AI-2 compounds and analogs based on Salmonella typhimurium LsrB structure

Abstract

This invention relates to crystals comprising apo-LsrB and holo-LsrB. The structure of holo-LsrB identifies a tetrahydroxytetrahydrofuran derived from 4,5-dihydroxy-2,3-pentanedione (DPD) as the active autoinducer-2 (AI-2) molecule in Salmonella typhimurium . The X-ray crystallographic data can be used in a drug discovery method. Additionally the invention provides AI-2 analogs based on this discovery as well as pharmaceutical compositions containing those analogs.

1 . A crystal comprising LsrB.  
     
     
         2 . The crystal of  claim 1  comprising an LsrB-ligand complex, the crystal diffracting X-rays to a resolution of greater than 5.0 Angstroms.  
     
     
         3 . The crystal of  claim 2  wherein the resolution is greater than 1.3 Angstroms.  
     
     
         4 . The crystal of  claim 2 , in which the ligand comprises a furan moiety.  
     
     
         5 . The crystal of  claim 2 , in which the ligand comprises autoinducer-2.  
     
     
         6 . The crystal of  claim 5  in which the ligand has the chemical formula:  
       
         
           
           
               
               
           
         
       
     
     
         7 . A method of using the crystal of  claim 1  to identify whether a ligand binds to LsrB which comprises obtaining the atomic coordinates in the crystal of at least a selected portion of LsrB; using the atomic coordinates to computer model the selected portion; and identifying a potential ligand that can bind to the selected portion of LsrB.  
     
     
         8 . The method of  claim 7 , wherein the selected portion comprises one or more amino acid residues selected from the group consisting of Lys35, Asp116, Asp166, Gln 167, Pro220 and Ala 222.  
     
     
         9 . The method of  claim 7  in which information regarding the selected portion is stored on a computer.  
     
     
         10 . The method of  claim 7  in which a computer is used for identifying the potential ligand or the docking of the potential ligand to the binding site, or both.  
     
     
         11 . The method of  claim 7 , further comprising obtaining a sample of the potential ligand and contacting a prokaryotic cell with said sample under conditions to whether said ligand can bind to LsrB.  
     
     
         12 . A ligand identified by the method of  claim 7 .  
     
     
         13 . A pharmaceutical composition comprising the ligand of  claim 12 .  
     
     
         14 . The pharmaceutical composition of  claim 13  in which the ligand is a compound having the chemical formula:  
       
         
           
           
               
               
           
         
       
     
     
         15 . A method of treatment comprising administering the pharmaceutical composition of  claim 13  to a human in an amount that is therapeutically effective to treat a bacterial infection.  
     
     
         16 . A compound represented by the formula:  
       
         
           
           
               
               
           
         
       
       wherein 
 X is CFH or CF 2 ;  
 Y is hydrogen, hydroxy, methyl or amino;  
 Z is hydroxy or amino; and  
 R is lower alkyl,  
 or a pharmaceutically-acceptable salt thereof.  
 
     
     
         17 . A compound represented by the formula:  
       
         
           
           
               
               
           
         
       
       wherein 
 W is hydroxyl or amino;  
 X is O, NH, S, CH 2 , CFH or CF 2 ;  
 Y is hydrogen, hydroxy, methyl or amino;  
 Z is hydroxy or amino; and  
 R 1  and R 2  are independently lower alkyl,  
 or a pharmaceutically-acceptable salt thereof.  
 
     
     
         18 . A compound represented by the formula:  
       
         
           
           
               
               
           
         
       
       wherein 
 W is hydroxyl or amino;  
 X is O, NH, S, CH 2 , CFH or CF 2 ;  
 Y is hydrogen, hydroxy, methyl or amino;  
 Z is hydroxy or amino; and  
 R 1  and R 2  are independently lower alkyl,  
 or a pharmaceutically-acceptable salt thereof.  
 
     
     
         19 . A compound represented by the formula:  
       
         
           
           
               
               
           
         
       
       wherein 
 X is O, NH, S, CH 2 , CFH or CF 2 ;  
 Y is hydrogen, hydroxy, methyl or amino;  
 Z is hydroxy or amino; and  
 R is lower alkyl,  
 or a pharmaceutically-acceptable salt thereof.  
 
     
     
         20 . A pharmaceutical composition comprising one or more compounds of any one of claims  16 - 19  in admixture with a pharmaceutically acceptable carrier.  
     
     
         21 . A method of regulating the activity of an autoinducer-2 (AI-2) receptor which comprises contacting said AI-2 receptor with an AI-2 analog for a time and in an amount sufficient to regulate said activity, wherein said AI-2 analog is a compound of any one of claims  16 - 19 .  
     
     
         22 . The method of  claim 21  wherein the AI-2 receptor is LsrB, LuxP or LuxQ.  
     
     
         23 . The method of  claim 21 , wherein the AI-2 receptor is found on a bacterial cell.  
     
     
         24 . The method of  claim 23 , wherein the activity regulated is selected from bacterial cell growth, siderophore expression, bacterial virulence, biofilm formation exopolysaccharide production in bacterial cells and bacterial colony morphology.  
     
     
         25 . The method  claim 24 , wherein the activity is the inhibition of siderophore expression.  
     
     
         26 . The method  claim 24 , wherein the exopolysaccharide production is rugose polysaccharide production.  
     
     
         27 . The method  claim 24 , wherein the activity is smooth colony morphology formation.  
     
     
         28 . The method of  claim 23 , wherein the bacterial cell is found in a warm blooded host.  
     
     
         29 . The method of  claim 23 , wherein the bacterial cell is selected from the group consisting of  Vibrio harveyi, Vibrio cholerae, Vibrio parahaemolyticus, Vibrio alginolyticus, Pseudomonas phosphoreum, Yersinia enterocolitica, Escherichia coli, Salmonella typhimurium, Salmonella typhi, Haemophilus influenzae, Helicobacter pylori, Bacillus subtilis, Borrelia burgfdorferi, Neisseria meningitidis, Neisseria gonorrhoeae, Yersinia pestis, Campylobacter jejuni, Deinococcus radiodurans, Mycobacterium tuberculosis, Enterococcus faecalis, Streptococcus pneumoniae, Streptococcus pyogenes  and  Staphylococcus aureus.    
     
     
         30 . A method for treating a subject infected with a pathogenic bacteria which comprises administering a therapeutically-effective amount of a pharmaceutical composition of  claim 20  to a subject for a time and in an amount sufficient to inhibit AI-2 activity.