WO2013040526A1

WO2013040526A1 - Antimicrobial compounds

Info

Publication number: WO2013040526A1
Application number: PCT/US2012/055677
Authority: WO
Inventors: Son T. Nguyen; Xiaoyuan DING; John D. Williams; Michelle M. Butler
Original assignee: Microbiotix, Inc.
Priority date: 2011-09-16
Filing date: 2012-09-16
Publication date: 2013-03-21

Abstract

The invention provides antimicrobial organic compounds and compositions thereof that kill or inhibit growth of cells of one or more microbial pathogens.

Description

ANTIMICROBIAL COMPOUNDS

Cross-Reference to Priority Applications

This application claims priority to US Provisional Appln. No. 61/535,739 filed September 16,

2011.

Statement of Federally Sponsored Research

The invention described herein was supported by SBIR grant number 1 R42 AI083032 and Research Project Cooperative Agreement 1 U01 AI082052 from the National Institutes of Health, as well as Contract No. HDTRA1-06-C-0042 from the Department of Defense. The United States Government has certain rights in the invention.

Field of the Invention

This invention is in the field of antimicrobial compounds. In particular, the invention provides organic compounds that inhibit growth of microbial cells, such as bacterial cells, fungal cells, and/or protozoan cells.

Background of the Invention

Microbial pathogens continue to pose a serious threat to public health as indicated by a worldwide resurgence of bacterial, fungal, and protozoan diseases. One aspect of this resurgence appears to be the result of prior widespread, and largely effective, therapeutic and prophylactic use of antibiotics, which, unfortunately, over time has also selected for resistant strains of various microbial pathogens. Of particular concern to the public health has been the emergence and proliferation of bacterial strains that are resistant to multiple antibiotics in the current arsenal of antimicrobial agents. Examples of bacteria that are resistant to multiple antibiotics include methicillin-resistant

Staphylococcus aureus ("MRSA") and strains of Group A streptococcus bacteria, such as

Streptococcus pyogenes, which have been isolated from highly aggressive infections in humans and popularly referred to as "flesh-eating" bacteria. Other multi-antibiotic resistant bacterial strains include strains of Enterococcus fecalis and Enterococcus fecium, which, along with antibiotic resistant Gram negative strains of Escherichia coli, constitute the most frequent etiological agents of nosocomial (hospital-acquired) diseases, such as septicemia, endocarditis, and infections of wounds and the urinary tract. S. aureus is currently the most frequent cause of nosocomial bacteremia and skin or wound infection. Streptococcus pneumoniae causes several serious and life-threatening diseases, including a contagious meningitis, bacteremia, and otitis media. Annual mortality from S. pneumoniae infection alone is estimated at between 3-5 million persons globally. Recently, a strain of Neisseria gonorrhoeae has been isolated that is resistant to all antibiotics previously used to treat gonorrhea. The emergence of such highly resistant bacterial strains illustrates the possibility of a worldwide scourge of untreatable bacterial infections and diseases. A wide variety of non-bacterial species of microbial cells are also responsible for a variety of severe, even fatal, diseases in human and non-human animal populations throughout the world. Strains of such non-bacterial species have also developed resistant to respective antimicrobial agents. For example, prominent fungal pathogens include, but are not limited to, species of Candida, such as C. albicans, C. parapsilosis, C. tropicalis, C. krusei, C. glabrata, and C. guillermondii; species of Aspergillus, such as A. fumgatus, A. niger, and A. flavus; species Cryptococcus, such as C.

neoformans, C. laurentii, C. albidus, and C. gatti; species of Histoplasma, such as H. capsulatum; and species of Pneumocystis, such as P. jiroveci. Fungal pathogens are of particular concern for immunocompromised individuals, such as patients of acquired immunodeficiency syndrome (AIDS), radiation therapy, and chemotherapy.

Despite decades of work to develop new drugs and vaccines, pathogenic protozoan species continue to be responsible for severe and even fatal diseases that annually affect millions of people worldwide. Treatment of an individual infected with protozoan cells can be particularly challenging as protozoa may exist in distinctly different forms at various stages in the protozoan life cycle. For example, Plasmodium falciparum, the etiological agent of malaria, exists in multiple forms during its presence in an infected human individual (sporozoites, merozoites, gametocytes) as well as in the mosquito vector (gametocytes, gametes, zygotes, ookinetes, oocysts, sporozoites). Other well-known pathogenic protozoans include, but are not limited to, trypanosomes, such as Trypanosoma brucei, T. brucie gambiense, and T. brucie rhodiense (cause of sleeping sickness) and T. cruzi (cause Chagas disease) and species of Leishamania (cause of leishmaniasis); species of Entamoeba, such as E. hisolytica (cause of amoebiasis); species of Toxoplasma, such as T. gondii (cause of toxoplasmosis); species of Cryptosporidium, such as C. parvum (cause of cryptosporidiosis); and species of Giardia, such as G. lamblia (cause of giardiasis).

The prevalence and persistence of microbial diseases throughout the world along with the increasing reports of multi-drug resistance strains attest to the urgent need for new antimicrobial agents.

Summary of the Invention

The invention addresses the above problem by providing antimicrobial compounds that inhibit growth of or kill cells of one or more microbial species, such as species of bacteria, fungi, and/or protozoa. An antimicrobial compound of the invention inhibits growth of or kills cells of one or more microbial species if the compound is brought into contact with the microbial cells.

Compounds of the invention are particularly useful in methods and compositions to inhibit growth of or kill cells of pathogenic microbial species (including opportunistic pathogenic species). An antimicrobial compound described herein may be used to inhibit growth of or kill cells of a pathogenic microbial species by administration to an individual (human or other mammal) that is susceptible to infection by or has been infected with cells of the pathogenic microbial species. An antimicrobial compound of the invention may also be applied to or incorporated into a liquid, solid, semi-solid composition that is susceptible to or is already contaminated with cells of one or more pathogenic microbial species. Compounds of the invention may also be used to treat solid surfaces, e.g., as a bacteriocide.

In an embodiment of the invention, an antimicrobial compound of the invention has the structure (I):

wherein:

X¹, X⁵, and X⁹ are independently NH, NR¹⁰; O, S, or S0₂,

X², X³, X⁴, X⁶, X⁷, X⁸, and X¹⁰ are each independently C or N,

L is a linker which is a divalent heteroaryl radical having at least one ring of at least 6 member atoms; and

R¹ to R⁹ are each independently hydrogen, halo, amino, amidino, guanidino, alkyl, haloalkyl, alkenyl, alkynyl, cycloalkyl, heterocycloalkyl, aryl, heteroaryl, hydroxy, alkoxy, aryloxy, heteroaryloxy, acyl, carboxy, alkoxycarbonyl, aryloxycarbonyl, amino, substituted amino, acylamino, amido, sulfonamido, mercapto, alkylthio, arylthio, hydroxamate, thioacyl, alkylsulfonyl, or aminosulfonyl; and

R¹⁰ is hydrogen, an alkyl, or acyl radical;

or salts thereof.

In one embodiment of the invention, an antimicrobial compound of the invention has the structure (I):

where Y is

wherein:

X¹ is NH;

X², X³, X⁴, X⁶ , and X¹⁰ are C;

X⁵ is NH or O;

X⁹ is O;

L is a linker which is a divalent pyridine or divalent pyrazine ring; and

R¹ to R⁴ and R⁹ are each independently hydrogen, halo, amino, amidino, guanidino, alkyl, haloalkyl, alkenyl, alkynyl, cycloalkyl, heterocycloalkyl, aryl, heteroaryl, hydroxy, alkoxy, aryloxy, heteroaryloxy, acyl, carboxy, alkoxycarbonyl, aryloxycarbonyl, amino, substituted amino, acylamino, amido, sulfonamido, mercapto, alkylthio, arylthio, hydroxamate, thioacyl, alkylsulfonyl, or aminosulfonyl; and

or salts thereof.

In an embodiment, a salt of a compound that has a structure described above is a pharmaceutically acceptable salt. In still another embodiment, an antimicrobial compound of the invention has a structure:

The compounds described herein are useful as antibacterial or bacteriostatic agents and may be used to treat bacterial infections. Accordingly, an individual infected with or exposed to bacterial infection, especially Pseudomonas, Escherichia, Streptococcus, Enterobacteria, or Klebsiella infection, may be treated by administering to the individual in need an effective amount of a compound according to the invention, e.g., administering one or more of the compounds of formula (I) described above.

The present invention also provides pharmaceutical compositions containing one or more of the antimicrobial compounds disclosed herein and a pharmaceutically acceptable carrier or excipient. The use of one or more of the antimicrobial inhibitor compounds in the preparation of a medicament for combating bacterial infection is contemplated. In addition, antimicrobial compounds as disclosed herein have many non-pharmaceutical uses, such as on surfaces (objects, countertops, floors, teeth, etc.) or added to solutions or mixtures (cleaning solutions, detergents, dentifrices, etc.), to inhibit microbial growth or eliminate infectious agents. An antimicrobial compound or combination of compounds described herein may be used as a supporting or adjunctive therapy for the treatment of bacterial or fungal infection in an individual (human or other animal). In the case of an individual with a healthy immune system, administration of an antimicrobial compound as described herein to inhibit the growth of microbes in or on an individual may be sufficient to permit the individual's own immune system to effectively clear or kill infecting or contaminating bacteria, fungi or protozoans from the tissue of the individual.

Alternatively, an antimicrobial compound described herein may be administered to an individual in conjunction (i.e., in a mixture, sequentially, or simultaneously) with an antibacterial agent, such as an antibiotic, an antibody, or immunostimulatory agent, to provide inhibition of microbial growth.

In yet another embodiment, a composition comprising an antimicrobial compound or a combination of antimicrobial compounds described herein may also comprise a second agent (second active ingredient, second active agent) that possesses a desired therapeutic or prophylactic activity other than that of the antimicrobial compound. Such a second active agent may include, but is not limited to, an antibiotic, an antibody, an antiviral agent, an anticancer agent, an analgesic (e.g., a non- steroidal anti-inflammatory drug (NSAID), acetaminophen, an opioid, a COX-2 inhibitor), an immunostimulatory agent (e.g., a cytokine), a hormone (natural or synthetic), a central nervous system (CNS) stimulant, an antiemetic agent, an anti-histamine, an erythropoietin, a complement stimulating agent, a sedative, a muscle relaxant agent, an anesthetic agent, an anticonvulsive agent, an antidepressant, an antipsychotic agent, and combinations thereof.

Compositions comprising an antimicrobial compound described herein may be formulated for administration to an individual (human or other animal) by any of a variety of routes including, but not limited to, intravenous, intramuscular, subcutaneous, intra-arterial, parenteral, intraperitoneal, sublingual (under the tongue), buccal (cheek), oral (for swallowing), topical (epidermis), transdermal (absorption through skin and lower dermal layers to underlying vasculature), nasal (nasal mucosa), intrapulmonary (lungs), intrauterine, vaginal, intracervical, rectal, intraretinal, intraspinal, intrasynovial, intrathoracic, intrarenal, nasojejunal, and intraduodenal.

Additionally, the invention provides pharmaceutically acceptable salts of the antimicrobial compounds described herein, solvated forms of the antimicrobial compounds described herein, multimeric forms of the antimicrobial compounds described herein, and prodrugs of the antimicrobial compounds described herein.

Detailed Description of the Invention

The invention is based on a discovery of a class of organic compounds, which when brought into contact of cells of one or more microbial species (e.g., bacteria, fungi, or protozoa), inhibit growth of or kill the cells of the one or more microbial species. Compounds of the invention are thus referred to as "anti-microbial" compounds. Antimicrobial compounds described herein are particularly useful in compositions and methods to kill or inhibit growth of cells of one or more pathogenic (including opportunistic pathogenic) bacteria, fungi, or protozoa. Antimicrobial compounds described herein may be used in compositions and methods to treat an individual (human or other mammal) that is infected with, at risk of infection by, or suspected of being infected with a pathogenic microbial species. Antimicrobial compounds described herein may also be used to treat or disinfect a liquid, solid, or semi-solid composition that is contaminated with or susceptible to contamination by cells of a pathogenic microbial species.

In order that the invention may be more clearly understood, the following terms and abbreviations are used as defined below.

Unless indicated otherwise, when the terms "about" and "approximately" are used in combination with an amount, number, or value, then that combination describes the recited amount, number, or value alone as well as the amount, number, or value plus or minus 10% of that amount, number, or value. By way of example, the phrases "about 40%" and "approximately 40%" disclose both "40%" and "from 36% to 44%, inclusive".

"Halo" or "halogen" means fluorine, chlorine, bromine, or iodine.

"Alkyl" means a straight or branched chain monovalent or a divalent radical of saturated and/or unsaturated carbon atoms. Examples of an "alkyl" radical include, but are not limited to, methyl (abbreviated "Me"), ethyl ("Et"), propyl ("Pr"), isopropyl ("zPr"), butyl ("Bu"), isobutyl (";^'Bu"), sec-butyl (sBu), ieri-butyl (iBu), and the like. An alkyl group may be unsubstituted or substituted by one or more suitable substituents found herein.

