Method of Identifying Inhibitors of DHODH

Abstract

The present invention provides a compound capable of binding to the ubiquinone binding site of DHODH which contains a non-aromatic ring system as a core structure, a group capable of interacting with structural elements of subsite 2 or 3 of the ubiquinone binding site of DHODH and a group capable of interacting hydrophobically with structural elements of subsite 1 of the ubiquinone binding site of DHODH. Furthermore, the present invention provides a compound capable of binding to the ubiquinone binding site of DHODH which contains an aromatic ring system as a core structure, a group capable of interacting with residues His 56 and/or Tyr 356 of subsite 3 of the ubiquinone binding site of DHODH and a group capable of interacting hydrophobically with structural elements of subsite 1 of the ubiquinone binding site of DHODH.

1 . A method for determining the three dimensional structure of a crystalline polypeptide comprising an ubiquinone binding site of DHODH complexed with at least one ligand, said method comprising: 
 obtaining at least one crystal of the polypeptide comprising the ubiquinone binding site of DHODH complexed with a ligand;    obtaining x-ray diffraction data for said crystal; and    solving the crystal structure of said crystal using said x-ray diffraction data and atomic coordinates for the DHODH complex with the ligand.    
     
     
         2 . A method of identifying a compound which is capable of inhibiting DHODH, said method comprising: 
 obtaining at least one crystal of a polypeptide comprising an ubiquinone binding site of DHODH complexed with a ligand;    obtaining the atomic coordinates of the polypeptide in said crystal;    using said atomic coordinates to define the ubiquinone binding site of DHODH complexed with a ligand; and    identifying at least one compound which fits the ubiquinone binding site.    
     
     
         3 . A method of  claim 2 , further comprising obtaining or synthesizing the compound to inhibit at least one biological activity of DHODH.  
     
     
         4 . A method of  claim 3 , wherein said activity is enzymatic activity.  
     
     
         5 . A method of identifying a compound that is capable of inhibiting DHODH comprising: 
 determining the ability of one or more functional groups and/or moieties of the compound, when present in, or bound to, an ubiquinone binding site of DHODH to interact with at least one subsite of the ubiquinone binding site of DHODH, wherein the ubiquinone binding site of DHODH is defined by atomic coordinates of a polypeptide comprising the ubiquinone binding site of DHODH, and    assessing whether said compound is able to interact with said at least one subsite, and/or has a calculated interaction energy with a desired or preselected range to determine a potential thereof for inhibiting DHODH.    
     
     
         6 . A method of  claim 2 , wherein the atomic coordinates of the polypeptide are used to generate a three-dimensional structure of the ubiquinone binding site of DHODH, and said structure is used to assess the ability of said compound to fit into the ubiquinone binding site.  
     
     
         7 . A method of  claim 2 , wherein the atomic coordinates of the polypeptide and ligand are used to generate a three-dimensional structure of the ligand in a binding conformation thereof, and wherein said structure is used to assess the ability of said compound to exhibit a similar spatial orientation, electrostatic and/or van der Waals interaction as the ligand and to fit into the binding site.  
     
     
         8 . A method of  claim 5 , wherein said determining the ability to interact, comprises determining whether said compound is of a size and shape to physically reside in the ubiquinone binding site, and/or whether said compound has a shape which is complementary to the ubiquinone binding site and can reside in the ubiquinone binding site without significant unfavorable sterical and/or van der Waals interaction.  
     
     
         9 . A method of  claim 8 , wherein said compound possesses an energetically stabilizing interaction with at least one moiety within the subsite.  
     
     
         10 . A method of  claim 9  wherein said compound possesses an energetically stabilizing interaction with at least two complementary moieties within the subsite and said moieties are capable of participating in an attractive and/or stabilizing interaction.  
     
     
         11 . A method of  claim 10 , where in said interaction comprises an electrostatic and/or a van der Waals interaction.  
     
     
         12 . A method of  claim 10 , wherein said interaction is an ion-ion, a salt bridge, ion-dipole, dipole-dipole, hydrogen bond, pi-pi interaction, hydrophobic interaction, and/or a covalent bond.  
     
     
         13 . A compound identified by the method of  claim 1 .  
     
     
         14 . A compound identified by the method of  claim 2 .  
     
     
         15 . A compound identified by the method of  claim 5 .  
     
     
         16 . A method of  claim 5 , wherein said compound is capable of interacting with at least two subsites.  
     
     
         17 . A method of  claim 5 , wherein said compound is capable of interacting with at least three subsites.  
     
     
         18 . A method of identifying a compound that is capable of inhibiting DHODH comprising: 
 identifying at least one functional group capable of interacting with at least one subsite of the DHODH ubiquinone binding site;    identifying a scaffold which presents the functional group in a suitable orientation for interacting with said at least one subsite of the DHODH ubiquinone binding site, and    attaching the identified functional group to the scaffold to identify a compound, wherein said compound is capable of inhibiting DHODH.    
     
     
         19 . A method of  claim 18 , wherein said ubiquinone binding site is defined by the atomic coordinates of a polypeptide comprising the DHODH ubiquinone binding site.