Bacterial efflux pump inhibitors and methods of treating bacterial infections

1. A compound having the structure of Formula (III):

wherein:

R 1 is:

X 1 is selected from the group consisting of —O— and —S—;

m 1 is an integer from 0 to 4;

n 1 is an integer from 0 to 1;

R 11 is selected from the group consisting of —NH 2 , —NH—CH(═NH), —NH—C(CH 3 )(═NH), —CH(═NH)NH 2 , and —NH—C(═NH)NH 2 ;

R 3 is selected from the group consisting of:

X 3 is selected from the group consisting of —CH 2 —, —C(CH 3 ) 2 —, —O—, and —S—;

m 3 is an integer from 1 to 2;

n 3 is an integer from 0 to 2;

R 31 is selected from the group consisting of C 1-10 alkyl, C 1-10 alkenyl, C 1-10 alkynyl, and C 1-10 cycloalkyl;

R 4 is selected from the group consisting of hydrogen, optionally substituted C 1-6 alkyl, and optionally substituted C 3-7 cycloalkyl;

Ar is an optionally substituted phenyl,

R 5 is selected from the group consisting of:

each optionally substituted with methyl, ethyl, n-propyl, isopropyl, cyclopropyl, tert-butyl, hydroxyl, methoxyl, ethoxyl, hydroxymethyl, trifluoromethyl, trifluoromethoxyl, or halogen moieties, and

wherein:

each A 5 is separately selected from the group consisting of ═CH— and ═N—, with the proviso that each A 5 containing ring contains no more than four ═N— groups;

each B 5 is separately selected from the group consisting of —C═, —N═, —O—, —S—, —NH—, and —N(R 6 )—, with the proviso that each B 5 containing ring contains no more than three heteroatoms;

R 6 is selected from the group consisting of hydrogen, C 1-6 alkyl, and C 3-6 cycloalkyl;

R 51 is selected from the group consisting of hydrogen, methyl, ethyl, and cyclopropyl;

m 5 is an integer from 1 to 3;

n 5 is an integer from 0 to 2;

p 5 is an integer from 0 to 4; and

any amino groups present in R 1 are optionally acylated with an amino acid having an (S)-configuration selected from aspartic acid and glutamic acid.

2. The compound of claim 1 , wherein R 3 is selected from the group consisting of:

wherein:

R 31 is selected from the group consisting of ethyl, propyl, isopropyl, isobutyl, tert-butyl, cyclopropyl, cyclobutyl, cyclopentyl, and cyclohexyl; and

m 3 is an integer from 1 to 2.

3. The compound of claim 1 , wherein —N(R 4 )(R 5 ) is selected from the group consisting of:

4. The compound of claim 3 , selected from the group consisting of:

5. A pharmaceutical composition, comprising a compound of 1 in an amount effective to inhibit an efflux pump of a microbe.

6. A pharmaceutical composition, comprising a compound of 1 in combination with an antimicrobial agent.

7. The compound of claim 1 , wherein:

n1 is 0;

m1 is an integer from 2 to 4; and

R 11 is —NH 2 .

8. The compound of claim 1 , wherein:

R 31 is selected from the group consisting of C 1-10 alkyl and C 3-10 cycloalkyl;

X 3 is —CH 2 —; and

n3 is an integer from 0 to 1.

9. The compound of claim 3 , wherein:

n1 is 0;

m1 is an integer from 2 to 4;

R 11 is —NH 2 ;

R 31 is selected from the group consisting of C 1-10 alkyl and C 3-10 cycloalkyl;

X 3 is —CH 2 —; and

n3 is an integer from 0 to 1.

10. The compound of claim 9 , wherein R 3 is

11. A compound having the structure of Formula (III):

wherein:

R 1 is:

X 1 is selected from the group consisting of —O— and —S—;

m 1 is an integer from 0 to 4;

n 1 is an integer from 0 to 1;

R 11 is selected from the group consisting of —NH 2 , —NH—CH(═NH), —NH—C(CH 3 )(═NH), —CH(═NH)NH 2 , and —NH—C(═NH)NH 2 ;

R 3 is selected from the group consisting of:

X 3 is selected from the group consisting of —CH 2 —, —C(CH 3 ) 2 — —O—, and —S—;

m 3 is an integer from 1 to 2;

n 3 is an integer from 0 to 2;

R 31 is selected from the group consisting of C 1-10 alkyl, C 1-10 alkenyl, C 1-10 alkynyl, and C 1-10 cycloalkyl;

R 4 is selected from the group consisting of hydrogen, optionally substituted C 1-6 alkyl, and optionally substituted C 3-7 cycloalkyl;

Ar is phenyl substituted with one or more groups independently selected from the group consisting of heterocyclyl, heteroaryl, chlorine, bromine, iodine, hydroxy, amino, cyano, nitro, alkylamido, acyl, C 1-6 alkoxy, C 1-6 alkyl, C 1-6 hydroxyalkyl, C 1-6 aminoalkyl, C 1-6 alkylamino, alkylsulfenyl, alkylsulfinyl, alkylsulfonyl, sulfamoyl, or trifluoromethyl, and

R 5 is

optionally substituted with methyl, ethyl, n-propyl, isopropyl, cyclopropyl, tert-butyl, hydroxyl, methoxyl, ethoxyl, hydroxymethyl, trifluoromethyl, trifluoromethoxyl, or halogen moieties;

each A 5 is separately selected from the group consisting of ═CH— and ═N—, with the proviso that each A 5 containing ring contains no more than four ═N— groups;

n 5 is an integer from 0 to 2; and

any amino groups present in R 1 are optionally acylated with an amino acid having an (S)-configuration selected from aspartic acid and glutamic acid.

