Ribosome Structure and Protein Synthesis Inhibitors

Abstract

The invention provides methods for producing high resolution crystals of ribosomes and ribosomal subunits as well as crystals produced by such methods. The invention also provides high resolution structures of ribosomal subunits either alone or in combination with protein synthesis inhibitors. The invention provides methods for identifying ribosome-related ligands and methods for designing ligands with specific ribosome-binding properties as well as ligands that may act as protein synthesis inhibitors. Thus, the methods and compositions of the invention may be used to produce ligands that are designed to specifically kill or inhibit the growth of any target organism.

1 . A computer system comprising:
 (a) a memory having stored therein data defining one or more target regions from the atomic co-ordinates for  Haloarcula marismortui  large ribosomal subunit found on Disk 1 under file name 1JJ2.RTF, 1JJ2.TXT, 1JJ2.PDB, PDB1FFK.DOC, PDB1FFK.ENT or deposited at the Protein Data Bank under accession number PDB ID: 1JJ2 or 1FFK, or derived from said  Haloarcula marismortui  atomic co-ordinates by molecular modeling; and   (b) a processor in electrical communication with the memory, the processor comprising a program for generating a three-dimensional model representative of the one or more target regions.   
     
     
         2 . The computer system of  claim 1 , further comprising a device for providing a visual representation of the model. 
     
     
         3 . (canceled) 
     
     
         4 . The computer system of  claim 1 , wherein the atomic co-ordinates further define at least a portion of a protein synthesis inhibitor in association with the one or more target regions. 
     
     
         5 . The computer system of  claim 4 , wherein the protein synthesis inhibitor is an antibiotic. 
     
     
         6 . The computer system of  claim 5 , wherein the protein synthesis inhibitor is anisomycin, blasticidin, carbomycin A, sparsomycin, spiramycin, tylosin, virginiamycin M, azithromycin, linezolid, or erythromycin. 
     
     
         7 . The computer system of  claim 4 , wherein the atomic co-ordinates comprise at least a portion of the atomic co-ordinates recorded on Disk No. 1 under file name anisomycin.pdb, blasticidin.pdb, carbomycin.pdb, sparsomycin.pdb, spiramycin.pdb, tylosin.pdb, virginiamycin.pdb, ANISOMYC.PDB, BLASTICI.PDB, CARBOMYC.PDB, SPARSOMY.PDB, SPIRAMYC.PDB, TYLOSIN.PDB, VIRGINIA.PDB, AZITHROM.PDB, LINEZOLI.PDB, azithromycin.pdb, linezolid.pdb, or erythromycin.pdb, or deposited at the Protein Data Bank under accession number PDB ID: 1FFZ, 1FG0, 1K73, 1KC8, 1K8A, 1 KD1, or 1K9M. 
     
     
         8 . The computer system of  claim 1 , wherein the one or more target regions comprises at least a portion of an active site in the ribosomal subunit. 
     
     
         9 . The computer system of  claim 8 , wherein the active site comprises at least a portion of a peptidyl transferase site. 
     
     
         10 . The computer system of  claim 9 , wherein the peptidyl transferase site is defined by a plurality of residues set forth in Table 5A or Table 5B. 
     
     
         11 . The computer system of  claim 1 , wherein the one or more target regions comprises at least a portion of an A-site. 
     
     
         12 . The computer system of  claim 11 , wherein the A-site is defined by a plurality of residues set forth in Table 6A or Table 6B. 
     
     
         13 . The computer system of  claim 1 , wherein the one or more target regions comprises at least a portion of a P-site. 
     
     
         14 . The computer system of  claim 13 , wherein the P-site is defined by a plurality of residues set forth in Table 7A or Table 7B. 
     
     
         15 . The computer system of  claim 1 , wherein the one or more target regions comprises at least a portion of a polypeptide exit tunnel. 
     
     
         16 . The computer system of  claim 15 , wherein the exit tunnel is defined by a plurality of residues set forth in Table 8A, Table 8B, Table 9 or Table 10. 
     
     
         17 - 18 . (canceled) 
     
     
         19 . The computer system of  claim 1 , wherein the one or more target regions is defined by a plurality of residues set forth in Table 11A, Table 11B, Table 12A, Table 12B, Table 13A, Table 13B, Table 14A, Table 14B, Table 15A, Table 15B, Table 16A, Table 16B, Table 17A, Table 17B, Table 18A, Table 18B, Table 19A, Table 19B, Table 20A or Table 20B. 
     
     
         20 . (canceled) 
     
     
         21 . The computer system of  claim 1 , wherein the atomic co-ordinates are produced by homology modeling using at least a portion of the atomic co-ordinates deposited at the Protein Data Bank under accession number PDB ID: 1FFK or 1JJ2. 
     
     
         22 . The computer system of  claim 1 , wherein the atomic co-ordinates are produced by molecular replacement using at least a portion of the atomic co-ordinates deposited at the Protein Data Bank under accession number PDB ID: 1FFK, 1FFZ or 1JJ2. 
     
     
         23 . The computer system of  claim 1 , wherein the one or more target regions is defined by atoms of a ribosomal RNA. 
     
     
         24 . The computer system of  claim 1 , wherein the one or more target regions is defined by atoms of a ribosomal protein. 
     
     
         25 . The computer system of  claim 1 , wherein the atomic co-ordinates define a residue that is present in a ribosome of a pathogen but absent from a ribosome of a host organism. 
     
     
         26 . The computer system of  claim 25 , wherein the host organism is a mammal. 
     
     
         27 . The computer system of  claim 26 , wherein the mammal is a human. 
     
     
         28 . The computer system of  claim 1 , wherein the atomic co-ordinates define residues that are conserved among one or more pathogens or disease states. 
     
     
         29 . The computer system of method of  claim 1 , wherein the atomic co-ordinates define a residue present in a prokaryotic ribosome but absent from a eukaryotic ribosome or a eukaryotic mitochondrial ribosome. 
     
     
         30 . The computer system of  claim 29 , wherein the eukaryotic ribosome is a mammalian ribosome. 
     
     
         31 . The computer system of  claim 1 , further comprising a program for performing drug design. 
     
     
         32 . A molecular model produced by the computer system of  claim 1 . 
     
     
         33 - 62 . (canceled) 
     
     
         63 . A computer system comprising:
 (a) a memory having stored therein data indicative of atomic co-ordinates derived from an electron density map defining at least a portion of a protein synthesis inhibitor when the protein synthesis inhibitor is interacting with one or more target regions a of a large subunit of a ribosome, wherein the atomic co-ordinates comprise at least a portion of the atomic co-ordinates recorded on Disk No. 1 under file name: anisomycin.pdb, blasticidin.pdb, carbomycin.pdb, sparsomycin.pdb, spiramycin.pdb, tylosin.pdb, virginiamycin.pdb, ANISOMYC.PDB, BLASTICI.PDB, CARBOMYC.PDB, SPARSOMY.PDB, SPIRAMYC.PDB, TYLOSIN.PDB, VIRGINIA.PDB, AZITHROM.PDB, LINEZOLI.PDB, azithromycin.pdb, linezolid.pdb, or erythromycin.pdb, or deposited at the Protein Data Bank under accession number PDB ID: 1FFZ, 1FG0, 1K73, 1KC8, 1K8A, 1KD1, or 1K9M, or derived from said atomic co-ordinates by molecular modeling; and   (b) a processor in electrical communication with the memory, the processor comprising a program for generating a three-dimensional model representative of at least a portion of the protein synthesis inhibitor.   
     
     
         64 . The computer system of  claim 63 , further comprising a device for providing a visual representation of the model. 
     
     
         65 - 67 . (canceled) 
     
     
         68 . The computer system of  claim 63 , wherein the one or more target regions comprises at least a portion of an active site. 
     
     
         69 . The computer system of  claim 68 , wherein the active site comprises at least a portion of a peptidyl transferase site. 
     
     
         70 . The computer system of  claim 63 , wherein the one or more target regions comprises at least a portion of an A-site. 
     
     
         71 . The computer system of  claim 63 , wherein the one or more target regions comprises a least a portion of a P-site. 
     
     
         72 . The computer system of  claim 63 , wherein the one or more target regions comprises at least a portion of a polypeptide exit tunnel. 
     
     
         73 - 106 . (canceled) 
     
     
         107 . The computer system of  claim 63 , wherein the atomic co-ordinates are produced by homology modeling using at least a portion of the atomic co-ordinates deposited at the Protein Data Bank under accession number PDB ID: 1FFZ, 1FG0, 1K73, 1KC8, 1K8A, 1KD1, or 1K9M. 
     
     
         108 . The computer system of  claim 63 , wherein the atomic co-ordinates are produced by molecular replacement using at least a portion of the atomic co-ordinates deposited at the Protein Data Bank under accession number PDB ID: 1FFZ, 1FG0, 1K73, 1KC8, 1K8A, 1KD1, or 1K9M.