"Haloalkyl" means an alkyl radical that is substituted with one or more identical or different halogen atoms, e.g., -CH₂C1, -CF₃, -CH₂CF₃, -CH₂CC1₃, and the like.

"Alkenyl" means a straight-chain, branched, or cyclic hydrocarbon radical that has from 2 to 8 carbon atoms (C₂ - C₈) and at least one double bond, e.g., ethenyl, 3-buten-l-yl, 3-hexen-l-yl, cyclopent-l-en-3-yl, and the like. An alkenyl group may be unsubstituted or substituted by one or more suitable substituents found herein.

"Alkynyl" means a straight-chain or branched hydrocarbon radical that has from 2 to 8 carbon atoms (C₂ - C₈) and at least one triple bond, e.g., ethynyl, 3-butyn-l-yl, 2-butyn-l-yl, 3-pentyn-l-yl, and the like. An alkynyl group may be unsubstituted or substituted with one or more suitable substituents found herein.

"Cycloalkyl" means a non-aromatic monovalent or divalent monocyclic or polycyclic radical that has 3 to 12 carbon atoms (C₃ - Ci₂), e.g., cyclopentyl, cyclohexyl, decalinyl, and the like. A cycloalkyl radical may be unsubstituted or may be substituted with one or more suitable substituents found herein. A cycloalkyl radical may also be fused to one or more aryl groups, heteroaryl groups, or heterocycloalkyl groups, which themselves may be unsubstituted or may be substituted with one or more suitable substituents found herein. "Heterocycloalkyl" means a non-aromatic monovalent or divalent, monocyclic or polycyclic radical that has 2 to 12 carbon atoms (C₂ - Ci₂) and 1 to 5 heteroatoms selected from nitrogen (N), oxygen (O), or sulfur (S), e.g., pyrrolodinyl, tetrahydropyranyl, morpholinyl, piperazinyl, oxiranyl, and the like. A hetercycloalkyl radical may be unsubstituted or may be substituted with one or more suitable substituents found herein. A heterocycloalkyl radical may also be fused to one or more aryl groups, heteroaryl groups, or heterocycloalkyl groups, which themselves may be unsubstituted or substituted with one or more suitable substituents found herein.

"Aryl" (abbreviated "Ar") means an aromatic monovalent or divalent monocyclic or polycyclic radical comprising between 5 and 18 carbon ring members, e.g., phenyl, biphenyl, naphthyl, phenanthryl, and the like. An aryl radical may be unsubstituted or substituted with one or more of the suitable substituents found herein. An aryl radical may also be fused to one or more heteroaryl groups or heterocycloalkyl groups, which themselves may be unsubstituted or substituted with one or more suitable substituents found herein.

"Heteroaryl" (abbreviated "HAr") means an aromatic monovalent or divalent monocyclic or polycyclic radical comprising between 5 and 18 carbon ring members and at least 1 nitrogen (N) heteroatom, e.g., pyrrolyl, pyrazolyl, imidazolyl, pyridyl, pyrazinyl, pyridizinyl, pyrimidinyl, quinolinyl, and the like. A heteroaryl radical may be unsubstituted or may be substituted with one or more of the suitable substituents found herein. A heteroaryl radical may also be fused to one or more aryl groups, heteroaryl groups, or heterocycloalkyl groups, which themselves may be unsubstituted or may be substituted with one or more suitable substituents found herein. It is noted that the divalent heteroaryl values for the linking moiety -L- in formula (I) must contain at least six ring members.

"Hydroxy" means the radical -OH.

"Alkoxy" means the radical -OR, wherein R is an alkyl or cycloalkyl group.

"Aryloxy" means the radical -OAr, wherein Ar is an aryl group.

"Heteroaryloxy" means the radical -O(HAr), where HAr is a heteroaryl group

"Acyl" means a -C(0)R radical, wherein R is alkyl, alkenyl, alkynyl, cycloalkyl, aryl, heteroaryl, or heterocycloalkyl, e.g. acetyl, benzoyl, and the like.

"Carboxy" means the radical -C(0)OH.

"Alkoxycarbonyl" means a -C(0)OR radical where R is alkyl, alkenyl, alkynyl, or cycloalkyl. "Aryloxycarbonyl" means a -C(0)OR radical where R is aryl or heteroaryl.

"Amino" means the radical -NH₂.

"substituted amino" means the radical -NRR', wherein R and R' are, independently, hydrogen, alkyl, alkenyl, alkynyl, cycloalkyl, aryl, heteroaryl, or heterocycloalkyl.

"Acylamino" means the radical -NHC(0)R, wherein R is alkyl, alkenyl, alkynyl, cycloalkyl, aryl, heteroaryl, or heterocycloalkyl, e.g., acetyl, benzoyl, acetylamino, benzoylamino, and the like.

"Amido" means the radical -C(0)NRR', wherein R and R' are, independently, hydrogen, alkyl, alkenyl, alkynyl, cycloalkyl, aryl, heteroaryl, or heterocycloalkyl. "Sulfonylamino" means the radical -NHS0₂R, wherein R is alkyl, alkenyl, alkynyl, cycloalkyl, aryl, heteroaryl, or heterocycloalkyl.

"Amidino" means the radical -C(NR)NR'R", wherein R, R', and R" are, independently, hydrogen, alkyl, alkenyl, alkynyl, cycloalkyl, aryl, or heteroaryl, and wherein R, R', and R" may form heterocycloalkyl rings, e.g. carboxamido, imidazolinyl, tetrahydropyrimidinyl.

"Guanidino" means the radical -NHC(NR)NR'R", wherein R, R', and R" are, independently, hydrogen, alkyl, alkenyl, alkynyl, cycloalkyl, aryl, or heteroaryl, and wherein R, R', and R" may form heterocycloalkyl rings.

"Mercapto" means the radical -SH.

"Alkylthio" means the radical -SR, wherein R is an alkyl or cycloalkyl group.

"Arylthio" means the radical -SAr, wherein Ar is an aryl group.

"Hydroxamate" means the radical -C(0)NHOR, whereub R is an alkyl or cycloalkyl group.

"Thioacyl" means a -C(S)R radical, wherein R is alkyl, alkenyl, alkynyl, cycloalkyl, aryl, heteroaryl, or heterocycloalkyl.

"Alkylsulfonyl" means the radical -S0₂R, wherein R is alkyl, alkenyl, alkynyl, cycloalkyl, aryl, heteroaryl, or heterocycloalkyl.

"Aminosulfonyl" means the radical -S0₂NRR', wherein R and R' are, independently, hydrogen, alkyl, alkenyl, alkynyl, cycloalkyl, aryl, heteroaryl, or heterocycloalkyl.

A "leaving group" (Lv) means any suitable group that will be displaced by a substitution reaction. One of ordinary skill in the art will know that any conjugate base of a strong acid can act as a leaving group. Illustrative examples of suitable leaving groups include, but are not limited to, -F, - CI, -Br, alkyl chlorides, alkyl bromides, alkyl iodides, alkyl sulfonates, alkyl benzenesulfonates, alkyl p-toluene-sulfonates, alkyl methanesulfonates, triflate, and any groups having a bisulfate, methyl sulfate, or sulfonate ion.

A "protecting group" refers to a group that protects one or more inherent functional group from premature reaction. Suitable protecting groups may be routinely selected by those skilled in the art in light of the functionality and particular chemistry used to construct the compound. Examples of suitable protecting groups are described, for example, in Greene and Wuts, Protective Groups in Organic Synthesis, 3d edition, John Wiley and Sons, New York, N.Y. (1999).

The term "suitable organic moiety" means any organic moiety recognizable, such as by routine testing, to those skilled in the art as not adversely affecting the antimicrobial activity of compounds described herein. Illustrative examples of suitable organic moieties include, but are not limited to, hydroxyl groups, alkyl groups, oxo groups, cycloalkyl groups, heterocycloalkyl groups, aryl groups, heteroaryl groups, acyl groups, sulfonyl groups, mercapto groups, alkylthio groups, alkoxyl groups, carboxyl groups, amino groups, substitued amino groups, disubstitued amino groups, carbamoyl groups, arylthio groups, heteroarylthio groups, and the like. In general, the various moieties or functional groups for variables in the structural formuals of compounds of the invention may be "optionally substituted" by one or more suitable "substituents". The term "substituent" or "suitable substituent" means any suitable substituent that may be recognized or selected, such as through routine testing, by those skilled in the art. Illustrative examples of useful substituents are those found in the exemplary compounds that described herein, as well as a halogen; Ci_6-alkyl; Ci_6-alkenyl; Ci_6-alkynyl; hydroxyl; Ci_6 alkoxyl; amino; nitro; thiol; thioether; imine; cyano; amido; phosphonato; phosphine; carboxyl; carbonyl; aminocarbonyl; thiocarbonyl; sulfonyl; sulfonamine; sulfonamide; ketone; aldehyde; ester; oxygen (=0); haloalkyl (e.g., trifluoro methyl); carbocyclic cycloalkyl, which may be monocyclic or fused or non-fused polycyclic alkyl (e.g., cyclopropyl, cyclobutyl, cyclopentyl, or cyclohexyl) or a heterocycloalkyl, which may be monocyclic or fused or non-fused polycyclic (e.g., pyrrolidinyl, piperidinyl, piperazinyl, morpholinyl, or thiazinyl); carbocyclic or heterocyclic, monocyclic or fused or non-fused polycyclic aryl (e.g., phenyl, naphthyl, pyrrolyl, indolyl, furanyl, thiophenyl, imidazolyl, oxazolyl, isoxazolyl, thiazolyl, triazolyl, tetrazolyl,

pyrazolyl, pyridinyl, quinolinyl, isoquinolinyl, acridinyl, pyrazinyl, pyridazinyl, pyrimidinyl, benzimidazolyl, benzothiophenyl, or benzofuranyl); amino (primary, secondary, or tertiary); nitro; thiol; thioether, O-lower alkyl (alkoxyl); O-aryl (aryloxy), aryl; aryl-lower alkyl; C0₂CH₃; CONH₂; OCH₂CONH₂; NH₂; S0₂NH₂; OCHF₂; CF₃; OCF₃; and the like. Such moieties may also be optionally substituted by a fused-ring structure or bridge, for example OCH₂-0. All of these substituents may optionally be further substituted with a substituent selected from groups such as hydroxyl groups, halogens, oxo groups, alkyl groups, acyl groups, sulfonyl groups, mercapto groups, alkylthio groups, alkyloxyl groups, cycloalkyl groups, heterocycloalkyl groups, aryl groups, heteroaryl groups, carboxyl groups, amino groups, substitued amino groups, disubstitued amino groups, carbamoyl groups, aryloxyl groups, heteroaryloxyl groups, arylthio groups, heteroarylthio groups, and the like.

The term "optionally substituted" is intended to expressly indicate that the specified group is unsubstituted or substituted by one or more suitable substituents, unless the optional substituents are expressly specified, in which case the term indicates that the group is unsubstituted or substituted with the

specified substituents. As defined above, various groups may be unsubstituted or substituted (i.e., they are optionally substituted) unless indicated otherwise herein (e.g., by indicating that the specified group is unsubstituted).

It is understood that the structure of an antimicrobial compounds described herein includes solvated forms of the compound. Examples of solvated forms of an antimicrobial compounds of the invention include, but are not limited to, the antimicrobial compounds in combination with a solvent selected from water, isopropanol, ethanol, methanol, dimethyl sulfoxide, ethyl acetate, acetic acid, ethanolamine, and acetone. It is understood that while a compound of the general structural formulas herein may exhibit the phenomenon of tautomerism, the structural formulas within this specification expressly depict only one of the possible tautomeric forms. It is therefore to be understood that the structural formulas herein are

intended to represent any tautomeric form of the depicted compound and is not to be limited merely to a specific compound form depicted by the structural formulas.

It is also understood that the structural formulas are intended to represent any configurational form of the depicted compound and is not to be limited merely to a specific compound form depicted by the structural formulas.

Some of the compounds of the present invention may exist as single stereoisomers (i. e., essentially free of other stereoisomers), racemates, or mixtures of enantiomers, diastereomers, or both when they contain one or more stereogenic centers as designated by R or S according to the Cahn- Ingold-Prelog rules whether the absolute or relative configuration is known. All such single stereoisomers, racemates and mixtures thereof are intended to be within the scope of the present invention.

Some of the compounds in the present invention may exist as geometric isomers as the result of containing a stereogenic double bond. In such cases, they may exist either as pure or mixtures of cis or trans geometric isomers or (E) and (Z) designated forms according to the Cahn-Ingold-Prelog rules and

include compounds that adopt a double bond configuration as a result of electronic derealization.

As generally understood by those skilled in the art, an optically pure compound having one or more chiral centers (i.e., one asymmetric atom producing unique tetrahedral configuration) is one that consists essentially of one of the two possible enantiomers (i.e., is enantiomerically pure), and an optically pure compound having more than one chiral center is one that is both diastereomerically pure and enantiomerically pure. If the compounds of the present invention are made synthetically, they may be used in a form that is at least 90% optically pure, that is, a form that comprises at least 90% of a single isomer (80% enantiomeric excess (e.e.) or diastereomeric excess (d.e.), more preferably at least 95% (90% e.e. or d.e.), even more preferably at least 97.5% (95% e.e. or d.e.), and most preferably at least 99% (98% e.e. or d.e.).

As noted above, antimicrobial compounds of the invention include active tautomeric and stereoisomeric forms of the compounds of the present invention, which may be readily obtained using techniques known in the art. For example, optically active (R) and (S) isomers may be prepared via a stereospecific synthesis, e.g., using chiral synthons and chiral reagents, or racemic mixtures may be resolved using conventional techniques.

If a compound of the present invention is a base, the desired salt of the compound may be prepared by any suitable method available in the art, for example, treatment of the free base with an inorganic acid or with an organic acid along with appropriate counter ion. Inorganic acids that may be used to form salts of compounds of the invention include, but art not limited to, hydrochloric acid, hydrobromic acid, sulfuric acid, nitric acid, and phosphoric acid. Organic acids that may be used to form salts of compounds of the invention include, but are not limited to, acetic acid, maleic acid, succinic acid, mandelic acid, fumaric acid, malonic acid, pyrvic acid, oxalic acid, glycolic acid, salicylic acid, a pyranosidyl acid (such as glucuronic acid or galacturonic acid), an alpha-hydroxy acid (such as citric acid or tartaric acid), an amino acid (such as aspartic acid or glutamic acid), an aromatic acid (such as benzoic acid or cinnamic acid), and a sulfonic acid (such as p-toluenesulfonic acid or ethanesulfonic acid).

If a compound of the present invention is an acid, then the desired salt form may be prepared by any suitable method, for example, treatment of the free acid with an inorganic or organic base and appropriate counter ion(s). Examples of bases that may be used to form salts of compounds of the invention include, but are not limited to, amines (primary, secondary or tertiary), an alkali metal hydroxide, and an alkaline earth metal hydroxide. Illustrative examples of suitable salts of compounds of the invention include, but are not limited to, organic salts derived from basic amino acids (such as lysine and arginine, ammonia, primary, secondary, and tertiary amines) and from cyclic amines (such as piperidine, morpholine and piperazine), and inorganic salts derived from sodium, calcium, potassium, magnesium, manganese, iron, copper, zinc, aluminum, and lithium.

Salts of antimicrobial compounds of the invention include pharmaceutically acceptable salts of the compound. By the term "pharmaceutically acceptable salts of the compound" as understood and used herein, is meant those salts of any antimicrobial compounds of the invention derived from an inorganic or organic acid or base recognized in the art as compatible for pharmaceutical compositions. For convenience, the terms "pharmaceutical" and "pharmaceutically acceptable" also are understood to encompass compounds acceptable for the practice of veterinary medicine as well. It is understood that pharmaceutically acceptable salts of the antimicrobial compounds described herein are not limited to only pharmaceutical uses. Examples of suitable acids for pharmaceutically acceptable salts of antimicrobial compounds of the invention include, but are not limited to, hydrochloric acid, hydrobromic acid, sulfuric acid, nitric acid, perchloric acid, fumaric acid, maleic acid, hydroxymaleic acid, malonic acid, glutamic acid, phosphoric acid, glycolic acid, lactic acid, salicylic acid, succinic acid, to luene-p- sulfonic acid, p-bromophenylsulfonic acid, carbonic acid, succinic acid, citric acid, benzoic acid, 2-acetoxybenzoic acid, acetic acid, phenylacetic acid, propionic acid, glycolic acid, stearic acid, tartaric acid, acetic acid, methanesulfonic acid, formic acid, naphthalene-2-sulfonic acid, benzenesulfonic acid, ethane-disulfonic acid, and sulfanilic acid. Salts of other acids, such as oxalic acid or isethionic acid, may not be pharmaceutically acceptable, but may find use in a variety of compositions and methods that are used to provide the benefit of the antimicrobial activity of a compound of the invention to a solution, semi-solid, or solid composition that is not a pharmaceutical composition. Salts derived from appropriate bases include alkali metal (e.g., sodium, potassium), alkaline earth metal (e.g., magnesium), ammonium and NR4+ (where R is a Ci .4 alkyl) salts, and the like. Reference, hereinafter, to a compound according to the invention (or an equivalent term) is understood to include any and all corresponding salts, including pharmaceutically acceptable salts, thereof.

The term "multimer" refers to multivalent or multimeric forms of antimicrobial compounds of the invention. Such "multimers" may be made by linking or placing multiple copies of an active (i.e., possessing antimicrobial activity) compound described herein in close proximity to each other, e.g., using a scaffolding provided by a carrier moiety. Multimers of various dimensions (i.e., bearing varying numbers of copies of an active compound) may be tested to arrive at a multimer of optimum size with respect to binding site interactions. Provision of such multivalent forms of active compounds may enhance binding site interactions. See, e.g., Lee et al., Biochem., 23: 4255 (1984). The artisan may control the multivalency and spacing by selection of a suitable carrier moiety or linker units. Useful moieties include molecular supports comprising a multiplicity of functional groups that can be reacted with functional groups associated with the active compounds of the invention. A variety of carrier moieties may be used to build highly active multimers including, but not limited to, proteins such as bovine serum albumin (BSA); peptides such as pentapeptides, decapeptides, pentadecapeptides, and the like; and non-biological compounds selected for their beneficial effects on absorbability, transport, or persistence within or on a target microbial cell. Functional groups on the carrier moiety, such as amino, sulfhydryl, hydroxyl, and substitued amino groups, may be selected to obtain stable linkages to the compounds of the invention, optimal spacing between the immobilized compounds, and optimal biological properties.

By "pharmaceutically acceptable" is meant any compound or mixture that is not biologically, chemically, or in any other way, incompatible with body chemistry and metabolism and also does not adversely affect the desired, effective antimicrobial activity of a compound of the invention or any other component of a composition comprising an antimicrobial compounds described herein that may be administered to an individual to effectively kill or inhibit growth of cells of a microbial pathogen infecting an individual.

The terms "oral", "orally", enteral", "enterally", "non-parenteral", "non-parenterally", and the like, refer to a route or mode for administering an effective amount of an antimicrobial compounds described herein, or composition thereof, to an individual anywhere along the alimentary canal of the individual. Examples of such "enteral" routes of administration include, without, limitation, from the mouth, e.g., swallowing a solid (e.g., pill, tablet, capsule) or liquid (e.g., syrup, elixir) composition; nasojejunal or gastrostomy tubes (into the stomach); intraduodenal administration; and rectal (e.g., using suppositories for release and absorption of a compound or composition in the lower intestinal tract of the alimentary canal). One or more enteral routes of administration may be employed in the invention. Thus, unless a particular type of "oral" formulation described herein is specified or indicated by the context, "oral" formulations are the same as "enteral" formulations and broadly encompass formulations that may be swallowed from the mouth as well as those that permit administration of an antimicrobial compounds of the invention anywhere along the alimentary canal. For the purposes of this discussion, sub-lingual (absorption under the tongue) and buccal (absorption through the inner cheek) administration of a anit-microbial compound of the invention may also be considered oral routes of administration.

The terms "parenteral" and "parenterally" refer to routes or modes of administration of an antimicrobial compounds of the invention, or composition thereof, to an individual other than along the alimentary canal. Examples of parenteral routes of administration include, without limitation, intravenous (i.v.), intramuscular (i.m.), intra-arterial (i.a.), intraperitoneal (i.p.), subcutaneous (s.c), transdermal (absorption through the skin or dermal layer), nasal or pulmonary (e.g., via inhalation or nebulization, for absorption through the respiratory mucosa or lungs), intra-articular (i.a.), direct injections or infusions into body cavities or organs, as well as by implantation of any of a variety of devices into the body that permit active or passive release into the body of an individual of an antimicrobial compounds described herein.

A "pharmaceutically acceptable prodrug" is a compound that may be converted under physiological conditions or by solvolysis to the specified compound or to a salt of such compound, or a compound that is biologically active with respect to an intended pharmacodynamic effect. A "pharmaceutically active metabolite" means a pharmacologically active product produced through metabolism in the body of a specified compound or salt thereof. Prodrugs and active metabolites of a compound may be identified using routine techniques known in the art. See, e.g., Bertolini et al., J. Med. Chem., 40: 2011-2016 (1997); Shan et al., /. Pharm. Set, 86(7):765-767 (1997); Bagshawe, Drug Dev. Res., 34: 220-230 (1995); Bodor, Advances in Drug Res., 13: 224-331 (1984); Bundgaard, Design of Prodrugs (Elsevier Press, 1985); and Larsen, Design and Application of Prodrugs, Drug Design and Development (Krogsgaard-Larsen et al., eds., Harwood Academic Publishers, 1991).

In the case where an antimicrobial compound of the invention is present in a solid form, it is understood by those skilled in the art that the compound and salts thereof may exist in different crystal or polymorphic forms, all of which are intended to be within the scope of the present invention and specified structural formulas.

The terms "patient" and "individual" are synonymous, unless noted otherwise, and mean any mammal, including without limitation, a human, who receives or may be a candidate to receive an antimicrobial compounds described herein or composition thereof. Thus, as used herein, a "patient" may or may not present a recognizable symptom of a microbial disease, but merely be at risk for infection by cells of a pathogenic microbial species that may cause a disease, e.g., due to exposure to a source of cells of the microbial pathogen.

As provided herein, an "effective amount" is intended to mean that amount of a compound that is sufficient to reduce, prevent or inhibit bacterial growth as compared with a negative control. A "therapeutically effective amount" of an antimicrobial compounds of the present invention, or of a prodrug, an active metabolite, or a salt thereof, is a quantity sufficient to, when administered to an individual to kill or inhibit growth of cells of a microbial pathogen. Also, as used herein, a

"therapeutically effective amount" of a compound of the present invention is an amount which prevents, inhibits, suppresses, or reduces a given clinical condition or disease symptom in an individual as known and understood by a skilled healthcare provider or as compared to a control, such as an individual that is not infected with a microbial pathogen. As defined herein, a therapeutically effective amount of a compound of the present invention may be readily determined by one of ordinary skill by routine methods known in the art.

"Therapy" and "therapeutic" as understood and used herein refer to treatment of a patient for a microbial infection or disease due to the microbial infection. For convenience, the terms are also understood to encompass prophylactic or precautionary use or administration of a compound of the invention. Such precautionary or prophylactic use is exemplified by administration of an antibiotic to an immunocompromised or immunodeficient patient to protect the patient from an infection; to a patient suspected, but not proven, of having a microbial infection; or to a patient that is susceptible to contracting a disease caused by infection of cells of a pathogenic species, for example, at open wounds; by contact with water, food, body fluids, corpses, or carcasses contaminated with cells of a pathoogenic microbial species; or by contact with infected individuals or body fluids of infected individuals containing cells of a pathogenic microbial species.

In the context of therapeutic use of the antimicrobial compounds described herein, the terms

"treatment", "to treat", or "treating" will refer to any use of the antimicrobial compounds calculated or intended to arrest or inhibit the growth of or kill cells of a pathogenic microbial species. Thus, treating an individual may be carried out after any diagnosis indicating possible bacterial, fungal, or protozoan infection, i.e., whether an infection by a particular microbe has been confirmed or whether the possibility of infection is only suspected, for example, after exposure to the microbe or to another individual infected by the microbe.

A composition or method described herein as "comprising" one or more named elements or steps is open-ended, meaning that the named elements or steps are essential, but other elements or steps may be added within the scope of the composition or method. To avoid prolixity, it is also understood that any composition or method described as "comprising" (or which "comprises") one or more named elements or steps also describes the corresponding, more limited composition or method "consisting essentially of" (or which "consists essentially of") the same named elements or steps, meaning that the composition or method includes the named essential elements or steps and may also include additional elements or steps that do not materially affect the basic and novel characteristic s) of the composition or method. It is also understood that any composition or method described herein as "comprising" or "consisting essentially of" one or more named elements or steps also describes the corresponding, more limited, and closed-ended composition or method "consisting of" (or "consists of") the named elements or steps to the exclusion of any other unnamed element or step. In any composition or method disclosed herein, known or disclosed equivalents of any named essential element or step may be substituted for that element or step.

It is also understood that an element or step "selected from the group consisting of" or otherwise recited in a list of elements or steps refers to one or more of the elements or steps in the list that follows, including combinations of any two or more of the listed elements or steps, unless otherwise stated.

The meaning of other terms will be understood by the context as understood by the skilled practitioner in the art, including the fields of organic chemistry, pharmacology, pharmaceuticals, and microbiology.

An antimicrobial compound of the invention has the following structure:

where Y is

wherein: X¹, X⁵, and X⁹ are independently NH, NR¹⁰; O, S, or S0₂,

X², X³, X⁴, X⁶, X⁷, X⁸, and X¹⁰ are each independently C or N,

L is a linker which is a divalent heteroaryl radical having at least one ring of 6 or more member atoms; and

R¹⁰ is hydro gen, an alkyl, or acyl radical;

or salts thereof.