12. The compound of claim 11 , selected from the group consisting of:

13. The compound of claim 11 , selected from the group consisting of:

14. The compound of claim 1 , wherein R 4 is hydrogen.

15. A compound having the structure of Formula (III):

wherein:

R 1 is:

X 1 is selected from the group consisting of —O— and —S—;

m 1 is an integer from 0 to 4;

n 1 is an integer from 0 to 1;

R 11 is selected from the group consisting of —NH 2 , —NH—CH(═NH), —NH—C(CH 3 )(═NH), —CH(═NH)NH 2 , and —NH—C(═NH)NH 2 ;

R 3 is selected from the group consisting of:

X 3 is selected from the group consisting of —CH 2 —, —C(CH 3 ) 2 — —O—, and —S—;

m 3 is an integer from 1 to 2;

n 3 is an integer from 0 to 2;

R 31 is selected from the group consisting of C 1-10 alkyl, C 1-10 alkenyl, C 1-10 alkynyl, and C 1-10 cycloalkyl;

Ar is an optionally substituted phenyl,

R 4 is bound to R 5 to form a five-membered or six-membered heterocyclic ring selected from the group consisting of:

any amino groups present in R 1 are optionally acylated with an amino acid having an (S)-configuration selected from aspartic acid and glutamic acid.

16. A method of treating a bacterial infection, comprising administering to a subject suffering from said bacterial infection an amount effective to inhibit an efflux pump of said bacteria of a compound of claim 1 or 11 .

17. The method of claim 16 , wherein the subject is a human.

18. The method of claim 16 , wherein the bacteria is selected from the group consisting of Pseudomonas aeruginosa, Pseudomonas fluorescens, Pseudomonas acidovorans, Pseudomonas alcaligenes, Pseudomonas putida, Stenotrophomonas maltophilia, Burkholderia cepacia, Aeromonas hydrophilia, Escherichia coli, Citrobacter freundii, Salmonella typhimurium, Salmonella typhi, Salmonella paratyphi, Salmonella enteritidis, Shigella dysenteriae, Shigella flexneri, Shigella sonnei, Enterobacter cloacae, Enterobacter aerogenes, Klebsiella pneumoniae, Klebsiella oxytoca, Serratia marcescens, Francisella tularensis, Morganella morganii, Proteus mirabilis, Proteus vulgaris, Providencia alcalifaciens, Providencia rettgeri, Providencia stuartii, Acinetobacter calcoaceticus, Acinetobacter haemolyticus, Yersinia enterocolitica, Yersinia pestis, Yersinia pseudotuberculosis, Yersinia intermedia, Bordetella pertussis, Bordetella parapertussis, Bordetella bronchiseptica, Haemophilus influenzae, Haemophilus parainfluenzae, Haemophilus haemolyticus, Haemophilus parahaemolyticus, Haemophilus ducreyi, Pasteurella multocida, Pasteurella haemolytica, Branhamella catarrhalis, Helicobacter pylori, Campylobacter fetus, Campylobacter jejuni, Campylobacter coli, Borrelia burgdorferi, Vibrio cholerae, Vibrio parahaemolyticus, Legionella pneumophila, Listeria monocytogenes, Neisseria gonorrhoeae, Neisseria meningitidis, Kingella, Moraxella, Gardnerella vaginalis, Bacteroides fragilis, Bacteroides distasonis, Bacteroides 3452A homology group, Bacteroides vulgatus, Bacteroides ovalus, Bacteroides thetaiotaomicron, Bacteroides uniformis, Bacteroides eggerthii , and Bacteroides splanchnicus.

19. A method for inhibiting growth of antibacterial-resistant bacteria, comprising contacting the bacteria with a compound of claim 1 or 11 and an antibacterial agent.

20. The method of claim 19 , wherein the antibacterial agent is selected from the group consisting of a quinolone, aminoglycoside, beta-lactam, coumermycin, chloramphenical, lipopeptide, glycopeptide, glycylcycline, ketolide, macrolide, oxazolidonone, rifamycin, streptogramin, and tetracycline.

21. The method of claim 20 , wherein the antibacterial agent is selected from the group consisting of ciprofloxacin, levofloxacin, moxifloxacin, ofloxacin, gatifloxacin, cinoxacin, gemifloxacin, norfloxacin, lomofloxacin, pefloxacin, garenoxacin, sitafloxacin, and DX-619.

22. A method for treating a bacterial infection in a subject, wherein the bacteria causing the infection exhibit antibiotic resistance through an efflux pump mechanism, comprising:

administering to a subject an antibiotic to which said bacteria are resistant; and

administering to said subject a compound of claim 1 or 11 in conjunction with said antibiotic.

23. The method of claim 22 , wherein the antibiotic is selected from the group consisting of a quinolone, aminoglycoside, beta-lactam, coumermycin, chloramphenical, lipopeptide, glycopeptide, glycylcycline, ketolide, macrolide, oxazolidonone, rifamycin, streptogramin, and tetracycline.

24. The method of claim 23 , wherein the antibiotic is selected from the group consisting of ciprofloxacin, levofloxacin, moxifloxacin, ofloxacin, gatifloxacin, cinoxacin, gemifloxacin, norfloxacin, lomofloxacin, pefloxacin, garenoxacin, sitafloxacin, and DX-619.

25. The compound of claim 11 , having the structure: