Three-dimensional structure of complement receptor type 2 and uses thereof

Abstract

Disclosed is a crystalline human CR2 protein in complex with C3d, and the three dimensional structure of the crystalline complex. Also disclosed are methods of use of the structure, particularly for structure-based identification of compounds that bind to CR2 and inhibit or enhance the binding of CR2 to a natural ligand, that bind to CR2 and agonize or antagonize the receptor, that bind to CR2 and inhibit or enhance CR2 dimerization, or that use the C3-binding ability of CR2 as a drug delivery vehicle. Also disclosed are therapeutic compounds obtained by such methods and uses for such compounds.

1 - 47 . (canceled)  
     
     
         48 . A drug delivery system, comprising: 
 a) a drug; and,    b) a portion of a CR2 protein consisting essentially of less than a full-length CR2 protein or soluble CR2 protein selected from the group consisting of: 
 i) a portion comprising positions on strand B and the B-C loop of SCR2 including: G79-G80-Y81-K82-183-R84-G85-S86-T87-P88-Y89 with respect to SEQ ID NO:4;  
 ii) a portion comprising position K100 with respect to SEQ ID NO:4 on the B strand of CR2;  
 iii) a portion comprising positions: V 130-F 31-P 132-L133, with respect to SEQ ID NO:4; and,  
 iv) a portion comprising any combination of portions (I)-(iii);  
 wherein the portion has the three dimensional structure of a portion of a CR2 short consensus repeat (SCR) 1-2 region sufficient to bind to C3d, C3 or other CR2-binding fragments of C3 that contain C3d or a portion thereof; and  
 wherein the drug is linked to the portion of the CR2 protein.  
   
     
     
         49 . The drug delivery system of  claim 48 , wherein the CR2 short consensus repeat (SCR) 1-2 region has a three dimensional structure selected from the group consisting of: 
 a) a structure defined by atomic coordinates of a three dimensional structure of a crystalline CR2 SCR1-2 region in complex with C3d;    b) a structure defined by atomic coordinates selected from the group consisting of: 
 i) atomic coordinates represented in a table selected from the group consisting of Table 2 and Table 3; and,  
 ii) atomic coordinates that define a three dimensional structure, wherein at least 50% of said structure has an average root-mean-square deviation (RMSD) from backbone atoms in secondary structure elements in at least one domain of a three dimensional structure represented by said atomic coordinates of (I) of equal to or less than about 1.0 Å; and  
 iii) a structure defined by atomic coordinates derived from CR2 protein molecules arranged in a crystalline manner in a space group R32 so as to form a unit cell of dimensions a=b=170.5 Å, c=173.8 Å.  
   
     
     
         50 . The drug delivery system of  claim 48 , wherein the CR2 short consensus repeat (SCR) 1-2 region has a three dimensional structure defined by atomic coordinates, wherein at least 75% of said structure has an average root-mean-square deviation (RMSD) from backbone atoms in secondary structure elements in at least one domain of a three dimensional structure represented by atomic coordinates of Table 2 or Table 3 of equal to or less than about 1.0 Å.  
     
     
         51 . The drug delivery system of  claim 48 , wherein the CR2 short consensus repeat (SCR) 1-2 region has a three dimensional structure defined by atomic coordinates, wherein at least 50% of said structure has an average root-mean-square deviation (RMSD) from backbone atoms in secondary structure elements in at least one domain of a three dimensional structure represented by atomic coordinates of Table 2 or Table 3 of equal to or less than about 0.5 Å.  
     
     
         52 . The drug delivery system of  claim 48 , wherein the CR2 short consensus repeat (SCR) 1-2 region has a three dimensional structure defined by atomic coordinates, wherein at least 75% of said structure has an average root-mean-square deviation (RMSD) from backbone atoms in secondary structure elements in at least one domain of a three dimensional structure represented by atomic coordinates of Table 2 or Table 3 of equal to or less than about 0.5 Å.  
     
     
         53 . The drug delivery system of  claim 48 , wherein the portion of CR2 forms a dimer with a second, identical portion of CR2.  
     
     
         54 . The drug delivery system of  claim 48 , wherein the portion of CR2 consists essentially of the SCR1-SCR2 region of CR2.  
     
     
         55 . The drug delivery system of  claim 48 , wherein the portion of CR2 consists essentially of a portion of the SCR1-SCR2 region of CR2.  
     
     
         56 . The drug delivery system of  claim 48 , wherein the portion of CR2 consists essentially of the B strand and B-C loop of SCR2.  
     
     
         57 . The drug delivery system of  claim 48 , wherein the portion of CR2 further comprises positions T101-N102-F103 of CR2, with respect to SEQ ID NO:4.  
     
     
         58 . The drug delivery system of  claim 48 , wherein the full-length CR2 comprises SEQ ID NO:1.  
     
     
         59 . The drug delivery system of  claim 48 , wherein the portion of CR2 consists essentially of an amino acid sequence that is at least about 75% identical to SEQ ID NO:1.  
     
     
         60 . The drug delivery system of  claim 48 , wherein the portion of CR2 consists essentially of an amino acid sequence that is at least about 85% identical to SEQ ID NO:1.  
     
     
         61 . The drug delivery system of  claim 48 , wherein the portion of CR2 consists essentially of an amino acid sequence that is at least about 95% identical to SEQ ID NO:1.  
     
     
         62 . The drug delivery system of  claim 48 , wherein the portion of CR2 consists essentially of SEQ ID NO:4.  
     
     
         63 . The drug delivery system of  claim 48 , wherein the portion of CR2 consists essentially of a fragment of SEQ ID NO:4 that has the three dimensional structure of a portion of a CR2 short consensus repeat (SCR) 1-2 region sufficient to bind to C3d, C3 or other CR2-binding fragments of C3 that contain C3d or a portion thereof.  
     
     
         64 . The drug delivery system of  claim 48 , wherein the portion of CR2 consists essentially of an amino acid sequence of, with respect to SEQ ID NO:4, from about position 79 to about position 133 of CR2, or a fragment thereof.  
     
     
         65 . The drug delivery system of  claim 48 , wherein the portion of CR2 consists essentially of positions 79-133 of SEQ ID NO:4.  
     
     
         66 . The drug delivery system of  claim 48 , wherein the drug is covalently linked to the portion of the CR2 protein.  
     
     
         67 . The drug delivery system of  claim 48 , wherein the drug is chemically linked to the portion of the CR2 protein.  
     
     
         68 . The drug delivery system of  claim 48 , wherein the drug is selected from the group consisting of an anti-inflammatory compound, a cytotoxic drug, a complement regulatory protein, a corticosteroid, an anti-ischemia compound, a compound for treatment of autoimmune disease, and a compound for treatment of vascular disease.  
     
     
         69 . The drug delivery system of  claim 48 , wherein the drug is a complement regulatory protein.  
     
     
         70 . A method to deliver a drug to a patient, comprising administering to the patient the drug delivery system of  claim 48.