A preferred antimicrobial compounds of the invention has a structure:

wherein:

X¹ is NH;

X², X³, X⁴, X⁶ , and X¹⁰ are C;

X⁵ is NH or O;

X⁹ is O;

L is a linker which is a divalent pyridine or divalent pyrazine ring; and

R¹ to R⁴ and R⁹ are each independently hydrogen, halo, amino, amidino, guanidino, alkyl, haloalkyl, alkenyl, alkynyl, cycloalkyl, heterocycloalkyl, aryl, heteroaryl, hydroxy, alkoxy, aryloxy, heteroaryloxy, acyl, carboxy, alkoxycarbonyl, aryloxycarbonyl, amino, substituted amino, ac amido, sulfonamido, mercapto, alkylthio, arylthio, hydroxamate, thioacyl, alkylsulfonyl, or aminosulfonyl; and

or pharmaceutically acceptable salts thereof.

Additionall tructure:

Synthesis of Compounds

Compounds described herein may be synthesized using established chemistries, and suitable synthesis schemes for the compounds include the following:

reflux

N-Boc-6-cyano-2-(5-bromopyridin-2-yl)indole

To a suspension of /V-Boc-6-cyano-indole-2-boronic acid (5.06 g, 17.67 mmol) in 10% EtOH/toluene (40 mL) in a round bottom flask fitted with a condenser was added Pd(PPh₃)₄ (510 mg, 0.44 mmol) under a slow stream of Ar. After stirring for a few minutes, a solution of 2-bromo-5-iodo pyridine (5.50 g, 19.44 mmol) in 10% EtOH/toluene (10 mL) was added, followed by a 2 M aqueous solution of Na₂C0₃ (17.7 mL, 35.4 mmol). The resulting brown mixture was brought to reflux in a preheated oil bath and stirred for 3 hours. After cooling, the dark brown mostly homogeneous solution was extracted with EtOAc over Na₂C0₃ solution (5% aq). The combined organic solution was washed with water (50 mL) and brine (30 mL), dried over MgS0₄, filtered and evaporated to a fourth of the original volume. The solid that formed was collected by filtration, washed with 20% EtOAc in hexanes (100 mL) and ether (100 mL) to yield 0.99 g of a cream-colored solid. The filtrate was evaporated, treated with di-i-butyl dicarbonate in pyridine at 60°C followed by acidic work-up, then subjected to column chromatography on silica gel (0-25% EtOAc hexane) to yield 280 mg of additional crude product. The combined crude products were recrystallized from boiling

EtOAc hexane to yield to yield 826 mg (12%) of product as a cream- colored solid: ¾-NMR (300 MHz, -DMSO): δ 8.58 (s, 1H), 8.49 (s, 1H), 7.96 (dd, 1H), 7.86 (d, 1H), 7.79 (d, 1H), 7.69 (dd, 1H), 7.03 (s, 1), 1.35 (s, 9H).

2,5-Bis(N-Boc-6-cyanoindol-2-yl)pyridine

A solution of A^r-Boc-6-cyano-2-(5-bromopyridin-2-yl)indole (401 mg, 1.0 mmol), N-Boc-6- cyanoindole-2-boronic acid (301 mg, 1.0 mmol), and Pd(PPh₃)₄ (15 mg) in 10% EtOH/toluene (12 mL) was sparged with argon gas for 10 minutes, then a 2.0 M aqueous solution of sodium carbonate (1.0 mL, 2.0 mmol) was added. The reaction was heated to 100 °C in a sealed tube for 1 hour, then cooled to room temperature and diluted with EtOAc (50 mL) and brine (50 mL). The organic layer was separated, dried over MgS04, filtered, and evaporated to yield an orange oil which was subjected to flash chromatography on silica gel with 2: 1 hex:EtOAc. Product-containing fractions were pooled and evaporated to yield a yellow solid that was recrystallized from boiling CH₂Cl₂ hexane to yield

228 mg (41 %) of product as a crystalline yellow solid: R_f 0.17 (3: 1 hex:EtOAc); ¾-NMR (300 MHz, CDC1₃): δ 8.76 (d, 1H), 8.56 (s, 1H), 8.51 (s, 1H), 7.86 (dd, 1H), 7.70-7.61 (m, 3H), 7.56-7.51 (m, 2H), 6.88 (s, 1H), 6.74 (s, lh), 1.48 (s, 9H), 1.45 (s, 9H).

2,5-bis(6-cyanoindol-2-yl)pyridine 2,5-Bis(A^LBoc-6-cyanoindol-2-yl)pyridine (220 mg, 0.39 mmol) was heated (dry) to 200 °C in a small flask for 30 minutes. The remaining solid was collected to provide 141 mg (100%) of product as a yellow powder: R_f 0.48 (5% MeOH/CHCl₃); 'H-NMR (DMSO/D₂0) δ 12.36 (s, 1H), 12.32 (s, 1H), 9.26 (d, 1H), 8.43 (dd, 1H), 8.23 (d, 1H), 7.92 (s, 1H), 7.90 (s, 1H), 7.79 (d, 1H), 7.77 (d, 1H), 7.41- 7.33 (m, 4H).

1 ,3-diaminopropane

2,5-bis[6-(3,4,5,6-tetrahydropyrimidin-2-yl)indol-2-yl]pyridine acetic acid salt.

To a solution of 2,5-bis(6-cyanoindol-2-yl)pyridine (130 mg, 0.36 mmol) in 1,3-diaminopropane (10 mL) was added phosphorous pentasulfide (45 mg, 0.26 mmol) and 2 drops of H₂0. The mixture was heated in a sealed tube at 120 °C for 2 hours, then cooled to room temperature, poured into water (200 mL), and refrigerated overnight. The resulting solids were filtered, rinsed with water (50 mL), and dried under vacuum. The solids thus obtained were dissolved in boiling acetic acid (8 mL), then cooled to room temperature and filtered through Celite. The yellow solution was diluted with MeOH (4 mL), then poured into Et₂0 (100 mL). The resulting yellow precipitate was filtered and dried under vacuum to constant weight to provide 219 mg (85%) of product as a bright yellow powder: ¾- NMR (DMSO/D₂0) δ 9,26 (s, 1H), 8.45 (d, 1H), 8.22 (d, 1H), 7.91 (d, 2H), 7.81 (t, 2H), 7.38-7.29 (m, 4H), 3.53 (s, br, 8H), 2.01 (s, br, 4H), 1.80 (s, 12H).

N-Boc-6-cyano-2-[5-(6-cyanobenzofuran-2-yl)pyridin-2-yl]indole

To a mixture of A^r-Boc-6-cyano-2-(5-bromopyridin-2-yl)indole (100 mg, 0.25 mmol),

cyanobenzofuran-2-boronic acid pinacol ester (70 mg, 0.26 mmol), and Pd(PhP₃)₄ (29 mg) were added sequentially to freshly distilled toluene (4 mL), freshly distilled ethanol (2 mL) and 2.0 M aqueous Na₂C0₃ (2 mL). The mixture was stirred and heated to 70 °C. After 1 hour, and additional amount of cyanobenzofuran-2-boronic acid pinacol ester (63 mg, 23 mmol) was added and the reaction was continued for another hour. The mixture was allowed to cool to room temperature. The organic material was extracted with ether, washed with water, and dried over MgS0₄. The solvents were evaporated and the product was purified by silica gel column chromatography (50%-90%

[DCM:EtOAc (2: 1)] in hexanes) to provide 85 mg (73%) of product as a pale yellow powder: R/. 0.17 (25% EtOAc in hexanes); 'H-NMR: (CDC1₃) 8.78 (d, 1H), 8.60 (s, 1H), 8.03 (d, 1H), 7.92-7.88 (m, 2H), 7.76 (d, 1H), 7.67 (d, 1H), 7.58-7.53 (m, 3H), 6.76 (s, 1H), 1.45 (s, 9H).

6-(3,4,5,6 etrahydropyrimidin-2-yl)-2-{5 6-(3,4,5,6 etrahydropyrimidin-2-yl)benzofuran-2- yl]pyridin-2-yl}indole acetic acid salt.

To a mixture of A^r-Boc-6-cyano-2-[5-(6-cyanobenzofuran-2-yl)pyridin-2-yl]indole (170 mg, 0.37 mmol) and phosphorous pentasulfide (100 mg, 0.45 mmol) was added 1,3-diaminopropane (2.5 mL). The tube was sealed and placed in an oil bath preheated at 80 °C. The temperature was raised to 130 °C and maintained as such for 3 hours before cooling to rt. The solution was slowly added to water (10 mL). The yellow precipitate was filtered and rinsed with water. The crude solid product was purified by C18 column chromatography with 0-50% MeCN/H₂0. Product-containing fractions were pooled and evaporated to yield 170 mg (77%) of product as yellow solid: ^-NMR (MeOD): 9.08 (s, 1H), 8.16 (d, 1H), 7.85 (d, 2H), 7.72 (d, 2H). 7.62 (d, 1H), 7.44 (d, 1H), 7.21 (s, 1H), 6.97 (s, 1H), 3.48 (bs, 8H), 1.98 (bs, 4H), 1.82 (s, 6H).

6-(5-methyl ,4,5,6 etrahydropyrimidin-2-yl)-2-{5 6-(5-methyl-3,4,5,6 etrahydropyrimidin-2- yl)benzofuran-2-yl]pyridin-2-yl}indole acetic acid salt

To a mixture of A^r-Boc-6-cyano-2-[5-(6-cyanobenzofuran-2-yl)pyridin-2-yl]indole (85 mg, 0.18 mmol) and phosphorous pentasulfide (65 mg, 0.29 mmol) was added 2-methyl- 1,3-diaminopropane (0.5 mL) and diphenyl ether (2 mL). The tube was sealed and placed in an oil bath preheated at 125 °C and stirred well for 3 h. Upon cooling, the mixture solidified, and water (10 mL) was slowly added. The suspension was thoroughly mixed. The yellow precipitate was filtered and rinsed with water, then ether. The crude solid product was purified by CI 8 column chromatography with 5%- 50% MeCN/H₂0. Product-containing fractions were pooled and evaporated to yield 33 mg (26%) of product as a yellow solid: 'H-NMR (MeOD): 9.01 (s, IH), 8.28 (d, IH), 7.97-7.87 (m, 3H), 7.79 (d, IH), 7.69 (d, IH), 7.55-7.48 (m, 2H), 7.28 (d, IH), 7.06 (s, IH), 4.64-3.58 (m, 4H), 3.17-3.10 (m, 4H), 2.15-2.09 (m, 2H), 1.83 (s, 9H, AcOH), 1.13-1.06 (m, 6H).

6-(5-hydroxy-3,4,5,6-tetrahydropyrimidin-2-yl)-2-{4-[2-(5-hydroxy-3,4,5,6- tetrahydropyrimidin-2-yl)benzofuran-2-yl]pyrid-2-yl}indole acetic acid salt.

To a mixture of A^r-Boc-6-cyano-2-[5-(6-cyanobenzofuran-2-yl)pyridin-2-yl]indole (60 mg, 0.13 mmol) and phosphorous pentasulfide (60 mg, 0.27 mmol) was added 2-hydroxy-l,3-diaminopropane (1 mL). The tube was sealed and placed in an oil bath preheated at 80 °C. The temperature was raised to 130 °C, then stirred for 3.5 hours and allowed to cool to room temperature. Water (10 mL) was added slowly, and the suspension that formed was loaded on a C18 column. The column was eluted with 30% MeCN in water over 1 h (30 mL/min) to provide 64 mg (72%) of product as a yellow solid: 'H-NMR (CD₃OD) 9.19 (d, IH), 8.42 (dd, IH), 8.16 (d, IH), 8.04 (s, IH), 7.94 (d, IH), 7.89 (s, IH), 7.81 (d, IH), 7.69 (s, IH), 7.66 (dd, IH), 7.39 (dd, IH), 7.22 (s, IH), 4.43 (m, 2H), 3.70 (dt, 4H), 3.57 (dt, 4H), 1.93 (s, 9H, AcOH).

2-cyanobenzofuran-6-boronic acid pinacol ester

To a 50 mL round bottom flask was added 2-cyano-6-bromobenzofuran (498 mg, 2.243 mmol), bis(pinacolato)diboron (683 mg, 2.691 mmol), PdC XdppfJ-CE^C . (110 mg, 0.134 mmol), potassium acetate (660 mg, 6.729 mmol) and 1,4-dioxane (11.0 mL). The yellow mixture was heated at 80 °C for 5 hours and cooled to room temperature. EtOAC (15 mL) was added to the dark reaction mixture and the organic layer was separated. The aqueous layer was extracted with EtOAc (3 x 25 mL), the combined organic layers were dried over anhydrous Na₂S0₄, filtered and concentrated by rotary evaporator to yellow residue, which was purified by column chromatography on silica gel (hexanes: ethyl acetate) to provide 419 mg (69%) of product as a white solid: R/. 0.35 (10: 1 hex:EtOAc); ¾ NMR (300 MHz, CDC1₃): 8.00 (s, 1H), 7.79 (d, 1H), 7.68 (d, 1H), 7.46 (s, 1H), 1.37 (s, 12H).

6-cyano-2-[5-(2-cyanobenzofuran-6-yl)pyridin-2-yl]indole

A 50 mL round bottom flask was charged with Pd(Ph₃P)₄ (57 mg, 0.05 mmol), 2-cyanobenzofuran-6- boronic acid pinacol ester (200 mg, 0.74 mmol) and Na₂C0₃ (299 mg, 2.8 mmol). The mixture was flushed with Argon for 2 min, then DME (3.3 mL), water (3.3 mL), and A^r-Boc-6-cyano-2-(5- bromopyridin-2-yl)indole (197 mg, 0.495 mmol) were added. The reaction mixture was heated at 78 °C for 3.5 hours and then cooled to room temperature. The yellow solid was filtered, washed with EtOAc and water, dried under vacuum to provide one batch of desired product as yellow solid (64 mg). The filtrate was extracted with EtOAc (3 x 10 mL). The combined organic layers were dried over anhydrous Na₂S0₄, filtered, concentrated and purified by column chromatography on silica gel (hexanes: ethyl acetate). The material thus obtained was combined with the previous batch to provide 195 mg (86%) of product as a yellow powder: Rf: 0.54 (3:2 hex:EtOAc); ¾ NMR (300 MHz, DMSO-d₆): 9.18 (d, 1H), 8.41-8.37 (m, 2H), 8.29 (s, 1H), 8.19 (s, 1H), 8.02 (d, 1H), 7.94-7.89 (m, 3H), 7.71 (dd, 1H), 7.22 (s, 1H), 1.32 (s, 9H).

6-(3,4,5,6 etrahydropyrimidin-2-yl)-2-{5 2-(3,4,5,6 etrahydropyrimidin-2-yl)benzofuran-6- yl]pyridin-2-yl}indole acetic acid salt. A 10 mL sealed tube was charged with 6-cyano-2-[5-(2-cyanobenzofuran-6-yl)pyridin-2-yl] indole (60 mg, 0.13 mmol), P₂Ss (29 mg, 0.065 mmol) and 1,3-diaminopropane (1.9 mL). The reaction mixture was heated at 120 °C for 3 hours and poured to 10 mL of brine. The yellow precipitate was filtered and dried to give crude product, which was purified by reverse phase C18 column chromatography with 5 -50 MeCN/H₂0 containing 0.2% AcOH to provide 55 mg, (79%) of product as yellow solid: ¾ NMR (300 MHz, DMSO-d₆): 12.51 (s, IH), 9.09 (s, IH), 8.35 (dd, IH), 8.25 (d, IH), 8.08 (s, IH), 7.91-7.88 (m, 2H), 7.81 (d, 2H), 7.54 (s, IH), 7.38-7.34 (m, 2H), 3.54-3.50 (m, 8H), 2.10-1.90 (m, 2H), 1.88 (s, 3H), 1.85-1.75 (m, 2H).

6-(5-fluoro ,4,5,6 etrahydropyrimidin-2-yl)-2-^

yl)benzofuran-2-yl]pyridin-2-yl}indole trifluoroacetic acid salt.

A mixture of 6-cyano-2-[4-(6-cyanobenzofuran-2-yl)pyridin-2-yl]indole (50 mg, 0.11 mmol), phosphorous pentasulfide (30 mg, 0.14 mmol), and 2-fluoro- 1,3-diaminopropane (0.3 mL) in a sealed tube was stirred and heated in an oil bath to 130 °C for 6.5 hours. The mixture was allowed to cool to room temperature, then ethanol (3 mL) was added. The suspension was mixed thoroughly and filtered. The solid was dissolved in DMSO (2 mL) containing 10% TFA and purified by HPLC with 5%-50% MeCN/H₂0 to provide 29 mg (36%) of product as an orange- colored solid: 'H-NMR (DMSO-d₆): 12.60 (bs, IH), 10.36 (bs, 2H), 10.17 (bs, 2H), 9.42 (d, IH), 8.59 (dd, IH), 8.26 (d, IH), 8.23 (s, IH), 8.08 (d, IH), 7.94-7.90 (m, 3H), 7.77 (dd, IH), 7.47 (dd, IH), 7.43 (d, IH), 5.64 (m, IH), 5.49 (m, IH), 3.91 (bd, 4H), 3.90-3.60 (m, 4H).

6-(4,5-dihydroimidazol-2-yl]pyridin-2-yl}indole trifluoroacetic acid salt.

A 10 mL sealed tube was charged with tert-butyl 6-cyano-2-(5-(2-cyanobenzofuran-6-yl)pyridin-2- yl)-lH-indole-l-carboxylate (53 mg, 0.12 mmol), P₂Ss (26 mg, 0.058 mmol) and ethylenediamine (1.2 mL). The reaction mixture was heated to 120 °C in oil bath and turned into a clear green solution. It was stirred at the same temperature for 3 hours, poured to 10 mL of brine and the yellow precipitates were filtered, and dried under vacuum to give crude product, which was purified by reverse phase CI 8 column chromatography 5%-50% MeCN/H₂0 containing 0.2% AcOH to provide 29 mg (45%) of product as a yellow powder: ¾ NMR (300 MHz, DMSO-d₆): 9.10 (d, IH), 8.35 (dd, IH), 8.23 (d, IH), 8.15 (s, IH), 8.09 (s, IH), 7.91 (d, IH), 7.81 (d, IH), 7.76 (d, IH), 7.60 (d, IH), 7.46 (s, IH), 7.35 (s, IH), 3.90-3.80 (m, 4H), 3.70-3.60 (m, 4H), 1.90 (s, 6H).

then AcOH

2,5-bis[6-(4,5-dihydroimidazol-2-yl)indol-2-yl]pyridine acetic acid salt.

A 10 mL sealed tube was charged with 2,5-bis(/Y-Boc-6-cyanoindol-2-yl)pyridine (116 mg, 0.21 mmol), P₂Ss (46 mg, 0.10 mmol) and ethylenediamine (2.0 mL). The reaction mixture was heated to 120 °C for 3 hours, then poured into 10 mL of brine. The yellow precipitates were filtered, washed with water and EtOAc 6-7 times, and dried under vacuum to give yellow solid. The solid was dissolved in water/ AcOH (100 mL/10 mL) and lyophilized to provide 90 mg (68%) of product as a yellow powder: ¾ NMR (300 MHz, DMSO-d₆): 9.20 (d, IH), 8.38 (d, IH), 8.16 (d, IH), 7.98 (s, IH), 7.93 (s, IH), 7.63-7.51 (m, 4H), 7.27 (s, IH), 7.18 (s, IH), 3.67 (s, 4H), 3.66 (s, 4H), 1.88 (s, 9H).

6-(4-methyl-4,5-dihydro i7-imidazol-2-yl)-2-{5 2-(5-methyl-4,5-dihydro-li7-imidazol-2- yl)benzofuran-6-yl]pyridin-2-yl}indole di-AcOH salt A 10 mL sealed tube was charged with 6-cyano-2-[5-(2-cyanobenzofuran-6-yl)pyridin-2-yl] indole (61 mg, 0.13 mmol), P₂Ss (30 mg, 0.066 mmol) and 1,3-diaminopropane (1.9 mL). The reaction mixture was heated to 120°C in oil bath and turned into a clear green solution. It was stirred at the same temperature for 3 hours, poured to 10 mL of brine and the yellow precipitates were filtered, and dried under vacuum to give crude product, which was purified by reverse phase CI 8 column

chromatography (H₂O/0.1% CH₃COOH: Acetonitrile/0.1 CH₃COOH) to provide isomer 1 (37 mg, 47%) and isomer 2 (15 mg, 19%) as yellow solids.

Data for isomer 1 :

¾ NMR (300 MHz, DMSO-d₆): 9.07 (s, IH), 8.31 (d, IH), 8.20 (d, IH), 8.10 (d, 2H), 7.89 (d, IH), 7.79-7.72 (m, 2H), 7.58 (d, IH), 7.45 (s, IH), 7.33 (s, IH), 4.34-4.26 (m, IH), 4.09-3.96 (m, 3H), 3.47 (dd, IH), 3.25 (dd, IH), 1.86 (s, 6H), 1.32 (d, 3H), 1.20 (d, 3H); ); LC-MS mJe 475.6 (M+l)⁺; m.p. 243-284 °C.

Data for isomer 2:

¾ NMR (300 MHz, DMSO-d₆): 9.08 (s, IH), 8.33 (dd, IH), 8.19 (d, IH), 8.12 (s, IH), 8.02 (s, IH), 7.90 (d, IH), 7.80 (dd, IH), 7.69 (d, IH), 7.56 (dd, IH), 7.43 (s, IH), 7.31 (s, IH), 4.21-4.13 (m, IH), 4.11-4.00 (m, IH), 3.93-3.30 (m, 4H), 1.88 (s, 6H), 1.28 (d, 3H), 1.21 (d, 3H); LC-MS mJe 475.6 (M+l)⁺; m.p. 186-292 °C.

Using similar procedures, the following compounds were prepared:

2,5-bis[6-(3,4,5,6-tetrahydropyrimidin-2-yl)indol-2-yl]pyrazine acetic acid salt

¾-NMR (MeOD-d₄): 9.24 (s, 2H),7.89 (s, 2H), 7.83 (d, 2H), 7.39 (s, 2H), 7.35 (d, 2H), 3.62 (t, 8H), 2.14 (pent, 4H), 1.90 (s, 6H); ESI-MS: 475.5 (M+l)

2,5-bis[6-(4,5-dihydro-l/ -imidazol-2-yl)indol-2-yl]pyrazine acetic acid salt

¾-NMR (DMSO): 12.14 (bs, 2H), 9.34 (s, 2H), 7.99 (s, 2H), 7.65 (d, 2H), 7.55 (d, 2H), 7.44 (s, 2H), 3.65 (s, 8H), 1.88 (s, 6H, AcOH); ESI-MS: 447.5 (M+l)

2,5-bis[6-(3,4,5,6 etrahydropyrimidin-2-yl)indol-2-yl]pyrimidine acetic acid salt

'H-NMR (DMSO): 9.43 (s, 2H), 7.93-7.85 (m, 3H), 7.83 (d, 1H), 7.50 (s, 1H), 7.37 (m, 3H), 3.53 (m, 8H), 2.02 (m, 4H), 1.68 (s, 6H); ESI-MS: 475.8 (M+l)

Uses and Compositions

Compounds of the invention possess antimicrobial activity, which means that the compounds kill or inhibit growth of cells of one or more species or strains of a microbial pathogen when the compounds are brought into contact with such cells. Accordingly, the compounds described herein are useful in compositions and methods for treating an individual who has been infected with a pathogenic microbial species, is at risk of infection by a pathogenic microbial species, or is suspected of having been infected with a pathogenic microbial species. Compounds described herein may also be used in compositions and methods to kill or inhibit growth of cells of one or more microbial species in solutions, semi-solids, and solid compositions that are or are susceptible to contamination by cells of microbial species and particularly pathogenic microbial species.

There are a variety of pathogenic microbial species and strains that are known etiological agents for various diseases that can occur once an infection has become established in or on the body of individual. In some cases, a microbial species may be an opportunistic microbial pathogen, i.e., cause a disease only under certain conditions. For example, cells of an opportunistic pathogenic microbial species may not normally be pathogenic or only mildly pathogenic in the case of a healthy individual whose immune system can effectively identify the invading microbial cells and mount an effective response to inactivate and/or otherwise remove the cells from the individual's body.

However, cells of the same microbial species may be able to establish an infection resulting in significant pathology in an individual whose immune system has been weakened or otherwise suppressed. Weakened or compromised immune systems may result from a variety conditions including, but not limited to, prior (primary) illness, cancer of the immune system, exposure to toxins, exposure to radiation, exposure to chemotherapy drugs, and use of immunosuppressive drugs. Such individuals include, without limitation, patients of acquired immunodeficiency syndrome (AIDS), cancer patients undergoing radiation therapy, cancer patients receiving immunosuppressive chemotherapy drugs, and also individuals who take drugs designed to inhibit or suppress the activity of one or more cytokines, for example to treat diseases associated with an overactive cytokine(s), such as rheumatoid arthritis, psoriasis, and Crohn's disease. Antimicrobial compounds described herein may be used to kill or inhibit growth of cells of one more species of bacteria. Accordingly, compounds described herein may be used to use to kill or inhibit growth of cells of pathogenic (including opportunistic pathogenic) bacteria. Such bacteria may be Gram positive, Gram negative, or Gram variable. A compound described herein may be used to kill or inhibit growth of cells of one more species or strains of pathogenic (including opportunistic pathogenic) bacteria including, but not limited to, Acinetobacter (for example, A. baumannii), Bacillus (for example, B. anthracis, B. cereus, B. pumilis, B. megaterium, and B. subtilis),

Burkholderia (for example, B. mallei, B. pseudomallei, and B. cepacia), Clostridium (for example, C. botulinum, C. tetani, C. perfringens, and C. difficile), Chlamydia (for example, C. trachomatis), Chlamydophila (for example, C. pneumoniae and C. psittiaci), Enterobacter (for example, E.

aerogenes and E. cloacae), Enterococcus (for example, E. fecium and E. fecalis), Escherichia (for example, E. coli), Haemophilus (for example, H. influenzae), Helicobacter (for example, H. pylori), Klebsiella (for example, K. pneumoniae), Legionella (for example, L. pneumophila), Mycobacterium (for example, M. leprae, M. bovis, and M. tuberculosis), Neisseria (for example, N. gonorrhoeae), Pseudomonas (for example, P. aeruginosa), Proteus (for example, P. mirabilis), Salmonella (for example, S. typhimurium and S. typhi), Shigella (for example, S. dysenteriae), Staphylococcus (for example, S. aureus), Stenotrophomonas (for example, S. maltophilia), Streptococcus (for example, S. pyogenes and S. pneumoniae), Vibrio (for example, V. cholerae), and Yersinia (for example, Y. pestis).

Antimicrobial compounds described herein may be used to kill or inhibit growth of cells of one more species of fungi. Examples of prominent fungal pathogens include, but are not limited to, species of Candida, such as C. albicans, C. parapsilosis, C. tropicalis, C. krusei, C. glabrata, and C. guillermondii; species of Aspergillus, such as A. fumgatus, A. niger, and A. flavus; species

Cryptococcus, such as C. neoformans, C. laurentii, C. albidus, and C. gatti; species of Histoplasma, such as H. capsulatum; and species of Pneumocystis, such as P. jiroveci. Fungal pathogens are of particular concern for immunocompromised or immunosuppressed individuals.

Antimicrobial compounds described herein may be used to kill or inhibit growth of cells of one or more species of protozoa. Treatment of an individual infected with protozoan cells can be particularly challenging as protozoa may exist in distinctly different forms at various stages in the protozoan life cycle. For example, Plasmodium falciparum, an etiological agent of malaria, exists in multiples forms during its presence in an infected human individual (sporozoites, merozoites, gametocytes) as well in the mosquito vector (gametocytes, gametes, zygotes, ookinetes, oocysts, sporozoites). Other species of Plasmodium that cause malaria or malaria-like diseases include P. vivax, P. ovale, P. malariae, and P. knowlesi (cause of malaria in macaques). In addition to species and strains of Plasmodium, other well known pathogenic protozoa include, but are not limited to, species and subspecies of trypanosomes, such as Trypanosoma brucei, T. brucie gambiense, and T. brucie rhodiense (cause of sleeping sickness) and T. cruzi (cause of Chagas disease); species of Leishamania (cause of leishmaniasis); species of Entamoeba (cause of amoebiasis), such as E.

hisolytica and E. dispar; species of Dientamoebia, such as D. fragilis; species of Cryptosporidium (cause of cryptosporidiosis); and species of Giardia, such as G. lamblia (cause of giardiasis).

Antimicrobial compounds described herein may be formulated for pharmaceutical and non- pharmaceutical uses. Antimicrobial compounds described herein include compounds that may exhibit antimicrobial activity against multiple species and strains. In addition, compounds described herein may also be effective at killing or inhibiting growth of cells of multiple pathogenic microbial species and also non-pathogenic microbial cells. Such broad spectrum antimicrobial activity may be desirable in both pharmaceutical and non-pharmaceutical uses. In pharmaceutical uses, a compound that can kill or inhibit growth of cells of multiple pathogenic microbial organisms may provide new treatments for a variety of diseases, including those for which drug resistance by the etiological agent is a growing problem. Killing or inhibiting growth of non-pathogenic microbial cells is a common activity of broad spectrum antibiotics in current use. Accordingly, persons skilled in this art understand that in view of the benefit provided to the medical field of a compound that kills or inhibits growth of cells of one or more microbial pathogens, any side-effect of also killing or inhibiting growth of non-pathogenic cells should be tolerable and acceptable for approval by regulatory agencies for use of the compound for treating a particular disease.

Use of an antimicrobial compounds described herein to kill or inhibit growth of cells of pathogenic and/or non-pathogenic wherein growth of any microbial species is also desirable in situations where growth of any microbial cells may interfere with proper operation, safety, efficiency, or appearance of a composition. Compositions for which it is desirable to inhibit growth of pathogenic and/or non-pathogenic microbial cells are exemplified by, but not limited to, catheters, lock solutions, pumps (including cardiopulmonary bypass pumps, implantable patient pumps, non- implantable (exterior) patient pumps (e.g., for drug or hormone delivery), and industrial pumps), dialysis equipment, water pipes, plumbing fixtures, fuel lines, air ducts, gas lines (including air lines, oxygen lines, respirators), cosmetic products (including cosmetic skin products, cosmetic hair products), foods, eye products (eye drops, contact lenses, implantable lenses), ear products (e.g., ear drops), oral products (e.g., mouthwashes, tooth pastes, dental appliances), nasal products (e.g., nose drops, nose gels, nose swabs), vaginal care products, medical and veterinarian clothing (e.g., face masks, caps, gowns, gloves, footwear, gloves, aprons), gas masks, adhesives, soaps, detergents, and paints. Accordingly, in the discussion herein, it is understood that use of an antimicrobial compounds described herein to kill or inhibit cells of one or more microbial pathogens does not preclude use of the compound to kill or inhibit growth of cells of pathogenic and non-pathogenic microbial organisms.

In a method according to the invention, killing or inhibiting growth of cells of a microbial pathogen comprises bringing an antimicrobial compounds described herein into contact with the cells of the microbial pathogen. A compound described herein may be formulated in a pharmaceutical composition (including veterinarian) composition for administration to an individual or formulated to provide antimicrobial activityantimicrobial activity to an inanimate liquid, semi-solid, or solid composition that is susceptible or has already been contacted with (i.e., contaminated with) cells of a microbial pathogen. Preferably, an antimicrobial compounds described herein is in contact with a solid, semi-solid, or liquid composition prior to contamination with cells of a microbial pathogen, however, an antimicrobial compounds described herein may also be brought into contact with a solid, semi-solid, or liquid composition that is already contaminated with cells of a microbial pathogen to kill or inhibit growth of the cells already present on or in the composition. An antimicrobial compounds described herein may be incorporated into any of a variety of compositions to provide the benefit of killing or inhibiting growth of cells of a pathogenic microbial species or strain to the particular composition or to a surface to which the composition may be applied. Compositions comprising an antimicrobial compounds described herein include, but are not limited to, solutions, suspensions, dry mixtures, ointments, creams, gels, jellies, lotions, pastes, tooth pastes, petroleum products, porous membranes, porous filters, microparticles, microspheres, liposomes, micelles, lipid bilayers, resin particles, plastics, paints, glues, adhesives, cellulose products, textiles (fiber, yarn, or cloth), and nanoparticles. An antimicrobial compounds described herein may also be formulated by standard methods for delivery to a surface in an aerosol of fine solid particles or liquid droplets mixed with a gas.

An antimicrobial compounds described herein may be brought into contact with a solid surface composed of or comprising any of a variety of materials that are capable of retaining and/or transmitting viable cells of one or more microbial pathogens that may be present on the solid surface. Such materials include, but are not limited to, enamel, plastic, glass, silicon, rubber, metal, stone, cement, nylon, cellulose, polymeric resin (including various cellulose and agarose resins), calcium phosphate (for example, as in, but not limited to, hydro xyapatite and bone), calcium carbonate (for example, as in, but not limited to, mollusk shells and mother-of-pearl), keratin (for example, as in, but not limited to, skin, hair, fur, wool, nails, claws, hooves, scales, beaks, and feathers), collagen (for example, as in, but not limited to, animal hides, tendons, and ligaments), chitin (for example, as in, but not limited to, exoskeletons and fungal cell walls), and combinations thereof. The compound may be applied to a solid surface by any of a variety methods available in the art for applying an organic compound to a particular surface. Such methods include methods of "treating" a surface, wherein it is understood that the terms "treat", "treating", and "treatment" in this context of combining a compound with a surface is distinct from the a medical treatment of an individual for disease. Such methods of treating a surface with an antimicrobial compounds described herein include, but are not limited to, coating a surface with the compound, immersing the surface in the compound, impregnating the surface with the compound, absorbing the compound into the surface, adsorbing the compound to the surface, and covalently conjugating the compound to the surface. The skilled practitioner is able to determine which method is optimally suited for combining ("treating") a particular surface with a particular antimicrobial compounds described herein.

While in theory an antimicrobial compounds described herein may be used as the isolated compound alone (raw compound), it is more likely that the compound will be employed in a composition with at least one other compound. Compositions of the invention may be in any of a variety of forms particularly suited for the intended mode of providing the benefit of the antimicrobial activity of a compound described herein to a solid composition, to a semi-solid composition, or to liquid composition. A carrier is any compound that provides a medium for using antimicrobial compounds described herein. A carrier may be liquid, solid, or semi-solid. To retain its utility, it will be necessary that the carrier (and any other component of a composition) does not significantly neutralize, inhibit, or block the antimicrobialinhibitory activity of a compound of the invention included in the composition. A suitable carrier for use in the compositions described herein includes, but is not limited to, an organic solvent, an aqueous buffer, water, emulsifying agent, and a solid dispersing agent. Solutions and suspensions comprising an antimicrobial compounds described herein may also be prepared using an appropriate organic solvent or emulsifying agent. A preferred organic solvent is dimethyl sulfoxide (DMSO). DMSO-based solutions comprising an antimicrobial compounds described herein are particularly useful in providing required concentrations of the compound in various compositions, assays (including growth assays), and procedures. Other organic solvents may also be used including, but not limited to, an alcohol, N-methylpyrrolidone (NMP), and Ν,Ν-dimethylacetamide (DMA). For most in vitro purposes, DMSO is more preferred. As a general guide for using an alcohol as a solvent for a compound described herein, ethanol is more preferred than isopropanol, which is more preferred than butanol or an aryl alcohol, which are more preferred than methanol.

For solid compositions, conventional solid carriers are preferred and include, but are not limited to, mannitol, lactose, starch, magnesium stearate, sodium saccharin, talc, cellulose, glucose, sucrose, magnesium carbonate, and the like.

A composition comprising an antimicrobial compounds described herein may also comprise a dispersing agent. The dispersing agent may be employed to disperse the antimicrobial compounds more uniformly in a composition and/or to enhance dispersion of the composition containing an anti- micriobial compound described herein over a surface to which the composition is applied. A dispersing agent may be a solid or liquid. Solid dispersing agents may include, without limitation, talc, starch, cellulose, metal oxide (e.g., zinc oxide, titanium oxide), graphite, and combinations thereof. A preferred dispersing agent for liquid compositions is a surfactant, which may be an anionic, cationic, amphoteric, or nonionic surfactant. See, for example, US Patent No. 6,921,745. Preferably, a surfactant is employed at the lowest concentration that provides optimal dispersion of the antimicrobial compounds throughout the composition or optimal dispersion of the composition containing on a surface. Preferred anionic surfactants useful in the compositions and methods described herein include, without limitation, linear alkyl benzene sulfonic acid; alkyl sulfate; polyoxyethylene alkyl ether sulfate having 1 to 10 moles of ethylene oxide; polyoxyethylene alkyl ether carboxylic acid having 1 to 10 moles ethylene oxide; polyoxyethylene alkyl amide ether carboxylic or fatty acid having 1 to 10 moles ethylene oxide; and potassium, sodium, magnesium, or alkanolamine salts thereof. Preferably, the alkyl and fatty groups in an anionic surfactant are, independently, 8 to 22 carbon atoms, and more preferably 10 to 18 carbon atoms.

Preferably, a nonionic surfactant useful in the compositions and methods described herein is a nonionic polyoxyethylene ether, including, but not limited to, a polyoxyethylene alkyl ether having an alkyl chain containing 8 to 22 carbon atoms, more preferably 10 to 18 carbon atoms, and having 1 to 30 moles, and more preferably 4 to 20 moles, of ethylene oxide; a polyoxyethylene oxypropylene alkyl ether having 1 to 30 moles, and more preferably 1 to 20 moles, of ethylene oxide, and having 1 to 10 moles, more preferably 1 to 5 moles, of propylene oxide; a fatty acid alkanol amide containing 8 to 22 carbon atoms, and more preferably 10 to 18 carbon atoms to which 1 to 3 moles of ethylene oxide or propylene oxide may be added; and an alkyl polyglucoside having an alkyl chain containing 8 to 22 carbon atoms, and more preferably 10 to 18 carbon atoms, and preferably having 1 to 10 sugars, and more preferably 1 to 2 sugars, condensed therein. A preferred species of nonionic surfactant useful in compositions and methods described herein is t-octylphen-oxypolyethoxyethanol (e.g., brand name TRITON® X-100 non-ionic surfactant, Sigma- Aldrich, St. Louis, Missouri, US).

Another nonionic surfactant useful in the compositions and methods described herein may be an ester between a fatty acid containing 8 to 22 carbon atoms, and preferably 10 to 18 carbon atoms, and a polyvalent alcohol having a hydrocarbon group containing 2 to 10 carbon atoms and 2 to 8 hydroxy groups. More preferably, the ester is a glycerin fatty acid ester, a polyglycerin fatty acid ester, a sorbitan fatty acid ester, a sucrose fatty acid ester, or a propylene glycol fatty acid ester.

Amphoteric surfactants that may find use in the compositions and methods described herein include, without limitation, those having an alkyl group containing 8 to 22 carbon atoms, such as alkyl amidopropyl-N,N-dimethyl acetate betaine (N-alkanoyl aminopropyl-N,N-dimethyl-N-carboxymethyl ammonium carbobetaine), alkyl amidopropyl-N,N-dimethyl-2-hydroxypropyl sulfobetaine (N- alkanoyl aminopropyl-N,N-dimethyl-N-(2-hydroxy-3-sulfopropyl) ammonium sulfobetaine), alkyl- Ν,Ν-dimethyl acetate betaine (N-alkyl-N,N-dimethyl-N-carboxymethyl ammonium carbobetaine), alkyl amidopropyl-N,N-dimethyl-2-propyl sulfobetaine (N-alkanoyl aminopropyl-N,N-dimethyl-N- (2-sulfopropyl) ammonium sulfobetaine), lauryl-N,N-dimethyl-hydroxypropyl sulfobetaine (N-lauryl- N,N-dimethyl-N-(2-hydroxy-3-sulfopropyl) ammonium sulfobetaine), and alkyl amine oxide. Among these, preferred species may include lauric acid amidopropyl-N,N-dimethyl acetate betaine (N-lauroyl aminopropyl-N,N-dimethyl-N-carboxymethyl ammonium carbobetaine), myristic acid amidopropyl- Ν,Ν-dimethyl acetate betaine (N-myristyloyl aminopropyl-N,N-dimethyl-N-carboxymethyl ammonium carbobetaine), cocamide amide propyl-N,N-dimethyl acetate betaine (N-coconut composition alkanoyl aminopropyl-N,N-dimethyl-N-carboxymethyl ammonium carbobetaine), lauryl- N,N-dimethyl-2-hydroxypropyl sulfobetaine (N-lauryl-N,N-dimethyl-N-(2-hydroxy-3 -sulfopropyl) ammonium sulfobetaine), lauric acid amide propyl-N,N-dimethyl-23-hydroxypropyl betaine (N- lauroyl aminopropyl-N,N-dimethyl-N-(2-hydroxy-3-sulfopropyl) ammonium sulfobetaine), and an alkyl amine oxide having two alkyl groups containing 2 or less carbon atoms and one long-chain alkyl group containing 8 to 22 carbon atoms, which optionally may have an amide linkage.

Cationic surfactants that may be used in compositions and methods described herein include, but are not limited to, a long-chain dialkyl dimethyl ammonium salt, long-chain monoalkyl monobenzyl dimethyl ammonium salt, and monoalkyl trimethyl ammonium salt having a long alkyl chain containing 6 to 24 carbon atoms, and preferably 6 to 18 carbon atoms, which may be interrupted therein with an amide or ester linkage. The counterion of such cationic species is preferably a halogen ion, sulfate ion, or alkyl sulfate containing 1 to 3 carbon atoms. The cationic surfactants of amine type useful in compositions and methods described herein include long-chain dialkyl monomethylamine salts having a long alkyl chain containing 8 to 24 carbon atoms, which optionally may be interrupted therein with an amide or ester linkage. Preferred counterions of such species include hydrochlorides, sulfates, and phosphates thereof.

Pharmaceutical compositions of the invention comprise at least one antimicrobial compounds described herein and may be prepared in a unit-dosage form appropriate for a desired mode of administration. The pharmaceutical formulations of the present invention may be administered for therapy (including for preventive therapy) by any suitable route including, but not limited to, oral, buccal, sublingual, rectal, mucosal (mucosa), nasal, topical, dermal, vaginal and parenteral (including, but not limited to, subcutaneous, intramuscular, intravenous, and intradermal). It will be appreciated that the preferred route will vary with the condition and age of the individual receiving the pharmaceutical composition, the nature of the condition to be treated, and the chosen antimicrobial compounds of the present invention. A pharmaceutically acceptable carrier used in a pharmaceutical composition of the invention must be "acceptable" in the sense of being compatible with the other agents and ingredients of the composition and not prohibitively deleterious to the patient to whom the pharmaceutical composition is administered.

An antimicrobial compound of the invention may be administered alone, but will generally be administered as pharmaceutical formulations suitable for administration. Pharmaceutical formulations known in the art contemplated herein. Pharmaceutical formulations of this invention comprise a therapeutically effective amount of at least one compound of the present invention, and an inert, pharmaceutically or cosmetically acceptable carrier or diluent. As used herein the language "pharmaceutically acceptable carrier" or a "cosmetically acceptable carrier" is intended to include any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents, and the like, compatible with pharmaceutical or cosmetic administration, respectively. Except insofar as any conventional media or agent is incompatible with an antimicrobial compounds of the invention, use thereof in the formulation is contemplated.

Descriptions of suitable pharmaceutically acceptable carriers, formulations, and factors involved in their selection, are found in a variety of readily available sources, e.g., Remington's Pharmaceutical Sciences, 17th ed., (Mack Publishing Company, Easton, Pennsylvania, 1985), which is incorporated herein by reference.

A preferred pharmaceutical composition comprises an effective amount of one or more antimicrobial compounds described herein in combination with a pharmaceutically acceptable carrier, and, optionally, one or more other active agents, diluents, fillers, or excipients. An excipient is a compound that improves or provides a desirable physical property to a composition. An excipient useful in a composition described herein includes, but is not limited, an emulsifying agent, pH buffering agent, a dispersing agent, co-solvent, a gelling agent, and a drying agent.

While it is possible that, for use in therapy, a compound of the invention may be administered as the raw chemical, preferably the compound is present as an active ingredient in a pharmaceutical composition. The invention thus further provides a pharmaceutical composition comprising an antimicrobial compounds described herein, or a pharmaceutically acceptable salt thereof, together with one or more pharmaceutically acceptable carriers therefor and, optionally, one or more other therapeutic or beneficial agents known in the art, such as, an antibiotic, an antifungal drug, an antiprotozoan drug, an anti-viral compound, an anticancer compound, a vitamin, a trace metal supplement, or an ion supplement to restore or maintain proper ionic balance in blood or other tissues. Other examples of suitable therapeutic agents that may be used in combination with antimicrobial compounds of this invention include, without limitation, penicillins and other beta lactamase inhibitors, carbapenems, cephalosporins, macrolides (including erythromycin and ketolides), sulfonamides, aminoglycosides, quinolones (such as fluoroquinolones), oxazolidinones, lipopeptides (such as daptomycin), tetracyclines, vancomycin, erythromycin, streptomycin, efflux pump inhibitors, lactoferrins, and cationic peptides. Such agents may be administered to an individual in the same pharmaceutical composition comprising an antimicrobial compounds of this invention or in a separate composition.

A composition comprising an antimicrobial compounds of the invention may further comprise one or more antibiotics such as, but not limited to, penicillin,cephalosporin, cloxacillin, dicloxacillin, methicillin, nafcillin, oxacillin, ampicillin, amoxicillin, bacampicillin, azlocillin, carbenicillin, mezlocillin, piperacillin, ticarcillin, azithromycin, clarithromycin, clindamycin, erythromycin, lincomycin, demeclocycline, doxycycline, minocycline, oxytetracycline, tetracycline, quinolone, cinoxacin, nalidixic acid, fluoroquinolone, ciprofloxacin, enoxacin, grepafloxacin, levofloxacin, lomefloxacin, norfloxacin, ofloxacin, sparfloxacin, trovafloxacin, bacitracin, colistin, polymyxin B, sulfonamide, trimethoprim-sulfamethoxazole, co-amoxyclav, cephalothin, cefuroxime, ceftriaxone, vancomycin, gentamicin, amikacin, metronidazole, chloramphenicol, nitrofurantoin, co-trimoxazole, rifampicin, isoniazid, pyrazinamide, kirromycin, thiostrepton, micrococcin, fusidic acid, thiolactomycin, fosmidomycin, and the like.

A composition comprising an antimicrobial compound of the invention may further comprise one or more antifungal agents such as, but not limited to, amphotericin B, fluconazole, itraconazole, ketoconazole, potassium iodide, flucytosine, caspofungin acetate, nystatin, and the like.

A composition comprising an antimicrobial compounds of the invention may further comprise one or more antiprotozoan agents such as, but not limited to chloroquine, doxycycline, mefloquine, metronidazole, eplornithine, furazolidone, hydroxychloroquine, iodoquinol, pentamidine, mebendazole, piperazine, halofantrine, primaquine, pyrimethamine sulfadoxine, doxycycline, clindamycin, quinine sulfate, quinidine gluconate, quinine dihydrochloride, hydroxychloroquine sulfate, proguanil, quinine, clindamycin, atovaquone, azithromycin, suramin, melarsoprol, eflornithine, nifurtimox, amphotericin B, sodium stibogluconate, pentamidine isethionate, trimethoprim-sulfamethoxazole, pyrimethamine, sulfadiazine, and the like

A composition comprising an antimicrobial compounds of the invention may further comprise one or more antiproliferative agents such as, but not limited to, altretamine, amifostine, anastrozole, arsenic trioxide, bexarotene, bleomycin, busulfan, capecitabine, carboplatin, carmustine, celecoxib, chlorambucil, cisplatin, cisplatin-epinephrine gel, cladribine, liposomal cytarabine, daunorubicin (same as daunomycin), liposomal daunoribin, dexrazoxane, docetaxel, doxorubicin, liposomal doxorubicin, epirubicin, estramustine, etoposide phosphate, etoposide VP- 16, exemestane, fludarabine, fluorouracil 5-FU, fulvestrant, gemicitabine, gemtuzumab-ozogamicin, goserelin acetate, hydroxyurea, idarubicin, ifosfamide, imatinib mesylate, irinotecan, letrozole, leucovorin, levamisole, melphalan L-PAM, mesna, methotrexate, methoxsalen, mitomycin C, mitoxantrone, paclitaxel, pamidronate, pegademase, pentostain, porfimer sodium, streptozocin, talc, tamoxifen, temozolamide, teniposide VM-26, topotecan, toremifene, tretinoin, ATRA, valrubicin, vinorelbine, zoledronate, steroids, and the like.

Additional combination therapies may also include a compound of this invention. Clearly, the combination therapies described herein are merely exemplary and are not meant to limit possibilities for other combination treatments or co-administration regimens.

Pharmaceutical compositions according to the invention include those suitable for administration to an individual by any medically acceptable route including, but not limited to, parenteral, subcutaneous, intramuscular, intravenous, auricular (ear), ocular, intra-articular, intrabronchial, intraabdominal, intracapsular, intracartilaginous, intracavitary, intracelial, intracerebellar, intracerebroventricular, intracolic, intracervical, intragastric, intrahepatic, intramyocardial, intraosteal, intrapelvic, intrapericardiac, intraperitoneal, intrapleural, intraprostatic, intrapulmonary (e.g., by inhalation or insufflation), intrarectal, intrarenal, intraretinal, intraspinal, intrasynovial, intrathoracic, intrauterine, intravesical, bolus, vaginal, oral, rectal, buccal, sublingual, intranasal, and transdermal. The pharmaceutical compositions may, where appropriate, be conveniently presented in discrete dosage units and may be prepared by any of the methods well known in the art of pharmaceutical compositions.

Pharmaceutical compositions suitable for oral administration may conveniently be presented as discrete units such as capsules, cachets, or tablets each containing a predetermined amount of a compound of the invention in a powder or granule form, in a solution, in a suspension, or as an emulsion. A compound of the invention may also be presented as a bolus, electuary, or paste. Tablets and capsules for oral administration may contain conventional excipients such as binding agents, fillers, lubricants, disintegrants, or wetting agents. The tablets may be coated according to methods well known in the art. Oral liquid preparations may be in the form of, for example, aqueous or oily suspensions, solutions, emulsions, syrups, or elixirs, or may be presented as a dry product for constitution with water or other suitable vehicle before use. Such liquid preparations may contain conventional additives such as suspending agents, emulsifying agents, non-aqueous vehicles (which may include edible oils), or preservatives.

The compounds according to the invention may also be formulated for parenteral administration (e.g., by injection as a bolus or by continuous infusion) and may be presented in unit dose form in ampoules, pre-filled syringes, small volume infusion, or in multi-dose containers with an added preservative. The compositions may take such forms as suspensions, solutions, or emulsions in oily or aqueous vehicles, and may contain formulatory agents such as suspending, stabilizing, and/or dispersing agents. Alternatively, the active ingredient may be in powder form, obtained by aseptic isolation of sterile solid or by lyophilization from solution, for constitution with a suitable vehicle, e.g., sterile, pyrogen-free water or pharmaceutically acceptable buffer, prior to use.

For topical administration to the epidermis, antimicrobial compounds according to the invention may be formulated as ointments, creams, gels, jellies, or lotions. A compound of the invention may also be incorporated into a transdermal patch. Such transdermal patches may contain penetration enhancers such as linalool, carvacrol, thymol, citral, menthol, t-anethole, and the like.

Ointments and creams may, for example, be formulated with an aqueous or oily base comprising one or more suitable thickening and/or gelling agents. Lotions may be formulated with an aqueous or oily base and will in general also contain one or more emulsifying agents, stabilizing agents, dispersing agents, suspending agents, thickening agents, or coloring agents.

Compositions suitable for topical administration of an antimicrobial compounds of the invention in the mouth include lozenges comprising the compound, optionally, in a flavored base, usually sucrose and acacia or tragacanth; pastilles comprising the compound in an inert base such as gelatin and glycerin or sucrose and acacia; and mouthwashes comprising the active ingredient in a suitable liquid carrier.

Pharmaceutical compositions suitable for rectal administration wherein the carrier is a solid are presented as unit dose suppositories. Suitable carriers include cocoa butter and other materials commonly used in the art, and the suppositories may be conveniently formed by admixture of a compound of the invention with the softened or melted carrier(s) followed by chilling and shaping in molds.

Pharmaceutical compositions suitable for vaginal administration may be presented as pessaries, tampons, creams, gels, pastes, foams, or sprays containing in addition to a compound of the invention such carriers as are known in the art to be appropriate.

For intra-nasal administration the compounds of the invention may be used as a liquid spray or dispersible powder or in the form of drops. Drops may be formulated with an aqueous or nonaqueous base also comprising one more dispersing agents, solubilizing agents, or suspending agents. Liquid sprays may conveniently be delivered from pressurized packs.

For administration by inhalation, the compounds according to the invention may conveniently be delivered from an insufflator, nebulizer, a pressurized pack, or other convenient means of delivering an aerosol spray. Pressurized packs may comprise a suitable propellant, such as dichlorodifluoromethane, trichlorofluoromethane, dichlorotetrafluoroethane, carbon dioxide or other suitable gas. In the case of a pressurized aerosol, the dosage unit may be determined by providing a valve to deliver a metered amount. Alternatively, for administration by inhalation or insufflation, the compounds according to the invention may take the form of a dry powder composition, for example, a powder mix of a compound of the invention and a suitable powder base such as lactose or starch. The powder composition may be presented in unit dosage form in, for example, capsules or cartridges, or, for example, gelatin or blister packs from which the powder may be administered with the aid of an inhalator or insufflator.

An antimicrobial compound of the invention may also be formulated into a pharmaceutical composition for treating an eye or ear infection. Diseases of the eye that may be treated by administering antimicrobial compounds of the invention to a patient include, but are not limited to, bacterial keratitis, infectious keratoconjunctivitis, bacterial conjunctivitis, ocular tuberculosis, and suppurative uveitis. Diseases of the ear that may be treated by administering a compound of the invention include, but are not limited to, otitis externa and otitis media. Eye and ear diseases may be treated by administering a compound to a patient by any of the various routes described herein or by direct administration to the infected eye or ear. Pharmaceutical compositions comprising an antimicrobial compounds of the invention for treating an eye or ear disease may be a liquid or lotion, which may be administered directly into or on the infected eye or ear. Such compositions may be formulated in a manner similar to any of those known and used to administer an antibiotic to an eye or ear, such as compositions comprising fluoroquinolones (see, e.g., Am. Fam. Physician, 62: 1870-1876 (2000), and references cited therein).

When desired, the above described compositions may be adapted to give a sustained or time- delayed release of compound of the invention using any of the sustained or time-delayed formats available in art. When a compound of the invention or a pharmaceutically acceptable salt thereof is used in combination with a second therapeutic compound, the dose of each compound may be either the same as or differ from that when the compound is used alone. Appropriate doses will be readily appreciated by those skilled in the art. The ratio between a compound of the present invention and a second therapeutic compound for co-administration to a patient will be readily appreciated by those skilled in the art. For example, one may use a ratio in the range from about 1 : 1 to about 1:50 (by weight) of antimicrobial compounds of the invention: second therapeutic compound or, vice versa, i.e., of the second compound: antimicrobial compounds of the invention. In additional embodiments, the ranges of ratios that may be used in preparing a composition for co-administration of an antimicrobial compounds of the invention with a second therapeutic compound include, without limitation: about 1: 1 to about 1:30 (by weight), about 1 : 1 to about 1: 20 (by weight), about 1 : 1 to about 1: 15 (by weight), about 1: 1 to about 1: 10 (by weight), about 1 : 1 to about 1 :5 (by weight), and about 1: 1 to about 1 :3 (by weight) of an antimicrobial compounds of the invention: second therapeutic compound, or vice versa. If yet a further therapeutic compound(s) is added, ratios are adjusted accordingly.

An antimicrobial compounds of the invention may be provided and packaged in any of a variety of forms as described above, including in a powder or lyophilized state for reconstitution with sterile water or buffer, in unit doses for convenient administration, with one or more pharmaceutically acceptable buffers or salts, and/or with instructions for using the packaged compound as an antibiotic to treat an infection by a microbial pathogen.

Toxicity and therapeutic efficacy of such compounds can be determined by standard pharmaceutical procedures in cell cultures or experimental animals, e.g., for determining the LD₅₀ (the dose lethal to 50% of the population) and the ED₅₀ (the dose therapeutically effective in 50% of the population). The dose ratio between toxic and therapeutic effects is the therapeutic index, and it can be expressed as the ratio LD₅o/ED₅o. Antimicrobial compounds that exhibit large therapeutic indices are preferred. While compounds that exhibit toxic side effects may be used, care should be taken to design a delivery system that targets such compounds to the site of affected tissue in order to minimize potential damage to uninfected cells of an individual and, thereby, reduce untoward side effects.

Data obtained from cell culture assays and animal studies can be used in formulating a range of dosage for use in humans. The dosage of such compounds lies preferably within a range of circulating concentrations that include the ED₅₀ with little or no toxicity. The dosage may vary within this range depending upon the dosage form employed and the route of administration utilized. For any compound used in a method of the invention, the therapeutically effective dose can be estimated initially from cell culture assays. A dose may be formulated in animal models to achieve a circulating plasma concentration range that includes the IC5₀ (i.e., the concentration of the test antimicrobial compounds that achieves a half-maximal inhibition of microbial growth). Such information can be used to more accurately determine useful doses for humans. Levels in plasma may be measured, for example, by high performance liquid chromatography.

The following examples are provided to illustrate various embodiments of the present invention and shall not be considered as limiting in scope.

Examples

Example 1. Determination of minimum inhibitory concentration (MIC) of select compounds The following compounds were synthesized using the established chemistries described herein and were tested for in vitro inhibition of a panel of Gram-negative and Gram-positive bacteria using the broth microdilution method (Methods for Dilution Antimicrobial Susceptibility Tests for Bacteria that Grow Aerobically, M7-A7; Approved Standard— Seventh Edition, Clinical and

Laboratory Standards Institute, Wayne, PA (2006)) using cation-adjusted Mueller-Hinton Broth (MP Biomedicals, LLC, Solon, OH). Minimum inhibitory concentrations (MIC) values were determined for Klebsiella pneumoniae 13882, Proteus mirabilis 25933, Burkholderia cepacia 39277,

Acinetobacter baumannii 19606, Stenotrophomonas maltophilia 13637, Pseudomonas aeruginosa Paol, Escherichia coli 700, Staphylococcus aureus 25923, and Enterococcus faecalis 29212.

Briefly, serial 2-fold dilutions of compounds were added to 96-well assay plates containing the bacteria of interest at a concentration of 1 x 10⁵ colony-forming units/mL of medium. The growth of the bacteria was assessed after 18-20 hours of incubation at 37°C. MIC values for antimicrobial compounds-treated cultures were calculated as the lowest concentration of drug at which growth was not apparent, as measured by optical density at 600 nm.

The results are shown in Table 1 below.

Table 1.

The data in Table 1 show the organic compounds of the present invention are effective in inhibiting growth of a broad range of microbial cells. Consideration of the foregoing data defined a new group of compounds of related structure that are useful as antimicrobial compounds, and particularly, inhibit growth of microbial cells, such as bacterial cells, fungal cells, and/or protozoan cells, and may have further potency and/or toxicity profiles that make them candidates for use as therapeutic agents. The new family of antimicrobial compounds can be described by the Formula I:

where Y is

wherein:

X¹, X⁵, and X⁹ are independently NH, NR¹⁰; O, S, or S0₂,

X², X³, X⁴, X⁶, X⁷, X⁸, and X¹⁰ are each independently C or N,

L is a linker which is a divalent heteroaryl radical having at least one ring of 6 or more member atoms; and R¹ to R⁹ are each independently hydrogen, halo, amino, amidino, guanidino, alkyl, haloalkyl, alkenyl, alkynyl, cycloalkyl, heterocycloalkyl, aryl, heteroaryl, hydroxy, alkoxy, aryloxy, heteroaryloxy, acyl, carboxy, alkoxycarbonyl, aryloxycarbonyl, amino, substituted amino, acylamino, amido, sulfonamido, mercapto, alkylthio, arylthio, hydroxamate, thioacyl, alkylsulfonyl, or aminosulfonyl; and

R¹⁰ is hydrogen, an alkyl, or acyl radical;

or salts thereof.

The compounds identified above are candidates for development as antimicrobial compounds, and particularly, compounds which inhibit growth of microbial cells, such as bacterial cells, fungal cells, and/or protozoan cells.

All publications, patent applications, patents, and other documents cited herein are incorporated by reference in their entirety. In case of conflict, the present specification, including definitions, will control. In addition, the materials, methods, and examples are illustrative only and not intended to be limiting.

Obvious variations to the disclosed compounds and alternative embodiments of the invention will be apparent to those skilled in the art in view of the foregoing disclosure. All such obvious variants and alternatives are considered to be within the scope of the invention as described herein.

Claims

1. An antimicrobial compound having the structure:

wherein:

X¹, X⁵, and X⁹ are independently NH, NR¹⁰; O, S, or S0₂,

X², X³, X⁴, X⁶, X⁷, X⁸, and X¹⁰ are each independently C or N,

R¹⁰ is hydrogen, an alkyl, or acyl radical;

or pharmaceutical salts thereof.

2. The antimicrobial compound of Claim 1, having the structure:

where Y is

wherein:

X¹ is NH;

X², X³, X⁴, X⁶ , and X¹⁰ are C;

X⁵ is NH or O;

X⁹ is O;

L is a linker which is a divalent pyridine or pyrazine radical; and

or salts thereof.

3. An antimicrobial compound having the structure:

47

4. A pharmaceutical composition comprising one or more antimicrobial compounds according to any one of Claims 1-3 and a pharmaceutically acceptable carrier or excipient.

5. The pharmaceutical composition of Claim 4 further comprising one or more additional active agents.

6. The pharmaceutical composition of Claim 5, wherein said one or more additional active agents are selected from: an antibiotic, an antibody, an antiviral agent, an anticancer agent, an analgesic, an immunostimulatory agent, a hormone, a central nervous system (CNS) stimulant, an antiemetic agent, an anti-histamine, an erythropoietin, a complement stimulating agent, a sedative, a muscle relaxant agent, an anesthetic agent, an

anticonvulsive agent, an antidepressant, an antipsychotic agent, and combinations thereof.

7. A method of inhibiting or reducing growth of a microorganism, said method comprising contacting the microorganism with an effective amount of at least one compound of any of the preceding claims.

8. The method of Claim 7, wherein said microorganism is a bacteria, fungi, or protozoa. The method according to Claim 8, wherein said bacteria is a species selected from the group consisting of: Pseudomonas, Escherichia, Streptococcus, Enterobacteria, Klebsiella, Proteus, Burkholderia, Acinetobacter, Stenotrophomonas, Staphylococcus, and Enterococcus.

The method according to Claim 8, wherein said fungi is a species selected from the group consisting of: Candida, Aspergillus, Cryptococcus, Histoplasma, and Pneumocystis.

The method according to Claim 8, wherein said protozoa is a species selected from the group consisting of Plasmodium, Trypanosoma, Leishamania, Entamoeba, Dientamoebia, Cryptosporidium, and Giardia.

A method for treating an individual that is infected with, at risk of infection by, or suspected of being infected with a pathogenic microbial species, said method comprising

administering to said individual, as an active ingredient, a compound according to any one of Claims 1-3.

The method of Claim 12, wherein said pathogenic microbial species is a bacteria, fungi, or protozoa.

The method according to Claim 13, wherein said bacteria is a species selected from the group consisting of: Pseudomonas, Escherichia, Streptococcus, Enterobacteria, Klebsiella, Proteus, Burkholderia, Acinetobacter, Stenotrophomonas, Staphylococcus, and Enterococcus.

The method according to Claim 13, wherein said fungi is a species selected from the group consisting of: Candida, Aspergillus, Cryptococcus, Histoplasma, and Pneumocystis.

The method according to Claim 13, wherein said protozoa is a species selected from the group consisting of Plasmodium, Trypanosoma, Leishamania, Entamoeba, Dientamoebia, Cryptosporidium, and Giardia.

Use of a compound according to any one of Claims 1-3 for inhibiting or reducing growth of a microorganism.

Use of a compound according to any one of Claims 1-3 for the treatment or prevention of pathogenic microbial infection in a human subject.

19. The use according to Claim 18, wherein said pathogenic microbial infection is bacterial, fungal, or protozoan.

20. The use according to Claim 19, wherein said bacterial infection is selected from the group consisting of: Pseudomonas, Escherichia, Streptococcus, Enterobacteria, Klebsiella,

Proteus, Burkholderia, Acinetobacter, Stenotrophomonas, Staphylococcus, and Enterococcus.

21. The use according to Claim 19, wherein said fungal infection is selected from the group consisting of: Candida, Aspergillus, Cryptococcus, Histoplasma, and Pneumocystis.

22. The use according to Claim 19, wherein said protozoan infection is selected from the group consisting of Plasmodium, Trypanosoma, Leishamania, Entamoeba, Dientamoebia,

Cryptosporidium, and Giardia.

23. Use of a compound according to any one of Claims 1-3 for the manufacture of a

medicament for treating microbial infection.