RelA Inhibitors for Biofilm Disruption

Abstract

Pharmaceutical compositions comprising a RelA enzyme inhibitor and a bactericidal antibiotic, wherein said RelA enzyme inhibitor binds to the RelA enzyme in bacteria to reduce biofilm formation and to degrade biofilms that have been formed. The pharmaceutical compositions can be used to treat bacterial biofilm diseases.

1 - 6 . (canceled) 
     
     
         7 . A method of treating a bacterial biofilm disease in a patient comprising administering to said patient an effective amount of a composition comprising a RelA enzyme inhibitor and a bactericidal antibiotic, wherein said RelA enzyme inhibitor binds to RelA enzyme. 
     
     
         8 . The method of  claim 7 , wherein the bacterial biofilm disease is selected from the group consisting of chronic otitis media with effusion, otorrhea, chronic pharyngitis, chronic sinusitis, chronic tonsillitis, cholesteatoma, native and artificial valve endocarditis, chronic obstructive pulmonary disease (COPD), cystic fibrosis pneumonias, bacterial vaginosis, pelvic inflammatory disease, endometritis, salpingitis, chronic prostatitis, periodontal disease, neuroborreliosis and other chronic bacterial infections of the central nervous system, septic arthritis, bony non-unions, infected catheters, infected arthroplasties, other infected implanted medical devices including pace makers, screws, plates, stents, grafts, wounds, chronic non-healing wounds including pressure ulcers, diabetic ulcers, burns, decubitus ulcers, chronic pelvic pain syndromes, and lower back pain associated with biofilm infections in the nucleus polposa of the vertebral disks. 
     
     
         9 . The method of  claim 7 , wherein the patient is a mammal. 
     
     
         10 . The method of  claim 7 , wherein the pharmaceutical composition is administered subcutaneously, orally, intravenously, or topically. 
     
     
         11 - 18 . (canceled) 
     
     
         19 . The method of  claim 7 , wherein the bacterial biofilm disease is selected from the group consisting of chronic otitis media with effusion, neuroborreliosis, and lower back pain associated with biofilm infections in the nucleus polposa of the vertebral disks. 
     
     
         20 . The method of  claim 7 , wherein the bacterial biofilm disease is selected from the group consisting of chronic otitis media with effusion and neuroborreliosis. 
     
     
         21 . The method of  claim 7 , wherein the patient is a human, horse, dog or cat. 
     
     
         22 . The method of  claim 7 , wherein the patient is a human. 
     
     
         23 . The method of  claim 7 , wherein the pharmaceutical composition is administered subcutaneously or topically. 
     
     
         24 . The method of  claim 7 , wherein the RelA enzyme inhibitor binds to the RelA enzyme with a predicted binding score which is less than or equal to −9 kcal/mole. 
     
     
         25 . The method of  claim 7 , wherein the RelA enzyme inhibitor binds to the RelA enzyme with a predicted binding score which is −13.57 to −9.5 kcal/mole. 
     
     
         26 . The method of  claim 7 , wherein the RelA enzyme inhibitor is selected from the group consisting of S3-G1A and S3-G1B: 
       
         
           
                 
                 
                 
               
                     
                 
                   Compound Structure 
                   IUPAC Name 
                   Assay Name 
                 
                     
                 
                   
                     
                       
                       
                           
                           
                       
                     
                   
                   (4-chlorophenyl)([(3-(4- hydroxyphenyl)-1H-pyrazol-5- yl]carbonyl)amino)acetic acid 
                   S3-G1A 
                 
                     
                 
                   
                     
                       
                       
                           
                           
                       
                     
                   
                   3-(6-amino-5-cyano-4-[2- (propylamino)pyrimidin-5- yl]pyridin-2-yl))-1H-pyrazole- 5-carboxylic acid 
                   S3-G1B 
                 
                     
                 
             
                
                
                
               
               
                
                
                
                
               
            
           
         
         a bioisostere of S3-G1A and S3-G1B; an enantiomer of S3-G1A, S3-G1B and the foregoing bioisosteres; a racemic mixture of enantiomers of S3-G1A and S3-G1B and the foregoing bioisosteres, and a pharmaceutically acceptable salt of S3-G1A and S3-G1B, the foregoing enantiomers, bioisosteres and racemic mixtures. 
       
     
     
         27 . The method of  claim 7 , wherein the RelA enzyme inhibitor is selected from the group consisting of a bioisostere of S3-G1A or S3-G1B an enantiomer of the bioisostere of S3-G1A or S3-G1B, a racemic mixture of enantiomers of the bioisostere of S3-G1A or S3-G1B, and a pharmaceutically acceptable salt of the bioisostere of S3-G1A or S3-G1B, and wherein the bioisostere of S3-G1A or S3-G1B is selected from the group consisting of one of the following compounds: 
       
         
           
                 
                 
               
                     
                 
                   Compound Structure 
                   IUPAC Name 
                 
                     
                 
                   
                     
                       
                       
                           
                           
                       
                     
                   
                   (S)-2-((3R,5S)-3-hydroxy-5-(4- hydroxyphenyl)tetrahydrofuran-3- carboxamido)-2-(4-(3- hydroxypropyl)phenyl)acetic acid 
                 
                     
                 
                   
                     
                       
                       
                           
                           
                       
                     
                   
                   (S)-2-(4-chlorophenyl)-2-(4-hydroxy-3- (4-hydroxyphenyl)-1H-pyrazole-5- carboxamido)acetic acid 
                 
                     
                 
                   
                     
                       
                       
                           
                           
                       
                     
                   
                   (S)-2-(4-chlorophenyl)-2-(4-hydroxy-3- (4-methoxyphenyl)-1H-pyrazole-5- carboxamido)acetic acid 
                 
                     
                 
                   
                     
                       
                       
                           
                           
                       
                     
                   
                   (S)-2-((3R,5S)-3-hydroxy-5-(4- hydroxyphenyl)tetrahydrofuran-3- carboxamido)-2-(4-(3-hydroxyprop-2- yn-1-yl)phenyl)acetic acid. 
                 
                     
                 
                   
                     
                       
                       
                           
                           
                       
                     
                   
                   (S)-2-(4-hydroxyphenyl)-2-(3-(4 hydroxyphenyl)-1H-pyrazole-5- carboxamido)acetic acid 
                 
                     
                 
             
                
                
                
               
               
                
                
                
                
                
                
                
                
                
                
               
            
           
         
       
     
     
         28 . The method of  claim 7 , wherein the bactericidal antibiotic is selected from the group consisting of an aminoglycoside, an aminomethylcycline, an aminophenicol, an ansamycin, a β-lactam, a carbapenem, a dapsone, a 2,4-diaminopyrimidine, a glycopeptide, a glycycycline, a ketolid, a lincomycin, a lincosamide, a macrolide, a nitrofuran, an oxazolidinone, a peptide, a polymyxin, a quinolone, a rifabutin, a streptogrammn, a sulfonamide, a sulfone, a tetracycline, and combinations thereof. 
     
     
         29 . The method of  claim 7 , wherein the RelA inhibitor is a compound selected from the group consisting of compounds of the Formulae I and II: 
       
         
           
           
               
               
           
         
         in Formula I, Ring (A) and Ring (C) are each bonded to carbon atoms of Ring (B) meta to one another; 
         n is 1 or 2, 
         q is 1 or 2, 
         R 1  and R 2  are each individually selected from the group consisting of hydrogen, carboxylic acid, carboxylic C 1-6  alkyl ester, hydroxyl, cyano, nitro, amino, C 1-6  alkyl amino, amino C 1-6  alkyl, optionally substituted C 2-6  alkene, optionally substituted C 1-6  alkyl, optionally substituted C 3-8  cycloalkyl, optionally substituted C 1-6  alkoxy, optionally substituted C 2-10  heterocyclyl, and optionally substituted C 6-10  aromatic hydrocarbon, wherein the optional substituent(s) are each individually selected from carboxylic acid, carboxylic C 1-3  alkyl ester, C 1-6  alkyl, halogen, C 1-6  alkoxy, hydroxyl, amino, C 1-6  alkyl amino and amino C 1-6  alkyl; preferably n is 1, q is 1, R 1  is selected from the group consisting of hydrogen, carboxylic acid, and carboxylic C 1-6  alkyl ester; and R 2  is selected from the group consisting of hydrogen, amino, C 1-6  alkyl amino and amino C 1-6  alkyl; 
         Ring (A) is a 6 membered ring selected from pyridine, pyrimidine, pyridazine, pyran, oxazine, thiazine, and piperazine; preferably Ring (A) is pyrimidine; 
         Ring (B) is a 6 membered ring selected from pyridine, pyrimidine, pyridazine, oxazine, or thiazine, Z 1  is a ring member of Ring (B) and Z 1  is nitrogen or a carbon substituted with hydrogen, cyano, amino or C 1-3  alkyl,   is a single bond, double bond or a bond in the aromatic ring, wherein R 3  and R 4  are substituents on ring carbon atoms and are each individually selected from hydrogen, cyano, amino or C 1-3  alkyl; preferably Ring (B) is pyridine, Z 1  is a carbon substituted with hydrogen, R 3  is a cyano and R 4  is an amino; and 
         Ring (C) is a 5 membered ring selected from oxazole, isoxazole, thiazole, pyrazole, imidazole, thiophene, pyrole, furan, tetrahydrofuran, tetrahydrothiophene, and pyrrolidine; preferably Ring (C) is pyrazole or tetrahydrofuran; 
       
       
         
           
           
               
               
           
         
         in Formula II, Ring (D) is substituted at a first ring carbon with phenyl-R 6  and Ring (D) is substituted at a second ring carbon with the carbonyl of the amide group, and wherein the first ring carbon and the second ring carbon are each bonded to the same third ring carbon of Ring (D), 
         R 5  is selected from the group consisting of hydrogen, carboxylic acid, carboxylic C 1-6  alkyl ester, halogen, cyano, nitro, hydroxyl, amino, amino C 1-6  alkyl, C 1-6  alkyl amino, optionally substituted C 2-6  alkene, optionally substituted C 1-6  alkyl, optionally substituted C 3-6  alkyne, optionally substituted C 3-8  cycloalkyl, optionally substituted C 1-6  alkoxy, optionally substituted C 2-20  heterocyclyl, and optionally substituted C 6-10  aromatic hydrocarbon, wherein the optional substituent(s) are each individually selected from carboxylic acid, carboxylic C 1-3  ester, C 1-6  alkyl, halogen, C 1-6  alkoxy, hydroxyl, amino, C 1-6  alkyl amino, and amino C 1-6  alkyl; preferably R 5  is halogen, hydroxyl, C 3-6  alkyne which is optionally substituted with hydroxyl, or C 1-6  alkyl which is optionally substituted with hydroxyl; 
         R 6  is selected from the group consisting of hydrogen, carboxylic acid, carboxylic C 1-6  alkyl ester, cyano, nitro, hydroxyl, amino, amino C 1-6  alkyl, C 1-6  alkyl amino, optionally substituted C 2-6  alkene, optionally substituted C 1-6  alkyl, optionally substituted C 3-8  cycloalkyl, optionally substituted C 1-6  alkoxy, optionally substituted C 2-20  heterocyclyl, and optionally substituted C 6-10  aromatic hydrocarbon, wherein the optional substituent(s) are each individually selected from carboxylic acid, carboxylic C 1-3  ester, C 1-6  alkyl, halogen, C 1-6  alkoxy, hydroxyl, amino, C 1-6  alkyl amino, and amino C 1-6  alkyl; preferably R 6  is C 1-6  alkoxy or hydroxyl; and 
         Ring (D) is an optionally substituted 5-membered heterocycle selected from oxazole, isoxazole, thiazole, pyrazole, imidazole, thiophene, pyrole, furan, tetrahydrofuran, tetrahydrothiophene, and pyrrolidine, wherein the optional substituent(s) are each individually selected from hydrogen, carboxylic acid, carboxylic C 1-3  ester, C 1-6  alkyl, halogen, C 1-6  alkoxy, hydroxyl, amino, C 1-6  alkyl amino, and amino C 1-6  alkyl;   is a single bond, double bond or a bond in the aromatic ring; preferably Ring (D) is pyrazole or tetrahydrofuran and Ring (D) is optionally substituted with a hydroxyl; 
         enantiomers of the compounds of the formulae I and II, and pharmaceutically acceptable salts of any of the foregoing compounds. 
       
     
     
         30 . The method of  claim 7 , wherein the bactericidal antibiotic is kanamycin, norfloxacin, or ampicillin. 
     
     
         31 . The method of  claim 26 , wherein the bactericidal antibiotic is selected from the group consisting of an aminoglycoside, an aminomethylcycline, an aminophenicol, an ansamycin, a β-lactam, a carbapenem, a dapsone, a 2,4-diaminopyrimidine, a glycopeptide, a glycycycline, a ketolid, a lincomycin, a lincosamide, a macrolide, a nitrofuran, an oxazolidinone, a peptide, a polymyxin, a quinolone, a rifabutin, a streptogramin, a sulfonamide, a sulfone, a tetracycline, and combinations thereof. 
     
     
         32 . The method of  claim 27 , wherein the bactericidal antibiotic is selected from the group consisting of an aminoglycoside, an aminomethylcycline, an aminophenicol, an ansamycin, a β-lactam, a carbapenem, a dapsone, a 2,4-diaminopyrimidine, a glycopeptide, a glycycycline, a ketolid, a lincomycin, a lincosamide, a macrolide, a nitrofuran, an oxazolidinone, a peptide, a polymyxin, a quinolone, a rifabutin, a streptogramin, a sulfonamide, a sulfone, a tetracycline, and combinations thereof. 
     
     
         33 . The method of  claim 26 , wherein the bactericidal antibiotic is kanamycin, norfloxacin, or ampicillin. 
     
     
         34 . The method of  claim 29 , wherein the bactericidal antibiotic is selected from the group consisting of an aminoglycoside, an aminomethylcycline, an aminophenicol, an ansamycin, a β-lactam, a carbapenem, a dapsone, a 2,4-diaminopyrimidine, a glycopeptide, a glycycycline, a ketolid, a lincomycin, a lincosamide, a macrolide, a nitrofuran, an oxazolidinone, a peptide, a polymyxin, a quinolone, a rifabutin, a streptogramin, a sulfonamide, a sulfone, a tetracycline, and combinations thereof.