WO2000058345A1 - NOVEL tRNA SYNTHETASE ENZYME, COMPOSITIONS CAPABLE OF BINDING TO SAID ENZYME, AND METHODS OF USE THEREOF - Google Patents

NOVEL tRNA SYNTHETASE ENZYME, COMPOSITIONS CAPABLE OF BINDING TO SAID ENZYME, AND METHODS OF USE THEREOF Download PDF

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WO2000058345A1
WO2000058345A1 PCT/US2000/008246 US0008246W WO0058345A1 WO 2000058345 A1 WO2000058345 A1 WO 2000058345A1 US 0008246 W US0008246 W US 0008246W WO 0058345 A1 WO0058345 A1 WO 0058345A1
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synthetase
trna synthetase
active site
coordinates
glycyl trna
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PCT/US2000/008246
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French (fr)
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Cheryl A. Janson
Neal Frederick Osborne
Xiayang Qiu
Christine M. Richardson
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Smithkline Beecham Corporation
Smithkline Beecham Plc
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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/195—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria
    • C07K14/305—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria from Micrococcaceae (F)
    • C07K14/31—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria from Micrococcaceae (F) from Staphylococcus (G)

Definitions

  • the invention relates to the identification of a novel enzyme active site and methods enabling the design and selection of inhibitors of that active site.
  • Transfer RNA (tRNA) synthetase enzymes are of interest as potential targets for antibacterial agents.
  • Mupirocin a selective inhibitor of bacterial isoleucyl tRNA synthetase, is marketed for the treatment of skin infections and the eradication of nasal carriage of MRSA (methicillin-resistant Staphylococcus aureus) in hospital staff and patients.
  • MRSA methicillin-resistant Staphylococcus aureus
  • Nucleic acid and amino acid sequences for glycyl tRNA synthetases are publicly available, including those of Thermus thermophilus, Mycoplasma genitalium, Homo sapiens, yeast, Bombyx mori and Caenorhabditis elegans, which are all characterized by a2 dimers, and Coxiella burnetti, Escherichia coii, Chlamydia trachomatous, Neisseria gonorrheae, Synechocystis sp., and Haemophilus influenzae, which are all characterized by being a2b2 tetramers.
  • the present invention provides a novel Staphylococcus aureus tRNA synthetase enzyme active site crystalline form.
  • the present invention provides a novel tRNA synthetase composition characterized by a catalytic site of 16 amino acid residues.
  • the invention provides a method for identifying inhibitors of the compositions described above which methods involve the steps of: providing the coordinates of the tRNA synthetase structure of the invention to a computerized modeling system; identifying compounds which will bind to the structure; and screening the compounds identified for tRNA synthetase inhibitory bioactivity.
  • the present invention provides an inhibitor of the catalytic activity of any composition bearing the catalytic domain described above.
  • Another aspect of this invention includes machine readable media encoded with data representing the coordinates of the three-dimensional structure of the tRNA synthetase crystal.
  • Fig. 1 provides the atomic coordinates of the Staph aureus glycyl tRNA synthetase.
  • Fig. 2 illustrates the cloning of the grs gene in pDB575. Briefly, the grs gene was
  • the GRS2 primer contains the Xbal site and stop codons in the three possible reading frames.
  • Fig. 3 illustrates the SDS-PAGE analysis of the GRS production by E. coii. E. coii HB 101 cells, harboring either pDB575 or pDBGRS, were induced with 1 mM IPTG.
  • Fig. 4 provides a projection of the ribbon structure of the Staphylococcus aureus glycyl tRNA synthetase dimer. The two monomers are shaded in dark and light gray.
  • Fig. 5 provides a schematic drawing of the molecular structure of the
  • Staphylococcus aureus glycyl tRNA synthetase dimer The two monomers are shaded in dark and light gray.
  • Fig. 6 provides the ribbon structure of the human glycyl tRNA synthetase monomer.
  • Fig. 7 provides a schematic drawing comparing the active sites of the human and
  • the present invention provides a novel glycyl tRNA synthetase crystalline structure, a novel Staph aureus tRNA synthetase active site, and methods of use of the crystalline form and active site to identify synthetase inhibitor compounds (peptide, peptidomimetic or synthetic compositions) characterized by the ability to competitively inhibit binding to the active site of a glycyl tRNA synthetase.
  • synthetase inhibitor compounds peptide, peptidomimetic or synthetic compositions
  • a novel human glycyl tRNA synthetase crystalline structure This structure can be used as described below for the Staph tRNA synthetase crystal structure.
  • the present invention provides a novel glycyl tRNA synthetase crystalline structure based on the Staph aureus tRNA synthetase.
  • the amino acid sequences of the synthetase are provided in SEQ ID NO: 1.
  • the crystal structure is a tightly associated S. aureus GRS dimer.
  • Each monomer has three structural domains: the N- terminal domain (residues 1-86 of SEQ ID NO: l), the active site domain (residues 150-340 of SEQ ID NO: l) and the C-terminal domain (residues 341-463 of SEQ ID NO:l).
  • the N- terminal domain having three a-helices and three b-strands, wraps around the active site domain with its second a-helix lying in the core of the dimer interface and its third b-strand adding to the central b-sheet of the active site domain to form the 7-stranded anti-parallel b sheet where the enzyme active site locates.
  • the C-terminal domain contains mainly a 5- stranded mixed b-sheet with three flanking helices and is believed to be important to anticodon recognition. While the overall architecture of the S. aureus GRS is similar to that of the T. thermophilus GRS, differences exit in the conformation of a number of surface loops, as well as the relative orientation of between the active site and C-terminal domains. With only 44% sequence identity, many amino acid side chains are also different, including several residues near the active site.
  • the Staph aureus synthetase is a dimer.
  • the present invention provides both a crystalline monomer and dimer structure of Staph aureus synthetase. Inhibitors that perturb or interact with this dimer interface are another target for the design and selection of anti-bacterial agents.
  • the crystal structure of Staph aureus tRNA synthetase has been resolved at 3.5 .
  • the structure was determined using the method of molecular replacement, and refined to an R-factor of 23.4% with goal geometry.
  • R-factor 23.4% with goal geometry.
  • further refinement of the atomic coordinates will change the numbers in Figure 1 and Tables I - III
  • refinement of the crystal structure from another crystal form will result in a new set of coordinates.
  • distances and angles in Figure 1 and Tables I - III will remain the same within experimental errors, and relative conformation of residues in the active site will remain the same within experimental error.
  • Figure 1 provides the atomic coordinates of the Staph aureus glycyl tRNA synthetase dimer, which contains 790 amino acids; with 130 residues disordered in the crystal.
  • the occupancy factor is 1.0 and the B factor is 19.60.
  • the tRNA synthetase is characterized by an active site which preferably contains a binding site for glycyl-adenylate and the receptor stem of tRNA (glycines).
  • the crystal structure described herein was solved in the absence of glycine, ATP or tRNA.
  • the region of the active site can be inferred from that of the homologous aspartyl tRNA synthetase.
  • the crystalline active site consists of 16 amino acid residues.
  • residues include Glul74, Arg206, Glu208, Phe216, Arg217, Thr218, Phe221 , Gln223, Glu225, Asp279, Glu290, Leu291, Arg297, Glu330, Ser332 and Arg337 [SEQ ID NO: l].
  • the atomic coordinates of the active site residues are provided in Table I.
  • Table II provides the distances between (D) atoms of the active site residues that are within 5.0 angstroms of one another.
  • Table III provides the angles (A) between active site atoms at are within 4.0 angstrom of each other. For simplicity, intra-residue angles are omitted.
  • the invention further provides homologues, co-complexes, mutants and derivatives of the Staph aureus tRNA synthetase crystal structure of the invention.
  • homologue means a protein having at least 30% amino acid sequence identity with synthetase or any functional domain of glycyl tRNA synthetase.
  • co-complex means glycyl tRNA synthetase or a mutant or homologue of glycyl tRNA synthetase in covalent or non-covalent association with a chemical entity or compound.
  • mutant refers to a glycyl tRNA synthetase polypeptide, i.e., a polypeptide displaying the biological activity of wild-type glycyl tRNA synthetase activity, characterized by the replacement of at least one amino acid from the wild-type synthetase sequence.
  • a mutant may be prepared, for example, by expression of Staph aureus synthetase cDNA previously altered in its coding sequence by oligonucleotide-directed mutagenesis.
  • Staph aureus glycyl tRNA synthetase mutants may also be generated by site-specific incorporation of unnatural amino acids into glycyl tRNA synthetase proteins using the general biosynthetic method of C. J. Noren et al, Science, 244: 182-188 (1989).
  • the codon encoding the amino acid of interest in wild-type glycyl tRNA synthetase is replaced by a "blank" nonsense codon, TAG, using oligonucleotide-directed mutagenesis.
  • a suppressor tRNA directed against this codon is then chemically aminoacylated in vitro with the desired unnatural amino acid.
  • the aminoacylated tRNA is then added to an in vitro translation system to yield a mutant glycyl tRNA synthetase enzyme with the site-specific incorporated unnatural amino acid.
  • Selenocysteine or selenomethionine may be incorporated into wild-type or mutant tRNA glycyl synthetase by expression of Staph aureus glycyl tRNA synthetase- encoding cDNAs in auxotrophic E. coii strains [W. A. Hendrickson et al, EMBO J., 9(5): 1665- 1672 (1990)].
  • the wild-type or mutagenized tRNA synthetase cDNA may be expressed in a host organism on a growth medium depleted of either natural cysteine or methionine (or both) but enriched in selenocysteine or selenomethionine (or both).
  • heavy atom derivative refers to derivates of glycyl tRNA synthetase produced by chemically modifying a crystal of glycyl tRNA synthetase.
  • a crystal is soaked in a solution containing heavy metal atom salts, or organometallic compounds, e.g., lead chloride, gold thiomalate, thimerosal or uranyl acetate, which can diffuse through the crystal and bind to the surface of the protein.
  • the location(s) of the bound heavy metal atom(s) can be determined by X-ray diffraction analysis of the soaked crystal. This information, in turn, is used to generate the phase information used to construct three-dimensional structure of the enzyme [T. L. Blundel and N. L. Johnson, Protein Crystallography, Academic Press (1976).
  • Another aspect of this invention involves a method for identifying inhibitors of a Staph glycyl tRNA synthetase characterized by the crystal structure and novel active site described herein, and the inhibitors themselves.
  • the novel synthetase crystalline structure of the invention permits the identification of inhibitors of synthetase activity.
  • Such inhibitors may be competitive, binding to all or a portion of the active site of the glycyl tRNA synthetase; or non-competitive and bind to and inhibit glycl tRNA synthetase whether or not it is bound to another chemical entity.
  • One design approach is to probe the glycyl tRNA synthetase crystal of the invention with molecules composed of a variety of different chemical entities to determine optimal sites for interaction between candidate glycyl tRNA synthetase inhibitors and the enzyme. For example, high resolution X-ray diffraction data collected from crystals saturated with solvent allows the determination of where each type of solvent molecule sticks. Small molecules that bind tightly to those sites can then be designed and synthesized and tested for their glycyl tRNA synthetase inhibitor activity [J. Travis, Science, 262: 1374 (1993)].
  • This invention also enables the development of compounds that can isomerize to short-lived reaction intermediates in the chemical reaction of a substrate or other compound that binds to or with glycyl tRNA synthetase.
  • the time-dependent analysis of structural changes in glycyl tRNA synthetase during its interaction with other molecules is permitted.
  • the reaction intermediates of glycyl tRNA synthetase can also be deduced from the reaction product in co-complex with glycyl tRNA synthetase.
  • Such information is useful to design improved analogues of known glycyl tRNA synthetase inhibitors or to design novel classes of inhibitors based on the reaction intermediates of the glycyl tRNA synthetase enzyme and glycyl tRNA synthetase inhibitor co-complex.
  • This provides a novel route for designing glycyl tRNA synthetase inhibitors with both high specificity and stability.
  • Another approach made possible by this invention is to screen computationally small molecule data bases for chemical entities or compounds that can bind in whole, or in part, to the glycyl tRNA synthetase enzyme.
  • the quality of fit of such entities or compounds to the binding site may be judged either by shape complementarity or by estimated interaction energy [E. C. Meng et al, J. Comp. Chem., . 13:505-524 (1992)].
  • glycyl tRNA synthetase may crystallize in more than one crystal form
  • the structure coordinates of glycyl tRNA synthetase, or portions thereof, as provided by this invention are particularly useful to solve the structure of those other crystal forms of tRNA synthetase. They may also be used to solve the structure of glycyl tRNA synthetase mutant co-complexes, or of the crystalline form of any other protein with significant amino acid -sequence homology to any functional domain of glycyl tRNA synthetase.
  • the unknown crystal structure whether it is another crystal form of glycyl tRNA synthetase, a glycl tRNA synthetase mutant, or a glycyl tRNA synthetase co- complex, or the crystal of some other protein with significant amino acid sequence homology to any functional domain of glycyl tRNA synthetase, may be determined using the glycyl tRNA synthetase structure coordinates of this invention as provided in Figure 1 and Tables I - III.
  • This method will provide an accurate structural form for the unknown crystal more quickly and efficiently than attempting to determine such information ab initio.
  • the synthetase structure permits the screening of known molecules and/or the designing of new molecules which bind to the synthetase structure, particularly at the active site, via the use of computerized evaluation systems.
  • computer modelling systems are available in which the sequence of the synthetase, and the synthetase structure (i.e., the bond angles, dihedral angles, distances between atoms in the active site region, etc. as provided by Figure 1 and Tables I - III herein) may be input.
  • a machine readable medium may be encoded with data representing the coordinates of Figure 1 and Tables I - III.
  • the computer then generates structural details of the site into which a test compound should bind, thereby enabling the determination of the complementary structural details of said test compound.
  • the design of compounds that bind to or inhibit glycyl tRNA synthetase according to this invention generally involves consideration of two factors.
  • the compound must be capable of physically and structurally associating with glycyl tRNA synthetase.
  • Non-covalent molecular interactions important in the association of glycyl tRNA synthetase with its substrate include hydrogen bonding, van der Waals and hydrophobic interactions.
  • the compound must be able to assume a conformation that allows it to associate with glycyl tRNA synthetase. Although certain portions of the compound will not directly participate in this association with glycyl tRNA synthetase, those portions may still influence the overall conformation of the molecule. This, in turn, may have a significant impact on potency.
  • Such conformational requirements include the overall three- dimensional structure and orientation of the chemical entity or compound in relation to all or a portion of the binding site, e.g., active site or accessory binding site of glycyl tRNA synthetase, or the spacing between functional groups of a compound comprising several chemical entities that directly interact with glycyl tRNA synthetase.
  • the potential inhibitory or binding effect of a chemical compound on glycyl tRNA synthetase may be analyzed prior to its actual synthesis and testing by the use of computer modelling techniques. If the theoretical structure of the given compound suggests insufficient interaction and association between it and glycyl tRNA synthetase, synthesis and testing of the compound is obviated. However, if computer modelling indicates a strong interaction, the molecule may then be synthesized and tested for its ability to bind to glycyl tRNA synthetase and inhibit using a suitable assay. In this mannei, synthesis of inoperative compounds may be avoided.
  • An inhibitory or other binding compound of glycyl tRNA synthetase may be computationally evaluated and designed by means of a series of steps in which chemical entities or fragments are screened and selected for their ability to associate with the individual binding pockets or other areas of glycyl tRNA synthetase.
  • One skilled in the art may use one of several methods to screen chemical entities or fragments for their ability to associate with glycyl tRNA synthetase and more particularly with the individual binding pockets of the glycyl tRNA synthetase active site or accessory binding site.
  • This process may begin by visual inspection of, for example, the active site on the computer screen based on the glycyl tRNA synthetase coordinates in Figure 1 and Tables I - III. Selected fragments or chemical entities may then be positioned in a variety of orientations, or docked, within a binding pocket of glycyl tRNA synthetase.
  • Docking may be accomplished using software such as Quanta and Sybyl, followed by energy minimization and molecular dynamics with standard molecular mechanics force fields, such as CHARMM and AMBER. Specialized computer programs may also assist in the process of selecting fragments or chemical entities. These include:
  • GRID [P. J. Goodford, "A Computational Procedure for Determining Energetically Favorable Binding Sites on Biologically Important Macromolecules", J. Med. Chem., 28:849-857 (1985)]. GRID is available from Oxford University, Oxford, UK.
  • MCSS [A. Miranker and M. Karplus, "Functionality Maps of Binding Sites: A Multiple Copy Simultaneous Search Method", Proteins: Structure, Function and Genetics. H:29-34 (1991)]. MCSS is available from
  • DOCK [I. D. Kuntz et al, "A Geometric Approach to Macromolecule- Ligand Interactions", J. Mol. Biol., 161:269-288 (1982)]. DOCK is available from University of California, San Francisco, CA.
  • Assembly may be proceed by visual inspection of the relationship of the fragments to each other on the three-dimensional image displayed on a computer screen in relation to the structure coordinates of glycyl tRNA synthetase. This would be followed by manual model building using software such as Quanta or Sybyl.
  • CAVEAT [P. A. Bartlett et al, "CAVEAT: A Program to Facilitate the
  • 3D Database systems such as MACCS-3D (MDL Information Systems, San Diego, Calif.).
  • inhibitory or other glycyl tRNA synthetase binding compounds may be designed as a whole or "de novo" using either an empty active site or optionally including some portion(s) of a known inhibitor(s).
  • LEGEND [Y. Nishibata and A. Itai, Tetrahedron, 47:8985 (1991)]. LEGEND is available from Molecular Simulations, Burlington, MA.
  • the synthetase inhibitor may be tested for bioactivity using standard techniques.
  • structure of the invention may be used in binding assays using conventional formats to screen inhibitors.
  • One particularly suitable assay format includes the enzyme-linked immunosorbent assay (ELISA).
  • ELISA enzyme-linked immunosorbent assay
  • Other assay formats may be used; these assay formats are not a limitation on the present invention.
  • the synthetase structure of the invention permit the design and identification of synthetic compounds and/or other molecules which are characterized by the conformation of the synthetase of the invention.
  • the coordinates of the synthetase structure of the invention may be provided in machine readable form, the test compounds designed and/or screened and their conformations superimposed on the structure of the synthetase of the invention.
  • suitable candidates identified as above may be screened for the desired synthetase inhibitory bioactivity, stability, and the like. Once identified and screened for biological activity, these inhibitors may be used therapeutically or prophylactically to block synthetase activity, and thus, bacterial replication.
  • the present invention also provides inhibitors of glycyl tRNA synthetase activity identified or designed by the methods of the invention. These inhibitors are useful as antibacterial agents.
  • One particularly desirable inhibitor is glycylsulfamoyladenosine.
  • the structure of this compound is as follows.
  • Glycylsulfmoyladenosine is an analogue of the Gly-AMP reaction intermediate and inhibits GRS catalytic activity as measured by any of the techniques described in the examples below.
  • Estimates of the potency of inhibition are obtained by performing enzyme assays in the presence of a range of inhibitor concentrations, and fitting the effect of inhibitor concentration on enzyme velocity to a four parameter logistic function that allows calculation of an IC 50 (the inhibitor concentration at which GRS activity is reduced by half).
  • This parameter is directly related to the dissociation constant for inhibitor binding (Kj or K d ) and has a value of around 2.4 mM for glycylsulfamoyladenosine when tested against the S. aureus GRS.
  • Binding of glycylsulfamoyladenosine to GRS can also be measured directly using stopped-flow fluorescence techniques because enzyme:inhibitor binary complex has around 5% higher tryptophan fluorescence than the free enzyme.
  • Example 1 The Expression of the Glycyl t-RNA Synthetase from Staphylococcus aureus in Escherichia coii.
  • the strategy for the expression of the glycyl t-RNA synthetase (GRS) from Staphylococcus aureus, using Escherichia coii as a host was based on the PCR amplification of the grs gene and the introduction of suitable restriction sites that allowed the cloning of the gr?-containing DNA fragment in the pDB575 expression vector. After the PCR amplification the insert of the resultant recombinant plasmid, (pDBGRS hereafter), was sequenced to verify the absence of artefacts introduced by the Taq polymerase. Expression was monitored by SDS-polyacrylamide gel analysis.
  • the Escherichia coii strains used were: DH5a (supE44, D/ ⁇ cU169 (f 80 / ⁇ cZDM15), hsdRXl, recAX, endAX, gyrA96, thi-X, relA X) and HB101 (thi-X, hsdS,20(r ,m B ), supE44, recAX3, ara-X4, leuB ⁇ , proA2, lacYX, rpsL20(st ⁇ ⁇ ), xyl-5, mtl-X).
  • E. coii cells were grown at 37°C in Luria Bertani broth (LB). These strains may all be obtained from commercial sources.
  • plasmids used were pBluescript SK- [Stratagene], pUC18 [J. Sambrook et al., Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York (1989)] and pDB575.
  • pDB575 A detailed description of pDB575 is provided in A.F. Chalker et al, Gene, 141:103-108 (1994).
  • pDB575 is a expression vector of E.coli based on pKK223-3 [Pharmacia] with the following modifications: (i) the polylinker between EcoRl and Hind ⁇ ll has been replaced with a longer one (EcoRX, NcoX, Kpnl, Ndel, SstX, Sstll, XbaX, ClaX, SmaX, BgllX, XmaXXX, Hindlll) (ii) it has a lacl q gene inserted; (iii) it is non-mobilizable, the pBR322 portion of pKK223-3 has been replaced by the equivalent fragment from pATIS3.
  • pDB575 allows the selection of the recombinant clones by ampicillin resistance and the gene expression is driven by the tac promoter.
  • LB Medium Per litre:
  • Plasmid DNA was prepared by the rapid alkaline method (Sambrook et al, 1989). Transformations of E. coii cells were carried out using the RbCl methods (Sambrook et al, 1989). DNA fragments were purified using the Geneclean Kit [BIO 101 Inc., La Jolla, CA, USA]. The plasmids for sequencing were purified using QIAGEN plasmid kit [QIAGEN]. DNA sequencing was carried out on supercoiled plasmid DNA by the dideoxy chain-termination method using the Thermo Sequenase cycle sequencing kit [Amersham Life Science, Inc. USA]. DNA was also sequenced by the Automated Sequencing Service of Pharmacy Faculty in the Complutense University of Madrid. Universal or synthetic oligonucleotides [MedProbe, Norway] were used as primers. Restriction enzymes and T4 DNA ligase were obtained from Promega and Boehringer respectively and the experiments were carried out following the instructions provided by the suppliers.
  • the grs gene from S. aureus cloned in the pBluescript SK- was amplified by PCR using the primers GRS 1 : (5'-GGGGTACCGCTAGCAGGAGAGGTAATTATGGCAAAAGATATG-3' ; SEQ ID NO:2) and GRS2: (5 -GCTCTAGATTAGTCATTTAATTAGAATTTTGTTTTTTCAGTTAAG- 3'; SEQ ID NO:3).
  • Kpn I and Xba I restriction sites were incorporated at the 5' and 3' ends respectively of each primer to facilitate ligation of the amplified DNA into vectors.
  • Plasmid DNA (100 ng) was amplified in 100 ml of PCR mixture containing 250 mM deoxynucleotide triphosphates (dNTPs), 0.9 mM oligonucleotide primers, the manufacturer's buffer and 2U of Taq polymerase (Promega). The following cycling parameters were used:
  • PCR Polymerase chain reaction
  • the cloning strategy is shown in Figure 2.
  • PCR amplification of the grs gene from S. aureus using the primers GRS1 and GRS2 resulted in a DNA fragment of 1.4 kb.
  • This fragment was purified and ligated to the Kpnl, Xbal sites of pDB575 to obtain the recombinant plasmid pDBGRS and the ligation mix was used to transform E. coii DH5a competent cells.
  • the construction of pDBGRS was initially confirmed by restriction analysis of the plasmid purified from the transformants.
  • the amplification with Taq DNA polymerase made the sequencing of the grs of pDBGRS an obligatory step to confirm that no changes were introduced due to the low fidelity of this enzyme. Sequence analysis was accomplished by using grs gene introduced in the expression plasmid pDB575 and/or in pUC18. The sequencing of both strands showed that no artefacts had been introduced during the amplification process
  • the plasmid pDBGRS and the negative control pDB575 were used to transform the E. coii HB 101 host strain.
  • Single clones of HB101 :pDBGRS and HB 101:pDB575 cells were grown overnight at 37°C in 2 ml of LB medium in the presence of 0.1 mg/ml ampicillin. The cells were then diluted 100-fold in 30 ml LB with ampicillin. When the cultures reached a value of 0.5 at OD 6 oothe grs expression was induced by addition of isopropyl-thio-galactoside (IPTG) at ImM of final concentration. After this induction 2 ml samples were taken at different times (2, 3 and 4 hours).
  • IPTG isopropyl-thio-galactoside
  • the cells were harvested in a microfuge for 3 min, the pellets were washed with 20 mM Tris-HCl pH 8 / ImM PMSF and resuspended in 300 ml of SDS-PAGE gel-loading buffer. The cells were broken by sonication (15 seconds). The samples were then boiled 10 minutes and after one spin, 10 ml fractions were analyzed by SDS-PAGE according to the methods of Laemmli [U. K. Laemmli, Nature 227, 680-685 (1970)]. The 12% polyacrylamide gels were stained with Coomassie blue. As shown in Figure 3 good expression levels were detected from the early stages after induction with IPTG.
  • the evidence was the presence of a prominent band (lanes 2, 4 and 6 in Figure 3) that was in good agreement with the M r predicted from the primary sequence.
  • the GRS protein has a theoretical molecular weight of about 53.7 kDa.
  • a 300 litre fermentation of E.coli HB 101 :pDB575GRS was carried out in double strength Luria Bertani medium (LB), containing 50 ug/ml ampicillin.
  • the vessel was inoculated at 2% (v/v) from a 15 hour secondary seed culture in single strength LB medium, containing 50 mg/ml ampicillin.
  • the production vessel was incubated at 37°C, agitated at 1.5 msec "1 and aerated at 1.0 VVM.
  • the OD at 550nm was monitored, and at 2.5 absorbance units, GRS expression was induced with the addition of isopropyl- thiogalactosidase to 1.0 mM and the cells harvested by centrifugation in a Westfalia CSA- 19, 2 hours post induction. A total of 990 grams of cell paste was recovered.
  • LB Medium per litre, contains the following components. The medium ingredients were supplied by Difco Laboratories, West Molesey, Surrey UK. Double strength Single strength Bacto Tryptone 20 g Bacto Tryptone 10 g
  • the supernatant from 1 was loaded onto a Q-Sepharose high performance (Pharmacia) column of 200ml packed into a Pharmacia XK-50 column.
  • the column was equilibrated with buffer A prior to loading.
  • the column is then washed with buffer A (1000ml) at 40 ml/min, and eluted with a linear gradient of buffer A to IM NaCl in buffer A over 140 minutes at lOml/min.
  • the eluate was fractionated into 5 minute fractions using a Pharmacia Superfrac.
  • the eluted fractions were assayed for GRS activity by measurement of aminoacylation of tRNA Gly , and for protein by the Bradford method. Active fractions were analyzed by reducing SDS PAGE (Pharmacia Phast System 10-15% gradient gel)
  • Eluted fractions are collected ( 1 minute fraction) and assayed for GRS activity and protein. Active fractions are pooled and diafiltered against (1,000 fold buffer exchange) buffer A using an Amicon ultrafiltration cell (350ml) under nitrogen. A final volume of 33 ml of protein was obtained containing 4.2 mg/ml of protein (by amino acid analysis). This product was greater than 95% purity by SDS PAGE and the activity showed an overall process yield of 60 % from 1). N-terminal amino acid analysis confirmed identity.
  • Glycyl tRNA Synthetase (GRS) activity The enzyme catalyses the aminoacylation of tRNA Gly , which proceeds through a two step mechanism. The first step involves the formation of a stable enzyme:glycyl adenylate complex resulting from the specific binding and reaction of ATP and L-glycine. Subsequently, the 3' terminal adenosine of enzyme-bound tRNAGly reacts with the aminoacyladenylate, leading to the esterification of the tRNA and release of AMP. These steps are summarized below. a) L-Gly + ATP.Mg + GRS P GRS: Gly-AMP + PPi.Mg b) GRS:Gly-AMP + tRNA Gly I GRS + Gly-tRNA Gly + AMP
  • This reaction can be assayed in order to characterize the enzyme or identify specific inhibitors of its activity in a number of ways: (1) Measurement of the formation of Gly-tRNA Gly can be specifically determined using radiolabelled glycine and separating free glycine from Gly-tRNA using precipitation/filtration techniques (e.g. in cold trichloroacetic acid; see, Calender & Berg (1966) Biochemistry 5, 1681-1690; Toth MJ & Schimmel P (1990) J. Biol. Chem. 265, 1000-1004].
  • precipitation/filtration techniques e.g. in cold trichloroacetic acid; see, Calender & Berg (1966) Biochemistry 5, 1681-1690; Toth MJ & Schimmel P (1990) J. Biol. Chem. 265, 1000-1004].
  • the full acylation reaction can also be measured by analyzing production of either PPi or AMP which are produced in stoichiometric ratio to the tRNA acylation. This may be achieved in a number of ways, for example using colorimetric [Hoenig (1989) J. Biochem. Biophys. Meth. 19, 249-252]; or enzyme coupled [Webb TM (1994) Anal. Biochem. 218, 449-454] measurement of Pi after addition of excess inorganic pyrophosphatase or using enzyme coupled assays to directly measure AMP or PPi production [Sigma Chemicals Catalogue, 1986].
  • the partial reaction (a) can be assayed through radiolabel isotopic exchange between ATP and PPi, since each of the steps in this part of the reaction are freely reversible.
  • This reaction is independent of tRNA binding, typically has a k CM around 20-fold higher than the full acylation reaction (a+b), and is readily measured using chromatographic principles which separate PPi from ATP (i.e. using activated charcoal; see, Calender & Berg, cited above; Toth & Schimmel, cited above).
  • D Ligand binding to GRS. It is also possible to define ligand interactions with GRS in experiments that are not dependent upon enzyme catalyzed turnover of substrates. This type of experiment can be done in a number of ways:
  • the ligands could either be inhibitors or variants of the natural ligands (i.e. fluorescent ATP derivatives or tRNAGly labelled with a fluorophore).
  • Assays were performed either using purified S. aureus GRS overexpressed in E. coii, or using crude cell lysate from E. coii overexpressing GRS. The latter contained around 10% of total protein as GRS.
  • Enzyme was stored at -70°C in 50 mM Tris-HCl buffer (pH 7.8), 10 mM MgCl 2 and 10 mM B-mercaptoethanol after flash freezing in liquid ⁇ 2 . In experiments to determine the activity of enzyme samples, these stocks were diluted over a wide range (100 fold to 10,000 fold) in 50 mM Tris pH 7.8, 10 mM MgCl 2 , 1 mM Dithiothreitol and stored on ice prior to assay.
  • the assay procedure was as follows. 50 ml of enzyme prepared and diluted as described above was mixed with reaction mixture (100 ml), comprising: 0.15 mCi L-[U- 14 ]-Glycine (Amersham International), 4 mg/ml E. coii MRE600 mixed tRNA (Boehringer Manheim), 5 mM ATP, 15 mM MgS0 4 , 3 M DTT, 75 mM KC1 and 50 mM Tris-HCl, pH 7.8. Unless otherwise states, all reagents were obtained from Sigma Chemical Company Ltd. Concentrations are given as in the final reaction mix.
  • Example 3 Crystallization of Staphylococcus aureus Glycyl tRNA Synthetase A. Crystallization A large crystal (0.25 x 0.25 x 0.18 mm 3 ) was formed using the following conditions. The protein used for the crystallization was supplied @ 5.8 mg/ml in a solution of 20mM tris, 5mM MgCl 2 , ImM DTT, ImM EDTA, 10% glycerol, pH 7.5). The crystal was obtained from a 1 : 1 mixture of the protein solution and a solution of 10% PEG 8000, 0.1M imidazole pH 8.0 and 0.2M calcium acetate using the hanging drop method, grown at room temperature.
  • the Staph aureus synthetase crystal was mounted in a sealed glass capillary with a small amount of mother liquor in each end of the capillary.
  • the CuK a X- ray having a wavelength of 1.54 A, was generated by a Rigaku-RU200 rotating anode machine operating at 100 mA x 50 kV electric power.
  • the crystal was exposed to the CuK a X-ray, and the diffracted X-ray was collected by a Siemens multiwire area detector.
  • the crystal diffracted to 3.5 .
  • the crystal has been determined to be an orthorhombic crystal system and P2,2,2, space group.
  • an asymmetric unit was calculated to have one protein molecule.
  • the crystal contains an estimated 60% solvent.
  • Solvent flattening and 2-fold non-crystallographic averaging was then used to improve the phases [Collaborative Computational Project, Number 4, Acta Crystaliogr. D50, 760-763 (1994)], which introduced about 30°C phase shifts and improved the averaged figure of merit from 0.4 to 0.8 and Rfree from 47% to 28%. An improved electron density map was then calculated.
  • the GRS model was subjected to one round of Xplor [A. Brunger et al, Science, 235:458-460 (1987) refinement using the standard positional, slowcool and overall B factor refining protocols.
  • the GRS was refined as a tightly contained dimer without any solvent molecules.
  • the R factor of the model is 23.9% with satisfactory geometry.
  • the rms deviations are 0.017 A for bond lengths, 2.0° for bond angles, 25.4 for dihedrals and 1.8°C for impropers.
  • the structure contains residues 1-86, 150-161 , 164-352 and 356-463 [SEQ ID NO:l], while the other 68 residues (15%) are disordered in the crystal and not included in the model.
  • the characterization of the compound as an inhibitor of the catalytic activity of GRS was performed using a procedure similar to that described in Example 2E above, except that multiple assays were performed in the presence of inhibitor concentrations ranging (in two-fold dilution steps) from 100 mM down to 0.1 mM (final concentrations). These were added from stocks prepared at 10-fold higher concentrations and added to each reaction mix. The stock of inhibitor was prepared freshly from a solid sample and dissolved in dimethylsulfoxide. The enzyme concentration used for these assays was selected so that around 50% of the tRNA available was acylated during the reaction time course.
  • acylation activity (relative to controls in the absence of inhibitor) were plotted as a function of inhibitor concentration and fitted to a four-parameter logistic function (using the Grafit package; Erithacus Software Ltd.) to yield IC 50 , the inhibitor concentration required to inhibit half the enzyme activity.
  • a model of the human glycyl tRNA synthetase was constructed using Quanta version 4.1 [Molecular Simulations Inc, Burlington, MA].
  • the human enzyme contains a number of large surface loops (see Fig. 6).
  • a comparison of the human and Staph enzyme aminoacylation sites is shown in Figure 7.
  • One of the most significant differences is that a glutamine in the prokaryotic enzyme is replaced by a methionine. The glutamine is believed to be capable of hydrogen bonding to the acyl phosphage moiety of glycyl adenylate.

Abstract

A novel Staphylococcus glycyl tRNA synthetase crystalline structure is identified. Also disclosed are methods of identifying inhibitors of these synthetases and/or active sites, and inhibitors identified by these methods.

Description

NOVEL tRNA SYNTHETASE ENZYME,
COMPOSITIONS CAPABLE OF BINDING TO SAID ENZYME,
AND METHODS OF USE THEREOF
Technical Field of the Invention
The invention relates to the identification of a novel enzyme active site and methods enabling the design and selection of inhibitors of that active site.
Background of the Invention Transfer RNA (tRNA) synthetase enzymes are of interest as potential targets for antibacterial agents. Mupirocin, a selective inhibitor of bacterial isoleucyl tRNA synthetase, is marketed for the treatment of skin infections and the eradication of nasal carriage of MRSA (methicillin-resistant Staphylococcus aureus) in hospital staff and patients. Glycyl tRNA synthetase, a class I enzyme, is unusual in that its oligomeric structure varies depending on the organism from which it was isolated. Nucleic acid and amino acid sequences for glycyl tRNA synthetases are publicly available, including those of Thermus thermophilus, Mycoplasma genitalium, Homo sapiens, yeast, Bombyx mori and Caenorhabditis elegans, which are all characterized by a2 dimers, and Coxiella burnetti, Escherichia coii, Chlamydia trachomatous, Neisseria gonorrheae, Synechocystis sp., and Haemophilus influenzae, which are all characterized by being a2b2 tetramers.
There is a need in the art for novel tRNA synthetase enzyme active sites and catalytic sequences to enable identification and structure-based design of synthetase inhibitors, which are useful in the treatment or prophylaxis of diseases, particularly bacterial diseases caused by bacteria of the genus Staphylococcus, as well as other bacteria which may share catalytic domains with those of the genus Staphylococcus.
Summary of the Invention
In one aspect, the present invention provides a novel Staphylococcus aureus tRNA synthetase enzyme active site crystalline form.
In still another aspect, the present invention provides a novel tRNA synthetase composition characterized by a catalytic site of 16 amino acid residues.
In yet another aspect, the invention provides a method for identifying inhibitors of the compositions described above which methods involve the steps of: providing the coordinates of the tRNA synthetase structure of the invention to a computerized modeling system; identifying compounds which will bind to the structure; and screening the compounds identified for tRNA synthetase inhibitory bioactivity.
In a further aspect, the present invention provides an inhibitor of the catalytic activity of any composition bearing the catalytic domain described above.
Another aspect of this invention includes machine readable media encoded with data representing the coordinates of the three-dimensional structure of the tRNA synthetase crystal.
Other aspects and advantages of the present invention are described further in the following detailed description of the preferred embodiments thereof.
Brief Description of the Drawings
Fig. 1 provides the atomic coordinates of the Staph aureus glycyl tRNA synthetase.
The occupancy factor is 1.0 and the B factor is 19.60 for each coordinate. Fig. 2 illustrates the cloning of the grs gene in pDB575. Briefly, the grs gene was
PCR amplified out of the pBluescript GRS vector using a GRS1 primer which provided the
Kpnl restriction site and the Shine-Dalgarno consensus sequence. The GRS2 primer contains the Xbal site and stop codons in the three possible reading frames.
Fig. 3 illustrates the SDS-PAGE analysis of the GRS production by E. coii. E. coii HB 101 cells, harboring either pDB575 or pDBGRS, were induced with 1 mM IPTG.
Sonicated samples were electrophoresed through 0.1% SDS-15% polyacrylamide gels. The gel was stained with Coomassie brilliant blue. Lanes 1, 3 and 5 show the sonicated extracts of HB101:pDB575 at 2, 3 and 4 hours after the induction. Lanes 2, 4 and 6 show the corresponding samples of the recombinant clone HB 101 :pDBGRS. Fig. 4 provides a projection of the ribbon structure of the Staphylococcus aureus glycyl tRNA synthetase dimer. The two monomers are shaded in dark and light gray. Fig. 5 provides a schematic drawing of the molecular structure of the
Staphylococcus aureus glycyl tRNA synthetase dimer. The two monomers are shaded in dark and light gray. Fig. 6 provides the ribbon structure of the human glycyl tRNA synthetase monomer.
Fig. 7 provides a schematic drawing comparing the active sites of the human and
Staph aureus glycyl tRNA synthetase enzymes. Detailed Description of the Invention
The present invention provides a novel glycyl tRNA synthetase crystalline structure, a novel Staph aureus tRNA synthetase active site, and methods of use of the crystalline form and active site to identify synthetase inhibitor compounds (peptide, peptidomimetic or synthetic compositions) characterized by the ability to competitively inhibit binding to the active site of a glycyl tRNA synthetase. Also provided herein is a novel human glycyl tRNA synthetase crystalline structure. This structure can be used as described below for the Staph tRNA synthetase crystal structure.
I. The Novel Synthetase Crystalline Three-Dimensional Structure
The present invention provides a novel glycyl tRNA synthetase crystalline structure based on the Staph aureus tRNA synthetase. The amino acid sequences of the synthetase are provided in SEQ ID NO: 1. As illustrated herein, the crystal structure is a tightly associated S. aureus GRS dimer. Each monomer has three structural domains: the N- terminal domain (residues 1-86 of SEQ ID NO: l), the active site domain (residues 150-340 of SEQ ID NO: l) and the C-terminal domain (residues 341-463 of SEQ ID NO:l). The N- terminal domain, having three a-helices and three b-strands, wraps around the active site domain with its second a-helix lying in the core of the dimer interface and its third b-strand adding to the central b-sheet of the active site domain to form the 7-stranded anti-parallel b sheet where the enzyme active site locates. The C-terminal domain contains mainly a 5- stranded mixed b-sheet with three flanking helices and is believed to be important to anticodon recognition. While the overall architecture of the S. aureus GRS is similar to that of the T. thermophilus GRS, differences exit in the conformation of a number of surface loops, as well as the relative orientation of between the active site and C-terminal domains. With only 44% sequence identity, many amino acid side chains are also different, including several residues near the active site.
As described above, the Staph aureus synthetase is a dimer. The present invention provides both a crystalline monomer and dimer structure of Staph aureus synthetase. Inhibitors that perturb or interact with this dimer interface are another target for the design and selection of anti-bacterial agents.
According to the present invention, the crystal structure of Staph aureus tRNA synthetase has been resolved at 3.5 . The structure was determined using the method of molecular replacement, and refined to an R-factor of 23.4% with goal geometry. For example, further refinement of the atomic coordinates will change the numbers in Figure 1 and Tables I - III, refinement of the crystal structure from another crystal form will result in a new set of coordinates. However, distances and angles in Figure 1 and Tables I - III will remain the same within experimental errors, and relative conformation of residues in the active site will remain the same within experimental error.
Figure 1 provides the atomic coordinates of the Staph aureus glycyl tRNA synthetase dimer, which contains 790 amino acids; with 130 residues disordered in the crystal. The occupancy factor is 1.0 and the B factor is 19.60.
The tRNA synthetase is characterized by an active site which preferably contains a binding site for glycyl-adenylate and the receptor stem of tRNA (glycines). The crystal structure described herein was solved in the absence of glycine, ATP or tRNA. However, the region of the active site can be inferred from that of the homologous aspartyl tRNA synthetase. Particularly, the crystalline active site consists of 16 amino acid residues. These residues include Glul74, Arg206, Glu208, Phe216, Arg217, Thr218, Phe221 , Gln223, Glu225, Asp279, Glu290, Leu291, Arg297, Glu330, Ser332 and Arg337 [SEQ ID NO: l]. The atomic coordinates of the active site residues are provided in Table I.
TABLE I O. ATOM X Y
1 174N 4.941000 3.175000 50.397999
2 174CA 5.955000 4.038000 49.859001
3 174CB 5.335000 4.880000 48.750000
4 174CG 6.198000 6.021000 48.222000
5 174CD 5.581000 6.686000 46.986000
6 1740E1 6.341000 7.002000 46.035999
7 1740E2 4.332000 6.862000 46.949001
8 174C 6.562000 4.919000 50.930000
9 1740 5.886000 5.710000 51.594002
10 206N 3.716000 -3.980000 50.544998
1 1 206CA 2.750000 -4.082000 49.455002
12 206CB 3.479000 -4.007000 48.122002
13 206CG 3.246000 -2.730000 47.368999
14 206CD 4.122000 -1.569000 47.855999
15 206NE 5.071000 -1.073000 46.834000
16 206CZ 4.798000 -0.830000 45.534000
17 206NH1 3.575000 -1.030000 45.014999
18 206NH2 5.765000 -0.360000 44.730999
19 206C 1.978000 -5.398000 49.502998
20 206O 2.574000 -6.489000 49.485001
21 208N 0.743000 -7.731000 47.730999
22 208CA 0.888000 -8.258000 46.355999
23 208CB 2.298000 -8.843000 46.164001
24 208CG 2.966000 -8.376000 44.889000
25 208CD 2.847000 -6.871000 44.637001
26 208OE1 3.887000 -6.191000 44.762001
27 208OE2 1.741000 -6.362000 44.299000
28 208C -0.174000 -9.223000 45.783001
29 208O -1.329000 -9.263000 46.256001
30 216N 13.129000 ■10.373000 44.237999
31 216CA 12.590000 -9.384000 43.311001
32 216CB 12.766000 -9.728000 41.810001
33 216CG 12.693000 -11.233000 41.452000
34 216CD1 11.571000 -11.762000 40.764999
35 216CD2 13.816000 -12.076000 41.622002
36 216CE1 11.579000 -13.076000 40.243999
37 216CE2 13.827000 -13.408000 41.095001
38 216CZ 12.713000 -13.890000 40.409000
39 216C 11.174000 -8.954000 43.654999
40 2160 10.867000 -7.753000 43.624001
41 217N 10.311000 -9.898000 44.009998 42 217CA 8.961000 -9.483000 44.380001
43217CB 7.932000 -9.752000 43.272999
44217CG 7.030000 -8.552000 42.960999
45217CD 5.864000 -8.929000 42.049999 TABLE I (continued) O. ATOM X Y z
46 217NE 4.737000 -9.519000 42.785000
47 217CZ 3.574000 -9.900000 42.235001
48 217NH1 3.363000 -9.770000 40.926998
49 217NH2 2.591000 -10.372000 42.997002
50 217C 8.523000 -10.098000 45.709999
51 2170 7.943000 -11.195000 45.757999
52 218N 8.772000 -9.337000 46.778000
53 218CA 8.472000 -9.725000 48.148998
54 218CB 9.711000 -9.500000 49.070999
55 2180G1 10.388000 -8.300000 48.671001
56 218CG2 10.689000 -10.687000 49.019001
57 218C 7.346000 -8.848000 48.647999
58 2180 7.290000 -7.657000 48.326000
59 221N 9.504000 -5.218000 51.894001
60 221CA 10.836000 -4.815000 51.400002
61 221CB 10.783000 -4.649000 49.875000
62 22 ICG 9.708000 -3.696000 49.418999
63 221CD1 9.956000 -2.330000 49.346001
64 221CD2 8.407000 -4.164000 49.141998
65 221CE1 8.926000 -1.445000 49.012001
66 221CE2 7.360000 -3.282000 48.805000
67 221CZ 7.619000 -1.928000 48.743000
68 221C 11.326000 -3.494000 51.951000
69 2210 10.551000 -2.673000 52.439999
70 223N 13.206000 0.141000 50.983002
71 223CA 13.480000 1.112000 49.938000
72 223CB 12.461000 2.215000 50.000000
73 223CG 11.053000 1.686000 50.096001
74 223CD 10.275000 1.809000 48.803001
75 2230E1 10.824000 1.639000 47.716000
76 223NE2 8.980000 2.098000 48.918999
77 223C 14.863000 1.698000 50.092999
78 2230 15.811000 0.967000 50.327999
79 225N 15.128000 5.689000 49.512001
80 225CA 14.827000 6.937000 48.806000
81 225CB 13.335000 7.143000 48.845001
82 225CG 12.636000 5.820000 48.712002
83 225CD 11.176000 5.961000 48.533001
84 225OE1 10.626000 6.903000 49.126999
85 225OE2 10.582000 5.139000 47.798000
86 225C 15.517000 8.213000 49.247002
87 2250 16.087000 8.285000 50.326000
88 279N 14.349000 4.904000 34.318001
89 279CA 14.639000 3.772000 35.201000
90 279CB 13.700000 2.601000 34.933998 TABLE I (continued) O. ATOM X Y z
91 279CG 12.310000 2.839000 35.416000
92 2790D1 12.056000 3.903000 36.01 1002
93 2790D2 11.468000 1.941000 35.206001
94 279C 16.046000 3.310000 34.823002
95 2790 16.563000 3.722000 33.782001
96 290N 14.061000 -3.246000 36.935001
97 290CA 14.561000 -1.978000 37.402000
98 290CB 13.425000 -0.977000 37.536999
99 290CG 12.391000 -1.284000 38.611000
100 290CD 11.205000 -0.284000 38.606998
101 290OE1 10.212000 -0.542000 37.867001
102 290OE2 11.260000 0.749000 39.338001
103 290C 15.324000 -2.075000 38.700001
104 2900 15.162000 -3.026000 39.450001
105 291N 16.257999 -1.155000 38.882000
106 291CA 17.030001 -1.073000 40.099998
107 291CB 18.528000 -0.882000 39.824001
108 291CG 19.368999 -2.096000 39.455002
109 291CD1 20.739000 -1.973000 40.076000
1 10 291CD2 18.683001 -3.342000 39.924999
111 291C 16.466000 0.189000 40.699001
112 2910 15.445000 0.171000 41.387001
113 297N 9.206000 14.779000 39.366001
114 297CA 7.788000 14.867000 39.709000
1 15 297CB 7.520000 14.064000 40.992001
116 297CG 8.285000 12.757000 41.123001
1 17 297CD 8.166000 12.209000 42.539001
1 18 297NE 6.771000 12.005000 42.935001
119 297CZ 6.197000 10.821000 43.125999
120 297NH1 6.901000 9.720000 42.958000
121 297NH2 4.913000 10.735000 43.479000
122 297C 7.342000 16.333000 39.926998
123 2970 6.193000 16.584999 40.372002
124 330N 12.945000 12.193000 42.535999
125 330CA 13.135000 1 1.123000 43.480999
126 330CB 1 1.811000 10.733000 44.127998
127 330CG 10.940000 9.803000 43.354000
128 330CD 9.806000 9.249000 44.179001
129 330OE1 9.784000 8.026000 44.432999
130 330OE2 8.930000 10.041000 44.563000
131 330C 13.907000 9.910000 43.026001
132 3300 13.355000 9.017000 42.432999
133 332N 14.529000 6.954000 43.724998
134 332CA 14.141000 5.801000 44.557999
135 332CB 12.663000 5.457000 44.334999 TABLE I (continued) O. ATOM X Y Z
136 3320G 12.375000 4.105000 44.611000
137 332C 15.000000 4.581000 44.297001
138 3320 15.668000 4.512000 43.289001
139 337N 16.296000 -5.378000 46.342999
140 337CA 16.743999 -5.561000 44.936001
141 337CB 15.916000 -4.737000 43.957001
142 337CG 14.513000 -5.233000 43.710999
143 337CD 14.111000 -5.006000 42.230000
144 337NE 12.699000 -4.631000 42.080002
145 337CZ 12.236000 -3.377000 42.169998
146 337NH1 13.073000 -2.349000 42.389000 447 337NH2 10.919000 -3.156000 42.146999
148 337C 18.207001 -5.259000 44.654999
149 3370 18.920000 -6.130000 44.188000
Table II provides the distances between (D) atoms of the active site residues that are within 5.0 angstroms of one another.
TABLE II
Distance
Atom 1 Atom 2 Between
174N 1 174CA D = 1.436
174N ] 174CB D = 2.404
174N ] I74C D = 2.440
174N ! 1740 D = 2.958
174N : I74CG D = 3.797
174N 223NE2 D = 4.434
174N : 174CD D = 4.937
174CA 174N D = 1.436
174CA 174C D = 1.514
174CA 174CB D = 1.524
174CA 1740 D = 2.41 1
174CA 174CG D = 2.583
174CA 223NE2 D = 3.715
174CA 174CD D = 3.925
174CA 1740E2 D = 4.368
174CA 1740E1 D = 4.853
174CA 223CD D = 4.975
174CB 174CA D = 1.524
174CB 174CG D = 1.525
174CB 174N D = 2.404
174CB 174C D = 2.502
174CB 174CD D = 2.537
174CB 1740E2 D = 2.860
174CB 1740 D = 3.013
174CB 1740E1 D = 3.589
174CB 223NE2 D = 4.588
174CG 174CB D = 1.525
174CG 174CD D = 1.533
174CG 1740E1 D = 2.400
174CG 1740E2 D = 2.410
174CG 174CA D = 2.583
174CG 174C D = 2.946
174CG 1740 D = 3.401
174CG 174N D = 3.797
174CG 2250E2 D = 4.492
174CG 2250E1 D = 4.605
174CG 223NE2 D = 4.860
174CG 225CD D = 4.988
174CD 1740E1 D = 1.257
174CD 1740E2 D = 1.262
174CD 174CG D = 1.533 TABLE II (continued)
Distance
Atom 1 Atom 2 Between
174CD 174CB D = 2.537
174CD 174CA D = 3.925
174CD 174C D = 4.432
174CD 1740 D = 4.720
174CD 174N D = 4.937
1740E1 174CD D = 1.257
1740E1 1740E2 D = 2.21 1
1740E1 174CG D = 2.400
1740E1 174CB D = 3.589
1740E1 330OE1 D = 3.934
1740E1 297NH1 D = 4.144
1740E1 330OE2 D = 4.255
1740E1 330CD D = 4.528
1740E1 297NH2 D = 4.745
1740E1 297CZ D = 4.803
1740E1 174CA D = 4.853
1740E1 2250E2 D = 4.956
1740E2 174CD D = 1.262
1740E2 1740E1 D = 2.211
1740E2 174CG D = 2.410
1740E2 174CB D = 2.860
1740E2 174CA D = 4.368
1740E2 174C D = 4.959
174C 1740 D = 1.234
174C 174CA D = 1.514
174C 174N D = 2.440
174C 174CB D = 2.502
174C 174CG D = 2.946
174C 223NE2 D = 4.225
174C 174CD D = 4.432
174C 2250E1 D = 4.869
174C 1740E2 D = 4.959
1740 174C D = 1.234
1740 174CA D = 2.41 1
1740 174N D = 2.958
1740 174CB D = 3.013
1740 174CG D = 3.401
1740 174CD D = 4.720
206N 206CA D = 1.460
206N 206CB D = 2.435
206N 206C D = 2.473
206N 206O D = 2.953
206N 206CG D = 3.445 TABLE II (continued)
Distance
Atom 1 Atom 2 Between
206N : 206CD D = 3.634
206N : 221CE2 D = 4.098
206N : 221CZ D = 4.764
206N : 221CD2 D = 4.900
206N : 206NE D = 4.905
206CA 206N D = 1.460
206CA 206CB D = 1.521
206CA 206C D = 1.526
206CA 206O D = 2.414
206CA 206CG D = 2.535
-206CA 206CD D = 3.279
206CA 208N D = 4.507
206CA 206NE D = 4.616
206CA 221CE2 D = 4.724
206CB 206CG D = 1.501
206CB 206CA D = 1.521
206CB 206N D = 2.435
206CB 206C D = 2.469
206CB 206CD D = 2.535
206CB 206O D = 2.973
206CB 206NE D = 3.578
206CB 221CE2 D = 4.007
206CB 208OE1 D = 4.028
206CB 206NH1 D = 4.304
206CB 206CZ D = 4.305
206CB 208CD D = 4.555
206CB 208N D = 4.638
206CB 221CZ D = 4.674
206CB 208OE2 D = 4.815
206CG 206CB D = 1.501
206CG 206CD D = 1.534
206CG 206NE D = 2.522
206CG 206CA D = 2.535
206CG 206NH1 D = 2.922
206CG 206CZ D = 3.064
206CG 206N D = 3.445
206CG 206C D = 3.644
206CG 206NH2 D = 4.350
206CG 206O D = 4.366
206CG 208OE1 D = 4.380
206CG 221CE2 D = 4.392
206CG 221CZ D = 4.653
206CG 208CD D = 4.977 TABLE II (continued)
Distance
Atom 1 Atom 2 Between
206CG 208OE2 D = 4.988
206CD 206NE D = 1.480
206CD 206CG D = 1.534
206CD 206CZ D = 2.529
206CD 206CB D = 2.535
206CD 206NH1 D = 2.943
206CD 206CA D = 3.279
206CD 221CZ D = 3.626
206CD 206N D = 3.634
206CD 206NH2 D = 3.732
206CD 221CE2 D = 3.784
206CD 206C D = 4.687
206CD 221CE1 D = 4.943
206NE 206CZ D = 1.350
206NE 206CD D = 1.480
206NE 206NH2 D = : 2.327
206NE 206NH1 D = : 2.356
206NE 206CG D = : 2.522
206NE 221CZ D = : 3.297
206NE 206CB D = 3.578
206NE 221CE2 D = : 3.742
206NE 221CE1 D = 4.443
206NE 206CA D = ; 4.616
206NE 206N D = : 4.905
206CZ 206NH2 D = 1.342
206CZ 206NH1 D = 1.344
206CZ 206NE D = : 1.350
206CZ 206CD D = : 2.529
206CZ 206CG D = : 3.064
206CZ 206CB D = : 4.305
206CZ 221CZ D = : 4.41 1
206CZ 221CE2 D = : 4.824
206NH1 206CZ D = = 1.344
206NH1 206NH2 D = : 2.308
206NH1 206NE D = 2.356
206NH1 206CG D = : 2.922
206NH1 206CD D = = 2.943
206NH1 206CB D = 4.304
206NH2 206CZ D = 1.342
206NH2 206NH1 D = : 2.308
206NH2 206NE D = 2.327
206NH2 206CD D = : 3.732
206NH2 206CG D = : 4.350 TABLE II (continued)
Distance
Atom 1 Atom 2 Between
206NH2 221CZ D = 4.690
206C 206O D = 1.243
206C 206CA D = 1.526
206C 206CB D = 2.469
206C 206N D = 2.473
206C 208N D = 3.179
206C 206CG D = 3.644
206C 208CA D = 4.390
206C 206CD D = 4.687
206C 208CB D = 4.808
206O 206C D = 1.243
206O 206CA D = 2.414
206O 208N D = 2.823
206O 206N D = 2.953
206O 206CB D = 2.973
206O 208CA D = 3.970
206O 208CB D = 4.080
206O 206CG D = 4.366
206O 208CD D = 4.871
206O 208OE1 D = 4.91 1
206O 208CG D = 4.984
206O 2180 D = 4.995
208N 208CA D = 1.480
208N 208CB D = 2.472
208N 208C D = 2.619
208N 206O D = 2.823
208N 208O D = 2.969
208N 206C D = 3.179
208N 208CG D = 3.665
208N 208OE2 D = 3.827
208N 208CD D = 3.839
208N 206CA D = 4.507
208N 208OE1 D = 4.590
208N 206CB D = 4.638
208CA 208N D = 1.480
208CA 208CB D = 1.539
208CA 208C D = 1.545
208CA 208O D = 2.436
208CA 208CG D = 2.546
208CA 208OE2 D = 2.925
208CA 208CD D = 2.952
208CA 206O D = 3.970
208CA 208OE1 D = 3.976
208CA 217NH2 D = 4.319 TABLE II (continued)
Distance
Atom 1 Atom 2 Between
208CA 206C D = 4.390
208CB 208CG D = 1.513
208CB 208CA D -= 1.539
208CB 208N D = 2.472
208CB 208C D = 2.530
208CB 208CD D = 2.554
208CB 208OE2 D = = 3.153
208CB 208OE1 D - = 3.395
Table III provides the angles (A) between active site atoms at are within 4.0 angstrom of each other. For simplicity, intra-residue angles are omitted.
TABLE III
Middle
Atom 1 Atom Atom 3 An °
174N 174CA 223NE2 A = 1 10.86
174C 174CA 223NE2 A = 99.00
174CB 174CA 223NE2 A = 115.83
1740 174CA 223NE2 A = 124.59
174CG 174CA 223NE2 A = 99.44
223NE2 174CA 174CD A = 104.16
174CD 1740E1 330OE1 A = 154.51
1740E2 1740E1 330OE1 A = 168.53
174CG 1740E1 330OE1 A = 121.98
174CB 1740E1 330OE1 A = 135.03
206NE 206CD 221CZ A = 65.40
206NE 206CD 221CE2 A = 77.07
206CG 206CD 221CZ A = 123.62
206CG 206CD 221CE2 A = 103.04
206CZ 206CD 221CZ A = 89.76
206CZ 206CD 221CE2 A = 97.69
206CB 206CD 221CZ A = 97.1 1
206CB 206CD 221CE2 A = 75.84
206NH1 206CD 221CZ A = 1 15.70
206NH1 206CD 221CE2 A = 118.95
206CA 206CD 221CZ A = 102.03
206CA 206CD 221CE2 A = 83.62
221CZ 206CD 206N A = 82.01
221CZ 206CD 206NH2 A = 79.18
221CZ 206CD 221CE2 A = 21.33
206N 206CD 221CE2 A = 67.03
206NH2 206CD 221CE2 A = 88.85
206CZ 206NE 221CZ A = 139.50
206CZ 206NE 221CE2 A = : 137.47
206CD 206NE 221CZ A = 90.50
206CD 206NE 221CE2 A = : 80.25
206NH2 206NE 221CZ A = : 1 11.86
206NH2 206NE 221CE2 A = : 118.33
206NH1 206NE 221CZ A = : 160.52
206NH1 206NE 221CE2 A = : 143.70
206CG 206NE 221CZ A = : 105.43
206CG 206NE 221CE2 A = : 86.74
221CZ 206NE 206CB A = : 85.57
221CZ 206NE 221CE2 A = : 21.43
206CB 206NE 221CE2 A = : 66.33 TABLE III (continued)
Middle
Atom 1 Atom Atom 3 Anεle°
206O 206C 208N A = 62.24
206CB 206C 208N A = 109.75
206N 206C 208N A = 158.20
208N 206C 206CG A = 110.24
206C 206O 208N A = 94.83
206C 206O 208CA A = 101.47
206CA 206O 208N A = 1 18.57
206CA 206O 208CA A = 1 17.74
208N 206O 206N A = 147.93
208N 206O 206CB A = 106.25
208N 206O 208CA A = 16.05
206N 206O 208CA A = 145.65
206CB 206O 208CA A = 98.04
208CG 208CB 217NH2 A = 48.77
208CA 208CB 217NH2 A = 110.66
208N 208CB 217NH2 A = 144.69
208C 208CB 217NH2 A = 83.16
208CD 208CB 217NH2 A = 77.30
208OE2 208CB 217NH2 A = 79.91
208OE1 208CB 217NH2 A = 85.93
208CB 208CG 217NH2 A = 107.02
208CB 208CG 217NE A = 137.67
208CB 208CG 217CZ A = 130.69
208CD 208CG 217NH2 A = 125.76
208CD 208CG 217NE A = 107.90
208CD 208CG 217CZ A = 1 10.82
208OE1 208CG 217NH2 A = 132.66
208OE1 208CG 217NE A = 94.86
208OE1 208CG 217CZ A = 109.17
208OE2 208CG 217NH2 A = 1 11.25
208OE2 208CG 217NE A = 116.51
208OE2 208CG 217CZ A = : 107.25
208CA 208CG 217NH2 A = : 108.41
208CA 208CG 217NE A = : 155.51
208CA 208CG 217CZ A = : 132.20
217NH2 208CG 217NE A = : 47.37
217NH2 208CG 217CZ A = : 25.22
217NH2 208CG 208C A = : 82.78
217NH2 208CG 208N A = : 124.97
217NE 208CG 217CZ A = : 25.28
217NE 208CG 208C A = : 130.13
217NE 208CG 208N A = = 167.41
217CZ 208CG 208C A = : 106.51
217CZ 208CG 208N A = : 149.73 TABLE III (continued)
Middle
Atom 1 Atom Atom 3 Anrie°
208OE1 208CD 217NE A = 90.82
208OE1 208CD 217NH2 A = 126.11
208OE1 208CD 217CZ A = 109.06
208OE2 208CD 217NE A = 126.48
208OE2 208CD 217NH2 A = 101.12
208OE2 208CD 217CZ A = 107.98
208CG 208CD 217NE A = 49.21
208CG 208CD 217NH2 A = 35.55
208CG 208CD 217CZ A = 47.86
208CB 208CD 217NE A = 81.84
208CB 208CD 217NH2 A = 62.69
208CB 208CD 217CZ A = 79.06
208CA 208CD 217NE A = 106.90
208CA 208CD 217NH2 A = 77.18
208CA 208CD 217CZ A = 96.69
217NE 208CD 208N A = 121.13
217NE 208CD 217NH2 A = 35.39
217NE 208CD 217CZ A = 19.93
217NE 208CD 208C A = 96.15
208N 208CD 217NH2 A = 95.88
208N 208CD 217CZ A = 1 14.89
217NH2 208CD 217CZ A = 19.60
217NH2 208CD 208C A = 62.59
217CZ 208CD 208C A = 82.05
208CD 208OE1 217NE A = 70.82
208OE2 208OE1 217NE A = 92.23
208CG 208OE1 217NE A = 48.48
208CB 208OE1 217NE A = 69.54
216CA 216N 217N A = 58.26
216C 216N 217N A = 27.55
216CB 216N 217N A = 75.00
217N 216N 216CG A = 80.08
217N 216N 216CD2 A = 103.56
217N 216N 2160 A = 39.66
216N 216CA 217N A = 91.16
216N 216CA 217CA A = : 99.04
216C 216CA 217N A = : 28.81
216C 216CA 217CA A = : 18.15
216CB 216CA 217N A = : 109.69
216CB 216CA 217CA A = : 1 12.13
2160 216CA 217N A = = 55.48
2160 216CA 217CA A = : 44.80 TABLE III (continued)
Middle Atom 1 Atom Atom 3 Angle"
217N 216CA 216CG A = : 95.23
217N 216CA 216CD2 A = : 108.18
217N 216CA 216CD1 A = : 78.50
217N 216CA 217CA A = : 10.69 216CG 216CA 217CA A = : 102.67
216CD2 216CA 217CA A = : 1 17.68
216CD1 216CA 217CA A = = 84.94
216CG 216CB 217N A = : 93.95
216CA 216CB 217N A = : 44.07 216N 216CB 217N A = 57.03
216C 216CB 217N A = 21.81
216CD2 216CB 217N A = 107.73
216CD1 216CB 217N A = 83.39
2160 216CB 217N A = 39.93 217N 216CB 216CE1 A = 89.83
217N 216CB 216CE2 A = 106.03
216CD2 216CG 217N A = 129.49
216CD1 216CG 217N A = 87.74
216CB 216CG 217N A = 61.66 216CE1 216CG 217N A = 108.27
216CE2 216CG 217N A = 134.65
216CA 216CG 217N A = 40.47
216CZ 216CG 217N A = 125.90
216N 216CG 217N A = 49.00 216C 216CG 217N A = 20.78
216CE1 216CD1 217N A = 138.03
216CG 216CD1 217N A = 71.23
216CD2 216CD1 217N A = 93.79
216CZ 216CD1 217N A = 132.89 216CB 216CD1 217N A = 56.14
216CE2 216CD1 217N A = 1 15.84
216CA 216CD1 217N A = 37.24
2160 216C 217N A = 122.31
2160 216C 217CA A = 89.58 2160 216C 217CB A = 89.33
2160 216C 217C A = 98.16
2160 216C 218N A = 87.89
217N 216C 216CA A = 1 17.72
217N 216C 217CA A = 32.73 217N 216C 216N A = 92.44
217N 216C 216CB A = 1 12.49
217N 216C 217CB A = 40.03
217N 216C 216CG A = 89.28 TABLE III (continued)
Middle
Atom l Atom Atom 3 Angle0
217N 216C 217C A = 29.43
217N 216C 218N A = 47.60
216CA 216C 217CA A = 150.43
216CA 216C 217CB A = 143.72
216CA 216C 217C A = 137.49
216CA 216C 218N A = 135.79
217CA 216C 216N A = 122.09
217CA 216C 216CB A = 136.80
217CA 216C 217CB A = 24.20
217CA 216C 216CG A = 1 16.56
217CA 216C 217C A = 19.82
217CA 216C 218N A = 34.59
216N 216C 217CB A = 130.54
216N 216C 217C A = 105.55
216N 216C 218N A = 103.71
216CB 216C 217CB A = 116.54
216CB 216C 217C A = 141.86
216CB 216C 218N A = 156.61
217CB 216C 216CG A = 101.05
217CB 216C 217C A = 42.91
217CB 216C 218N A = 58.76
216CG 216C 217C A = 1 18.52
216CG 216C 218N A = 133.95
217C 216C 218N A = 19.50
216C 2160 217N A = 29.92
216C 2160 217CA A = 62.89
216C 2160 217CB A = 70.34
216C 2160 217C A = 63.58
216C 2160 337NE A = 131.52
216C 2160 217CG A = 92.78
217N 2160 216CA A = 63.29
217N 2160 217CA A = 32.97
217N 2160 216CB A = ■■ 70.39
217N 2160 216N A = : 54.43
217N 2160 217CB A = 43.89
217N 2160 217C A = : 35.89
217N 2160 337NE A = : 159.88
217N 2160 217CG A = ■ 66.32
216CA . 2160 217CA A = : 96.25
216CA . 2160 216N A = : 18.49
216CA . 2160 217CB A = : 101.39
216CA . 2160 217C A = : 95.31
216CA . 2160 337NE A = : 98.87
216CA . 2160 217CG A = : 122.42 TABLE III (continued)
Middle
Atom 1 Atom Atom 3 Angle0
217CA 2160 216CB A = 100.29
217CA 2160 216N A = 85.83
217CA 2160 217CB A = 23.38
217CA 2160 217C A = 16.01
217CA 2160 337NE A = 162.34
217CA 2160 217CG A = 39.79
216CB 2160 217CB A = 94.84
216CB 2160 217C A = 106.26
216CB 2160 337NE A = 89.50
216CB 2160 217CG A = 110.18
216N 2160 217CB A = 97.41
216N 2160 217C A = 81.13
216N 2160 337NE A = 111.1 1
216N 2160 217CG A = 120.03
217CB 2160 217C A = 39.18
217CB 2160 337NE A = 142.07
217CB 2160 217CG A = 22.64
217C 2160 337NE A = 164.24
217C 2160 217CG A = 52.47
337NE 2160 217CG A = 122.91
216C 217N 218N A = 1 14.66
217CA 217N 218N A = 44.76
2160 217N 218N A = 95.72
216CA 217N 218N A = 131.08
217C 217N 218N A = 22.69
217CB 217N 218N A = 77.75
Mutants and Derivatives
The invention further provides homologues, co-complexes, mutants and derivatives of the Staph aureus tRNA synthetase crystal structure of the invention.
The term "homologue" means a protein having at least 30% amino acid sequence identity with synthetase or any functional domain of glycyl tRNA synthetase. The term "co-complex" means glycyl tRNA synthetase or a mutant or homologue of glycyl tRNA synthetase in covalent or non-covalent association with a chemical entity or compound.
The term "mutant" refers to a glycyl tRNA synthetase polypeptide, i.e., a polypeptide displaying the biological activity of wild-type glycyl tRNA synthetase activity, characterized by the replacement of at least one amino acid from the wild-type synthetase sequence. Such a mutant may be prepared, for example, by expression of Staph aureus synthetase cDNA previously altered in its coding sequence by oligonucleotide-directed mutagenesis. Staph aureus glycyl tRNA synthetase mutants may also be generated by site-specific incorporation of unnatural amino acids into glycyl tRNA synthetase proteins using the general biosynthetic method of C. J. Noren et al, Science, 244: 182-188 (1989). In this method, the codon encoding the amino acid of interest in wild-type glycyl tRNA synthetase is replaced by a "blank" nonsense codon, TAG, using oligonucleotide-directed mutagenesis. A suppressor tRNA directed against this codon is then chemically aminoacylated in vitro with the desired unnatural amino acid. The aminoacylated tRNA is then added to an in vitro translation system to yield a mutant glycyl tRNA synthetase enzyme with the site-specific incorporated unnatural amino acid.
Selenocysteine or selenomethionine may be incorporated into wild-type or mutant tRNA glycyl synthetase by expression of Staph aureus glycyl tRNA synthetase- encoding cDNAs in auxotrophic E. coii strains [W. A. Hendrickson et al, EMBO J., 9(5): 1665- 1672 (1990)]. In this method, the wild-type or mutagenized tRNA synthetase cDNA may be expressed in a host organism on a growth medium depleted of either natural cysteine or methionine (or both) but enriched in selenocysteine or selenomethionine (or both).
The term "heavy atom derivative" refers to derivates of glycyl tRNA synthetase produced by chemically modifying a crystal of glycyl tRNA synthetase. In practice, a crystal is soaked in a solution containing heavy metal atom salts, or organometallic compounds, e.g., lead chloride, gold thiomalate, thimerosal or uranyl acetate, which can diffuse through the crystal and bind to the surface of the protein. The location(s) of the bound heavy metal atom(s) can be determined by X-ray diffraction analysis of the soaked crystal. This information, in turn, is used to generate the phase information used to construct three-dimensional structure of the enzyme [T. L. Blundel and N. L. Johnson, Protein Crystallography, Academic Press (1976).
II. Methods of Identifying Inhibitors of the Novel Glycyl tRNA Synthetase
Crystalline Structure
Another aspect of this invention involves a method for identifying inhibitors of a Staph glycyl tRNA synthetase characterized by the crystal structure and novel active site described herein, and the inhibitors themselves. The novel synthetase crystalline structure of the invention permits the identification of inhibitors of synthetase activity. Such inhibitors may be competitive, binding to all or a portion of the active site of the glycyl tRNA synthetase; or non-competitive and bind to and inhibit glycl tRNA synthetase whether or not it is bound to another chemical entity.
One design approach is to probe the glycyl tRNA synthetase crystal of the invention with molecules composed of a variety of different chemical entities to determine optimal sites for interaction between candidate glycyl tRNA synthetase inhibitors and the enzyme. For example, high resolution X-ray diffraction data collected from crystals saturated with solvent allows the determination of where each type of solvent molecule sticks. Small molecules that bind tightly to those sites can then be designed and synthesized and tested for their glycyl tRNA synthetase inhibitor activity [J. Travis, Science, 262: 1374 (1993)]. This invention also enables the development of compounds that can isomerize to short-lived reaction intermediates in the chemical reaction of a substrate or other compound that binds to or with glycyl tRNA synthetase. Thus, the time-dependent analysis of structural changes in glycyl tRNA synthetase during its interaction with other molecules is permitted. The reaction intermediates of glycyl tRNA synthetase can also be deduced from the reaction product in co-complex with glycyl tRNA synthetase. Such information is useful to design improved analogues of known glycyl tRNA synthetase inhibitors or to design novel classes of inhibitors based on the reaction intermediates of the glycyl tRNA synthetase enzyme and glycyl tRNA synthetase inhibitor co-complex. This provides a novel route for designing glycyl tRNA synthetase inhibitors with both high specificity and stability. Another approach made possible by this invention, is to screen computationally small molecule data bases for chemical entities or compounds that can bind in whole, or in part, to the glycyl tRNA synthetase enzyme. In this screening, the quality of fit of such entities or compounds to the binding site may be judged either by shape complementarity or by estimated interaction energy [E. C. Meng et al, J. Comp. Chem., .13:505-524 (1992)].
Because glycyl tRNA synthetase may crystallize in more than one crystal form, the structure coordinates of glycyl tRNA synthetase, or portions thereof, as provided by this invention are particularly useful to solve the structure of those other crystal forms of tRNA synthetase. They may also be used to solve the structure of glycyl tRNA synthetase mutant co-complexes, or of the crystalline form of any other protein with significant amino acid -sequence homology to any functional domain of glycyl tRNA synthetase.
One method that may be employed for this purpose is molecular replacement. In this method, the unknown crystal structure, whether it is another crystal form of glycyl tRNA synthetase, a glycl tRNA synthetase mutant, or a glycyl tRNA synthetase co- complex, or the crystal of some other protein with significant amino acid sequence homology to any functional domain of glycyl tRNA synthetase, may be determined using the glycyl tRNA synthetase structure coordinates of this invention as provided in Figure 1 and Tables I - III. This method will provide an accurate structural form for the unknown crystal more quickly and efficiently than attempting to determine such information ab initio.
Thus, the synthetase structure provided herein permits the screening of known molecules and/or the designing of new molecules which bind to the synthetase structure, particularly at the active site, via the use of computerized evaluation systems. For example, computer modelling systems are available in which the sequence of the synthetase, and the synthetase structure (i.e., the bond angles, dihedral angles, distances between atoms in the active site region, etc. as provided by Figure 1 and Tables I - III herein) may be input. Thus, a machine readable medium may be encoded with data representing the coordinates of Figure 1 and Tables I - III. The computer then generates structural details of the site into which a test compound should bind, thereby enabling the determination of the complementary structural details of said test compound.
More particularly, the design of compounds that bind to or inhibit glycyl tRNA synthetase according to this invention generally involves consideration of two factors. First, the compound must be capable of physically and structurally associating with glycyl tRNA synthetase. Non-covalent molecular interactions important in the association of glycyl tRNA synthetase with its substrate include hydrogen bonding, van der Waals and hydrophobic interactions.
Second, the compound must be able to assume a conformation that allows it to associate with glycyl tRNA synthetase. Although certain portions of the compound will not directly participate in this association with glycyl tRNA synthetase, those portions may still influence the overall conformation of the molecule. This, in turn, may have a significant impact on potency. Such conformational requirements include the overall three- dimensional structure and orientation of the chemical entity or compound in relation to all or a portion of the binding site, e.g., active site or accessory binding site of glycyl tRNA synthetase, or the spacing between functional groups of a compound comprising several chemical entities that directly interact with glycyl tRNA synthetase.
The potential inhibitory or binding effect of a chemical compound on glycyl tRNA synthetase may be analyzed prior to its actual synthesis and testing by the use of computer modelling techniques. If the theoretical structure of the given compound suggests insufficient interaction and association between it and glycyl tRNA synthetase, synthesis and testing of the compound is obviated. However, if computer modelling indicates a strong interaction, the molecule may then be synthesized and tested for its ability to bind to glycyl tRNA synthetase and inhibit using a suitable assay. In this mannei, synthesis of inoperative compounds may be avoided. An inhibitory or other binding compound of glycyl tRNA synthetase may be computationally evaluated and designed by means of a series of steps in which chemical entities or fragments are screened and selected for their ability to associate with the individual binding pockets or other areas of glycyl tRNA synthetase.
One skilled in the art may use one of several methods to screen chemical entities or fragments for their ability to associate with glycyl tRNA synthetase and more particularly with the individual binding pockets of the glycyl tRNA synthetase active site or accessory binding site. This process may begin by visual inspection of, for example, the active site on the computer screen based on the glycyl tRNA synthetase coordinates in Figure 1 and Tables I - III. Selected fragments or chemical entities may then be positioned in a variety of orientations, or docked, within a binding pocket of glycyl tRNA synthetase. Docking may be accomplished using software such as Quanta and Sybyl, followed by energy minimization and molecular dynamics with standard molecular mechanics force fields, such as CHARMM and AMBER. Specialized computer programs may also assist in the process of selecting fragments or chemical entities. These include:
1. GRID [P. J. Goodford, "A Computational Procedure for Determining Energetically Favorable Binding Sites on Biologically Important Macromolecules", J. Med. Chem., 28:849-857 (1985)]. GRID is available from Oxford University, Oxford, UK.
2. MCSS [A. Miranker and M. Karplus, "Functionality Maps of Binding Sites: A Multiple Copy Simultaneous Search Method", Proteins: Structure, Function and Genetics. H:29-34 (1991)]. MCSS is available from
Molecular Simulations, Burlington, MA.
3. AUTODOCK [D. S. Goodsell and A. J. Olsen, "Automated Docking of Substrates to Proteins by Simulated Annealing", Proteins; Structure, Function, and Genetics. 8 : 195-202 ( 1990)] . AUTODOCK is available from
Scripps Research Institute, La Jolla, CA.
4. DOCK [I. D. Kuntz et al, "A Geometric Approach to Macromolecule- Ligand Interactions", J. Mol. Biol., 161:269-288 (1982)]. DOCK is available from University of California, San Francisco, CA.
Once suitable chemical entities or fragments have been selected, they can be assembled into a single compound or inhibitor. Assembly may be proceed by visual inspection of the relationship of the fragments to each other on the three-dimensional image displayed on a computer screen in relation to the structure coordinates of glycyl tRNA synthetase. This would be followed by manual model building using software such as Quanta or Sybyl.
Useful programs to aid one of skill in the art in connecting the individual chemical entities or fragments include: 1. CAVEAT [P. A. Bartlett et al, "CAVEAT: A Program to Facilitate the
Structure-Derived Design of Biologically Active Molecules", in Molecular Recognition in Chemical and Biological Problems", Special Pub., Royal Chem. Soc. 78, pp. 182-196 (1989)]. CAVEAT is available from the University of California, Berkeley, CA.
2. 3D Database systems such as MACCS-3D (MDL Information Systems, San
Leandro, CA). This area is reviewed in Y. C. Martin, "3D Database Searching in Drug Design", J. Med. Chem.. 35:2145-2154 (1992). 3. HOOK (available from Molecular Simulations, Burlington, MA).
Instead of proceeding to build a glycyl tRNA synthetase inhibitor in a step-wise fashion one fragment or chemical entity at a time as described above, inhibitory or other glycyl tRNA synthetase binding compounds may be designed as a whole or "de novo" using either an empty active site or optionally including some portion(s) of a known inhibitor(s).
These methods include:
1. LUDI [H.-J. Bohm, "The Computer Program LUDI: A New Method for the
De Novo Design of Enzyme Inhibitors", J. Comp. Aid. Molec. Design, 6:61-78 (1992)]. LUDI is available from Biosym Technologies, San Diego,
CA.
2. LEGEND [Y. Nishibata and A. Itai, Tetrahedron, 47:8985 (1991)]. LEGEND is available from Molecular Simulations, Burlington, MA.
3. LeapFrog (available from Tripos Associates, St. Louis, MO).
Other molecular modelling techniques may also be employed in accordance with this invention. See, e.g., N. C. Cohen et al, "Molecular Modeling Software and Methods for Medicinal Chemistry", J. Med. Chem.. 33:883-894 (1990). See also, M. A. Navia and M. A. Murcko, "The Use of Structural Information in Drug Design", Current Opinions in Structural Biology, 2:202-210 (1992). For example, where the structures of test compounds are known, a model of the test compound may be superimposed over the model of the structure of the invention. Numerous methods and techniques are known in the art for performing this step, any of which may be used. See, e.g., P.S. Farmer, Drug Design,
Ariens, E.J., ed., Vol. 10, pp 119-143 (Academic Press, New York, 1980); U.S. Patent No. 5,331,573; U.S. Patent No. 5,500,807; C. Verlinde, Curr. Biol.. 2:577-587 (1994); and I. D. Kuntz, Science, 257: 1078-1082 (1992). The model building techniques and computer evaluation systems described herein are not a limitation on the present invention. Thus, using these computer evaluation systems, a large number of compounds may be quickly and easily examined and expensive and lengthy testing avoided. Moreover, the need for actual synthesis of many compounds is effectively eliminated.
Once identified by the modelling techniques, the synthetase inhibitor may be tested for bioactivity using standard techniques. For example, structure of the invention may be used in binding assays using conventional formats to screen inhibitors. One particularly suitable assay format includes the enzyme-linked immunosorbent assay (ELISA). Other assay formats may be used; these assay formats are not a limitation on the present invention.
In another aspect, the synthetase structure of the invention permit the design and identification of synthetic compounds and/or other molecules which are characterized by the conformation of the synthetase of the invention. Using known computer systems, the coordinates of the synthetase structure of the invention may be provided in machine readable form, the test compounds designed and/or screened and their conformations superimposed on the structure of the synthetase of the invention. Subsequently, suitable candidates identified as above may be screened for the desired synthetase inhibitory bioactivity, stability, and the like. Once identified and screened for biological activity, these inhibitors may be used therapeutically or prophylactically to block synthetase activity, and thus, bacterial replication.
III. INHIBITORS OF GLYCYL tRNA SYNTHETASE (GRS) ACTIVITY
The present invention also provides inhibitors of glycyl tRNA synthetase activity identified or designed by the methods of the invention. These inhibitors are useful as antibacterial agents.
One particularly desirable inhibitor is glycylsulfamoyladenosine. The structure of this compound is as follows.
Figure imgf000029_0001
Glycylsulfmoyladenosine
Glycylsulfmoyladenosine is an analogue of the Gly-AMP reaction intermediate and inhibits GRS catalytic activity as measured by any of the techniques described in the examples below. Estimates of the potency of inhibition are obtained by performing enzyme assays in the presence of a range of inhibitor concentrations, and fitting the effect of inhibitor concentration on enzyme velocity to a four parameter logistic function that allows calculation of an IC50 (the inhibitor concentration at which GRS activity is reduced by half). This parameter is directly related to the dissociation constant for inhibitor binding (Kj or Kd) and has a value of around 2.4 mM for glycylsulfamoyladenosine when tested against the S. aureus GRS. Binding of glycylsulfamoyladenosine to GRS can also be measured directly using stopped-flow fluorescence techniques because enzyme:inhibitor binary complex has around 5% higher tryptophan fluorescence than the free enzyme. Experiments of this type yield the following elementary rate constants for inhibitor binding; koa = 1.1 x IO6 s"'.M"', A'off = 2.9s"1. The ratio of these yields an estimate for I j of 2.6 mM, almost identical to the result obtained in enzyme inhibition experiments.
The following examples illustrate various aspects of this invention. These examples do not limit the scope of this invention which is defined by the appended claims.
Example 1 - The Expression of the Glycyl t-RNA Synthetase from Staphylococcus aureus in Escherichia coii.
The strategy for the expression of the glycyl t-RNA synthetase (GRS) from Staphylococcus aureus, using Escherichia coii as a host was based on the PCR amplification of the grs gene and the introduction of suitable restriction sites that allowed the cloning of the gr?-containing DNA fragment in the pDB575 expression vector. After the PCR amplification the insert of the resultant recombinant plasmid, (pDBGRS hereafter), was sequenced to verify the absence of artefacts introduced by the Taq polymerase. Expression was monitored by SDS-polyacrylamide gel analysis. A. Bacterial strains, Plasmids and Medium
The Escherichia coii strains used were: DH5a (supE44, D/αcU169 (f 80 /αcZDM15), hsdRXl, recAX, endAX, gyrA96, thi-X, relA X) and HB101 (thi-X, hsdS,20(r ,m B), supE44, recAX3, ara-X4, leuBβ, proA2, lacYX, rpsL20(stττ), xyl-5, mtl-X). E. coii cells were grown at 37°C in Luria Bertani broth (LB). These strains may all be obtained from commercial sources.
The plasmids used were pBluescript SK- [Stratagene], pUC18 [J. Sambrook et al., Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York (1989)] and pDB575. A detailed description of pDB575 is provided in A.F. Chalker et al, Gene, 141:103-108 (1994). Briefly, pDB575 is a expression vector of E.coli based on pKK223-3 [Pharmacia] with the following modifications: (i) the polylinker between EcoRl and Hindϊll has been replaced with a longer one (EcoRX, NcoX, Kpnl, Ndel, SstX, Sstll, XbaX, ClaX, SmaX, BgllX, XmaXXX, Hindlll) (ii) it has a laclq gene inserted; (iii) it is non-mobilizable, the pBR322 portion of pKK223-3 has been replaced by the equivalent fragment from pATIS3. pDB575 allows the selection of the recombinant clones by ampicillin resistance and the gene expression is driven by the tac promoter. LB Medium. Per litre:
Figure imgf000031_0001
For plasmid propagation 0.1 mg/ml of ampicillin was added to the medium. B. DNA manipulations
Plasmid DNA was prepared by the rapid alkaline method (Sambrook et al, 1989). Transformations of E. coii cells were carried out using the RbCl methods (Sambrook et al, 1989). DNA fragments were purified using the Geneclean Kit [BIO 101 Inc., La Jolla, CA, USA]. The plasmids for sequencing were purified using QIAGEN plasmid kit [QIAGEN]. DNA sequencing was carried out on supercoiled plasmid DNA by the dideoxy chain-termination method using the Thermo Sequenase cycle sequencing kit [Amersham Life Science, Inc. USA]. DNA was also sequenced by the Automated Sequencing Service of Pharmacy Faculty in the Complutense University of Madrid. Universal or synthetic oligonucleotides [MedProbe, Norway] were used as primers. Restriction enzymes and T4 DNA ligase were obtained from Promega and Boehringer respectively and the experiments were carried out following the instructions provided by the suppliers.
The grs gene from S. aureus cloned in the pBluescript SK- was amplified by PCR using the primers GRS 1 : (5'-GGGGTACCGCTAGCAGGAGAGGTAATTATGGCAAAAGATATG-3'; SEQ ID NO:2) and GRS2: (5 -GCTCTAGATTAGTCATTTAATTAGAATTTTGTTTTTTCAGTTAAG- 3'; SEQ ID NO:3). Kpn I and Xba I restriction sites were incorporated at the 5' and 3' ends respectively of each primer to facilitate ligation of the amplified DNA into vectors. Plasmid DNA (100 ng) was amplified in 100 ml of PCR mixture containing 250 mM deoxynucleotide triphosphates (dNTPs), 0.9 mM oligonucleotide primers, the manufacturer's buffer and 2U of Taq polymerase (Promega). The following cycling parameters were used:
94°C 5 min
94°C 1 min, 55°C 2 min, 72°C 2 min (35 cycles) 72°C 10 min Polymerase chain reaction (PCR) was performed using the DNA Thermal Cycler [Perkin Elmer Cetus]. PCR-amplified DNA fragments were purified using Wizard™ Preps DNA Purification System for Rapid Purification of DNA Fragments [Promega].
C. Cloning of the grs gene of S. aureus in the expression vector pDB575 of E. coii.
The cloning strategy is shown in Figure 2. PCR amplification of the grs gene from S. aureus using the primers GRS1 and GRS2 resulted in a DNA fragment of 1.4 kb. This fragment was purified and ligated to the Kpnl, Xbal sites of pDB575 to obtain the recombinant plasmid pDBGRS and the ligation mix was used to transform E. coii DH5a competent cells. The construction of pDBGRS was initially confirmed by restriction analysis of the plasmid purified from the transformants. The amplification with Taq DNA polymerase made the sequencing of the grs of pDBGRS an obligatory step to confirm that no changes were introduced due to the low fidelity of this enzyme. Sequence analysis was accomplished by using grs gene introduced in the expression plasmid pDB575 and/or in pUC18. The sequencing of both strands showed that no artefacts had been introduced during the amplification process.
D. Small-scale production of GRS from 5. aureus in E. coii
The plasmid pDBGRS and the negative control pDB575 (vector without insert) were used to transform the E. coii HB 101 host strain. Single clones of HB101 :pDBGRS and HB 101:pDB575 cells were grown overnight at 37°C in 2 ml of LB medium in the presence of 0.1 mg/ml ampicillin. The cells were then diluted 100-fold in 30 ml LB with ampicillin. When the cultures reached a value of 0.5 at OD6oothe grs expression was induced by addition of isopropyl-thio-galactoside (IPTG) at ImM of final concentration. After this induction 2 ml samples were taken at different times (2, 3 and 4 hours). The cells were harvested in a microfuge for 3 min, the pellets were washed with 20 mM Tris-HCl pH 8 / ImM PMSF and resuspended in 300 ml of SDS-PAGE gel-loading buffer. The cells were broken by sonication (15 seconds). The samples were then boiled 10 minutes and after one spin, 10 ml fractions were analyzed by SDS-PAGE according to the methods of Laemmli [U. K. Laemmli, Nature 227, 680-685 (1970)]. The 12% polyacrylamide gels were stained with Coomassie blue. As shown in Figure 3 good expression levels were detected from the early stages after induction with IPTG. The evidence was the presence of a prominent band (lanes 2, 4 and 6 in Figure 3) that was in good agreement with the Mr predicted from the primary sequence. The GRS protein has a theoretical molecular weight of about 53.7 kDa. Example 2 - Fermentation and Purification of Glycyl tRNA Synthetase
A. Fermentation
A 300 litre fermentation of E.coli HB 101 :pDB575GRS was carried out in double strength Luria Bertani medium (LB), containing 50 ug/ml ampicillin. The vessel was inoculated at 2% (v/v) from a 15 hour secondary seed culture in single strength LB medium, containing 50 mg/ml ampicillin. The production vessel was incubated at 37°C, agitated at 1.5 msec"1 and aerated at 1.0 VVM. The OD at 550nm was monitored, and at 2.5 absorbance units, GRS expression was induced with the addition of isopropyl- thiogalactosidase to 1.0 mM and the cells harvested by centrifugation in a Westfalia CSA- 19, 2 hours post induction. A total of 990 grams of cell paste was recovered.
LB Medium, per litre, contains the following components. The medium ingredients were supplied by Difco Laboratories, West Molesey, Surrey UK. Double strength Single strength Bacto Tryptone 20 g Bacto Tryptone 10 g
Bacto Yeast Extract 10 g Bacto Yeast Extract 5 g
Sodium Chloride 5 g Sodium Chloride 5 g
B. Purification
1) Lysis 125 g of cells of E. coii overexpressing S. aureus GRS obtained as described above, were resuspended in 600ml of 20mM Tris, ImM EDTA, ImM DTT, 5mM MgCl2pH 7.5 (buffer A). Lysozyme ( Sigma Chemicals: hen egg) was added to a final concentration of 2mg/ml. Cells were incubated at 37°C for 20min. The cells were then frozen in an ethanol/dry ice water bath and thawed. Dnase (Sigma; bovine pancreas type 1) was added to a final concentration of 10 Kunitz units per ml and held at 37°C for 5 minutes. The solution was centrifuged in a Beckman J A-HS centrifuge at 14,000 g for 60 minutes using a Beckman JA-14 rotor.
2) Anion exchange
All chromatography was performed on a Waters 650E chromatography system, fitted with a UV detector (Pharmacia S2) and conductivity monitor (Pharmacia). UV (at 280nm) and conductivity were monitored during all operations. All operations were performed at 4°C.
The supernatant from 1 ) was loaded onto a Q-Sepharose high performance (Pharmacia) column of 200ml packed into a Pharmacia XK-50 column. The column was equilibrated with buffer A prior to loading. The column is then washed with buffer A (1000ml) at 40 ml/min, and eluted with a linear gradient of buffer A to IM NaCl in buffer A over 140 minutes at lOml/min. The eluate was fractionated into 5 minute fractions using a Pharmacia Superfrac. The eluted fractions were assayed for GRS activity by measurement of aminoacylation of tRNAGly, and for protein by the Bradford method. Active fractions were analyzed by reducing SDS PAGE (Pharmacia Phast System 10-15% gradient gel)
3) Hydrophobic interaction chromatography Two active fractions from 2) were pooled and the ammonium
-sulphate concentration adjusted to IM by addition (1 to 1) of 2 M ammonium sulphate. The material was loaded onto a 50ml column of butyl Toyopearl 650S (Tosohaas) equilibrated with buffer A plus IM ammonium sulphate (column Pharmacia XK-26). The column was washed with 100ml of the equilibration buffer and then eluted with a linear gradient of equilibration buffer to buffer A over 140 minutes at 5ml/min.
4) Concentration/buffer exchange
Eluted fractions are collected ( 1 minute fraction) and assayed for GRS activity and protein. Active fractions are pooled and diafiltered against (1,000 fold buffer exchange) buffer A using an Amicon ultrafiltration cell (350ml) under nitrogen. A final volume of 33 ml of protein was obtained containing 4.2 mg/ml of protein (by amino acid analysis). This product was greater than 95% purity by SDS PAGE and the activity showed an overall process yield of 60 % from 1). N-terminal amino acid analysis confirmed identity.
C. Measurement of Glycyl tRNA Synthetase (GRS) activity. The enzyme catalyses the aminoacylation of tRNAGly, which proceeds through a two step mechanism. The first step involves the formation of a stable enzyme:glycyl adenylate complex resulting from the specific binding and reaction of ATP and L-glycine. Subsequently, the 3' terminal adenosine of enzyme-bound tRNAGly reacts with the aminoacyladenylate, leading to the esterification of the tRNA and release of AMP. These steps are summarized below. a) L-Gly + ATP.Mg + GRS P GRS: Gly-AMP + PPi.Mg b) GRS:Gly-AMP + tRNAGly I GRS + Gly-tRNAGly + AMP
This reaction can be assayed in order to characterize the enzyme or identify specific inhibitors of its activity in a number of ways: (1) Measurement of the formation of Gly-tRNAGly can be specifically determined using radiolabelled glycine and separating free glycine from Gly-tRNA using precipitation/filtration techniques (e.g. in cold trichloroacetic acid; see, Calender & Berg (1966) Biochemistry 5, 1681-1690; Toth MJ & Schimmel P (1990) J. Biol. Chem. 265, 1000-1004].
(2) The full acylation reaction can also be measured by analyzing production of either PPi or AMP which are produced in stoichiometric ratio to the tRNA acylation. This may be achieved in a number of ways, for example using colorimetric [Hoenig (1989) J. Biochem. Biophys. Meth. 19, 249-252]; or enzyme coupled [Webb TM (1994) Anal. Biochem. 218, 449-454] measurement of Pi after addition of excess inorganic pyrophosphatase or using enzyme coupled assays to directly measure AMP or PPi production [Sigma Chemicals Catalogue, 1986].
(3) The partial reaction (a) can be assayed through radiolabel isotopic exchange between ATP and PPi, since each of the steps in this part of the reaction are freely reversible. This reaction is independent of tRNA binding, typically has a kCM around 20-fold higher than the full acylation reaction (a+b), and is readily measured using chromatographic principles which separate PPi from ATP (i.e. using activated charcoal; see, Calender & Berg, cited above; Toth & Schimmel, cited above). D. Ligand binding to GRS. It is also possible to define ligand interactions with GRS in experiments that are not dependent upon enzyme catalyzed turnover of substrates. This type of experiment can be done in a number of ways:
(1) Effects of ligand binding upon enzyme intrinsic fluorescence (e.g. of tryptophan). Binding of either natural ligands or inhibitors may result in enzyme conformational changes which alter enzyme fluorescence. Using stopped-flow fluorescence equipment, this can be used to define the microscopic rate constants that describe binding. Alternatively, steady-state fluorescence titration methods can yield the overall dissociation constant for binding in the same way that these are accessed through enzyme inhibition experiments. (2) Spectral effects of ligands. Where the ligands themselves are either fluorescent or possess chromophores that overlap with enzyme tryptophan fluorescence, binding can be detected either via changes in the ligand fluorescence properties (e.g. intensity, lifetime or polarization) or fluorescence resonance energy transfer with enzyme tryptophans. The ligands could either be inhibitors or variants of the natural ligands (i.e. fluorescent ATP derivatives or tRNAGly labelled with a fluorophore).
(3) Thermal analysis of the enzyme:ligand complex. Using calorimetric techniques (e.g. Isothermal Calorimetry, Differential Scanning Calorimetry) it is possible to detect thermal changes, or shifts in the stability of GRS which reports and therefore allows the characterization of ligand binding.
E. Aminoacylation Assays for GRS Activity
Assays were performed either using purified S. aureus GRS overexpressed in E. coii, or using crude cell lysate from E. coii overexpressing GRS. The latter contained around 10% of total protein as GRS. Enzyme was stored at -70°C in 50 mM Tris-HCl buffer (pH 7.8), 10 mM MgCl2 and 10 mM B-mercaptoethanol after flash freezing in liquid Ν2. In experiments to determine the activity of enzyme samples, these stocks were diluted over a wide range (100 fold to 10,000 fold) in 50 mM Tris pH 7.8, 10 mM MgCl2, 1 mM Dithiothreitol and stored on ice prior to assay. The assay procedure was as follows. 50 ml of enzyme prepared and diluted as described above was mixed with reaction mixture (100 ml), comprising: 0.15 mCi L-[U- 14]-Glycine (Amersham International), 4 mg/ml E. coii MRE600 mixed tRNA (Boehringer Manheim), 5 mM ATP, 15 mM MgS04, 3 M DTT, 75 mM KC1 and 50 mM Tris-HCl, pH 7.8. Unless otherwise states, all reagents were obtained from Sigma Chemical Company Ltd. Concentrations are given as in the final reaction mix. After addition of the enzyme to start the reaction, assay samples were incubated at 37°C and, at the desired time, duplicate aliquots (50ml) were removed and quenched with 7% trichloroacetic acid (100 ml) and left on ice for 30 min. The precipitates were harvested using a Packard Filtermate 196 Cell Harvester [Packard Instruments Ltd.] onto glass fibre filters which were washed successively with 7% trichloroacetic acid and ethanol. The filters were dried at 70°C for 1 hour and the levels of radioactivity measured by scintillation counting (Packard Topcount).
Example 3 - Crystallization of Staphylococcus aureus Glycyl tRNA Synthetase A. Crystallization A large crystal (0.25 x 0.25 x 0.18 mm3) was formed using the following conditions. The protein used for the crystallization was supplied @ 5.8 mg/ml in a solution of 20mM tris, 5mM MgCl2, ImM DTT, ImM EDTA, 10% glycerol, pH 7.5). The crystal was obtained from a 1 : 1 mixture of the protein solution and a solution of 10% PEG 8000, 0.1M imidazole pH 8.0 and 0.2M calcium acetate using the hanging drop method, grown at room temperature.
B. X-ray Diffraction Characterization
Initially, the Staph aureus synthetase crystal was mounted in a sealed glass capillary with a small amount of mother liquor in each end of the capillary. The CuKa X- ray, having a wavelength of 1.54 A, was generated by a Rigaku-RU200 rotating anode machine operating at 100 mA x 50 kV electric power. The crystal was exposed to the CuKa X-ray, and the diffracted X-ray was collected by a Siemens multiwire area detector. The crystal diffracted to 3.5 . By registering the position and intensity of many tens of thousands diffraction spots using the computer program XENGEN, the crystal has been determined to be an orthorhombic crystal system and P2,2,2, space group. The unit cell dimensions are a- 81.5 A, b=123.1A, c = 127.5 A. By established methods, an asymmetric unit was calculated to have one protein molecule. The crystal contains an estimated 60% solvent. C. Structure Solution
It was determined that the amino acid sequences of S. aureus and T. thermophilus are 44% identical. Since the crystal structure of the T. thermophilus GRS has been published [D. T. Logan et al, EMBO J., 14:4156-4167 (1995)], it served as a search model for structure solution using molecular replacement methods. The GRS dimer was used as the initial search model, the rotation search was carried out including all the data in 10.0 - 4.0 A and the solution was evident from the 25s peak height. The subsequent translation search also yielded a pronounced solution at 15s and an R-factor of 49.4% using all the data to 3.5 A resolution. Rigid body refinement reduced the R-factor to 47.8%. Solvent flattening and 2-fold non-crystallographic averaging was then used to improve the phases [Collaborative Computational Project, Number 4, