Heterocyclic compounds and uses thereof as d-alanyl-d-alanine ligase inhibitors

Abstract

The invention is based on the discovery of a new class of heterocyclic compounds having, for example, antibacterial properties. The D-Ala-D-Ala ligase enzyme is a critical pathway enzyme in the bacterial cell-wall synthesis. The compounds can bind to and inhibit the enzyme D-Ala-D-Ala ligase. The new compounds' activity combined with their ability to cross bacterial cell membranes makes them suitable for use as antibacterial drugs or other antibacterial applications.

1 . A compound comprising the formula:  
       
         
           
           
               
               
           
         
       
       wherein 
 A and B are independently selected from the group consisting of N and CR 7 , provided that A and B are not both N, wherein  
 R 7  is hydrogen or a carbon-, nitrogen-, sulfur-, halogen-, and/or oxygen-containing function group;  
 R 1  and R 2  are identical or different —NR 5 R 6  groups, wherein each R 5  and R 6  is independently hydrogen or a carbon-containing functional group;  
 R 3  is selected from the group consisting of hydrogen, alkyl, amino, hydroxy, alkoxy, and alkylamino;  
 R 4  is a carbon-, nitrogen-, sulfur-, halogen-, and/or oxygen-containing functional group, provided that, 
 if A is CH, B is nitrogen, and R 5  and R 6  are both hydrogen, then R 4  is not methyl, isobutyl, phenyl, 4-methylphenyl, 4-chlorophenyl, 4-bromophenyl, 2-(2,5-dimethoxyphenyl)-ethyl, or —CH(OCH 3 ) 2 ; and  
 
 if A and B are both CH groups, then R 4  is an amino group other than —NH 2 , (3,4-dichlorophenyl)methylamino, or (3,4-dichlorophenyl)methyleneimino.  
 
     
     
         2 . The compound of  claim 1 , wherein R 4  is a substituted or unsubstituted, linear, branched, or cyclic, alkyl, alkenyl, alkynyl, aryl, aralkyl, or alkaryl group.  
     
     
         3 . The compound of  claim 1 , wherein R 5  and R 6  are both hydrogen.  
     
     
         4 . The compound of  claim 1 , wherein R 4  includes at least one aryl group.  
     
     
         5 . The compound of  claim 4 , wherein R 4  is selected from the group consisting of:  
       
         
           
           
               
               
           
         
       
     
     
         6 . The compound of  claim 4 , wherein R 4  is:  
       
         
           
           
               
               
           
         
       
       wherein R 8-12  are independently selected from the group consisting of hydrogen and carbon-, nitrogen-, sulfur-halogen- and/or oxygen-containing functional groups.  
     
     
         7 - 11 . (canceled)  
     
     
         12 . The compound of  claim 4 , wherein R 4  is selected from the group consisting of —CH 2 O-aryl, —CH 2 S-aryl, —CH═CH-aryl, and —NH(CH 2 -aryl).  
     
     
         13 . (canceled)  
     
     
         14 . The compound of  claim 1 , wherein R 4  is selected from the group consisting of —N(CH 3 )R 21 , —N(CH 2 CH 3 )R 21 , —N(CH(CH 3 ) 2 )e 21 , and —N(benzyl)R 21 , where R 21  is a carbon-, nitrogen-, sulfur-, halogen-, and/or oxygen-containing functional group.  
     
     
         15 . The compound of  claim 1 , wherein R 4  is selected from the group consisting of —CH 2 NH 2 , —NHCH 2 CH 2 NR 22 R 23   7  and —CH 2 NHC(═O)R 22 , wherein R 22 , and R 23  are independently selected from the group consisting of hydrogen and carbon-, nitrogen-, sulfur halogen- and/or oxygen-containing functional groups.  
     
     
         16 . The compound of  claim 15 , wherein R 22  is hydrogen and R 23  is —C(═O)R 24 , where R 24  is hydrogen or a carbon-, nitrogen-, sulfur-halogen- and/or oxygen-containing functional group.  
     
     
         17 - 22 . (canceled)  
     
     
         23 . A compound comprising the formula:  
       
         
           
           
               
               
           
         
       
       wherein 
 R 1  and R 2  are identical or different —NR 5 R 6  groups, wherein each R 5  and R 6  is independently hydrogen or a carbon-containing functional group; and  
 R 4  is an amino group other than —NH 2  or  
                     
 
     
     
         24 . A method of inhibiting D-Ala-D-Ala ligase, the method comprising exposing D-Ala-D-Ala ligase to a compound of formula I or formula II:  
       
         
           
           
               
               
           
         
       
       wherein 
 A and B are independently selected from the group consisting of N and CR 7 , provided that A and B in formula II are not both N. wherein R 7  is hydrogen or a carbon-, nitrogen-, sulfur-, halogen-, and/or oxygen-containing function group;  
 R 1  and R 2  are identical or different —NR 5 R 6  groups, wherein each R 5  and R 6  is independently hydrogen or a carbon-containing functional group; and  
 R 3  and R 4  are independently selected from the group consisting of hydrogen and carbon-, nitrogen-, sulfur-, halogen-, and/or oxygen-containing functional groups; provided that R 3  and R 4  are not both hydrogen.  
 
     
     
         25 . The method of  claim 24 , wherein R 1  and R 2  are both —NH 2 .  
     
     
         26 . The method of  claim 24 , wherein R 3  is hydrogen.  
     
     
         27 . The method of  claim 24 , wherein 
 R 3  and R 4  are independently selected from the group consisting of -branched and straight-chain alkyl, —O-alkyl, —O-alkyl-COOH, —O-alkyl-NR 7 R 8 , —O-alkyl-OH, —NR 7 R 8 , —NR 7 -alkyl-NR 8 R 9 , —NR 7 -alkyl-COOH, —NR 7 -alkyl-OH; —CONR 7 R 8 , —CONR 7 -alkyl-NR 8 R 9 , CONR 7 -alkyl-COOH, —CONR 7 -alkyl-OH, —S-alkyl, —S-alkyl-COOH, —S-alkyl-NR7R′, -alkyl-OH, —O-aryl, —O-aryl-COOH, —O-aryl-NR 7 R 8 , —O-aryl-OH, —S-aryl, —S-aryl-COOH, —S-aryl-NR 7 R 8 , —S-aryl-OH, —NR 7 -aryl-NR 8 R 9 , —NR 7 -aryl-COOH, —NR 7 -aryl-OH; —CONR 7 -aryl-NR 8 R 9 , —CONR 7 -aryl-COOH, —CONR-aryl-OH, —CH 2 NR 5 C 6 H 4 COOH; provided that R 3  and R 4  cannot simultaneously be identical branched or straight chain alkyl groups;    R 1  and R 2  are independently selected from the group consisting of hydrogen, —NH 2 , and —NR 11 R 12 , wherein at least one of R 1  and R 2  is —NH 2 ;    R 5  is lower alkyl, —H, or —CH 2 NR 10 C 6 H 4 CONHR 6 ; wherein R 6  is selected from the group consisting of -alkyl, -alkyl-COOH, -alkyl-NH 2 , and -alkyl-OH;    R 7 , R 8 , R 9 , R 10 , R 11 , and R 12  are independently selected from the group consisting of straight-chain alkyl, branched alkyl, aryl, and acyl groups, optionally substituted with one or more oxygen, nitrogen, sulfur, or halogen-based functional groups; and    A is selected from the group consisting of N and CH.    
     
     
         28 . A method of treating a patient, the method comprising administering to the patient an effective amount of a compound of formula I or formula II:  
       
         
           
           
               
               
           
         
       
       wherein 
 A and B are independently selected from the group consisting of N and CR 7 , provided that A and B in formula II are not both N, wherein R 7  is hydrogen or a carbon-, nitrogen-, sulfur-halogen- and/or oxygen-containing function group;  
 R 1  and R 2  are identical or different —NR 5 R 6  groups, wherein each R 5  and R 6  is independently hydrogen or a carbon-containing functional group; and  
 R 3  and R 4  are independently selected from the group consisting of hydrogen and carbon-, nitrogen-, sulfur-, halogen-, and/or oxygen-containing functional groups; provided that R 3  and R 4  are not both hydrogen.  
 
     
     
         29 . The method of  claim 28 , wherein R 1  and R 2  are both —NH 2 .  
     
     
         30 . The method of  claim 28 , wherein R 3  is hydrogen.  
     
     
         31 . The method of  claim 28 , wherein 
 R 3  and R 4  are independently selected from the group consisting of: -branched and straight-chain alkyl, —O-alkyl, —O-alkyl-COOH, —O-alkyl-NR 7 R 8 , —O-alkyl-OH, —NR 7 R 8 , —NR 7 -alkyl-NR 8 R 9 , —NR 7 -alkyl-COOH, —NR 7 -alkyl-OH; —CONR 7 R 8 , —CONR 7 -alkyl-NR 8 R 9 , —CONR 7 -alkyl-COOH, —CONR 7 -alkyl-OH, —S-alkyl, —S-alkyl-COOH, —S-alkyl-NR 7 R 8 , -S-alkyl-OH, —O-aryl, —O-aryl-COOH, —O-aryl-NR 7 R 8 , —O-aryl-OH, —S-aryl, —S-aryl-COOH, -Saryl-NR 7 R 8 , —S-aryl-OH, —NR 7 -aryl-NR 8 R 9 , —NR 7 -aryl-COOH, —NR 7 -aryl-OH; —CONR 7 -aryl-NR 8 R 9 , —CONR 7 -aryl-COOH, —CONR 7 -aryl-OH, —CH 2 NR 5 C 6 H 4 COOH; provided that R 3  and R 4  cannot simultaneously be identical branched or straight chain alkyl groups;    R 1  and R 2  are independently selected from the group consisting of hydrogen, —NH 2 , and —NR 11 R 12 , wherein at least one of R 1  and R 2  is —NH 2 ;    R 5  is lower alkyl, —H, or —CF 2 NR 10 C 6 H 4 CONHR 6 ; wherein R 6  is selected from the group consisting of alkyl, -alkyl-COOH, -alkyl-NH 2 , and -alkyl-OH;    wherein R 7 , R 8 , R 9 , R 10 , R 11 , and R 12  are independently selected from the group consisting of straight-chain alkyl, branched alkyl, aryl, and acyl groups, optionally substituted with one or more oxygen, nitrogen, sulfur, or halogen-based functional groups; and    A is selected from the group consisting of N and CH.    
     
     
         32 . A formulation comprising the compound of  claim 1  combined with an excipient suitable for administration to a subject.  
     
     
         33 . A method of treating a subject having a microbial infection, the method comprising administering to the subject an effective amount of the formulation of  claim 32 .  
     
     
         34 . The method of  claim 33 , wherein the subject is an animal.  
     
     
         35 . A method of inhibiting bacteria growth in a non-living system, the method comprising contacting the system with an effective amount of the compound  claim 1  to inhibit bacterial growth.  
     
     
         36 . The method of  claim 24 , wherein the D-Ala-D-Ala ligase comprises a sequence at least 90% identical to the sequence of a D-Ala-D-Ala ligase from a species selected from the group consisting of  Escherichia coli, Chlamydia pneumoniae, Chlamydia trachomatis, Yersinia pestis, Haemophilus influenzae, Haemophilus ducreyi, Pseudomonas aeruginosa, Pseudomonasputida, Xylellafastidiosa, Bordetellapertussis, Thiobacillusferrooxidans, Neisseriameningitidis, Neisseria gonorrhoeae, Buchn era aphidicola, Bacillus halodurans, Geobactersulfurreducens, Rickettsia prowazekii, Zymomonas mobilis, Aquifex aeolicus thermophile, Thermotoga maritima, Clostridium difficile, Enterococcus faecium, Streptomyces toyocaensis, Amycolatopsis orientalis, Enterococcus gallinarum, Enterococcushirae, EnterococcusJaecium, Enterococcus faecalis, Streptococcus pneumoniae, Streptococcus pyogenes, Staphylococcus aureus, Bacillus subtilis, Bacillus stearothermophilus, Deinococcus radiodurans, Synechocystis  sp.,  Salmonella typhimurium, Mycobacterium tuberculosis, Mycobacterium avium, Mycohacterium smegmatis, Legionella pneumophila, Leuconostoc mesenteroides, Borrelia burgdorferi, Treponema pallidum, Vibriocholerae , and  Helicobacter pylori.    
     
     
         37 . A method of making a compound of  claim 1 , comprising taking any one of the intermediate compounds described herein and reacting it with one or chemical reagents in one or more steps to produce a compound of  claim 1 .  
     
     
         38 . A product made by the method of  claim 37.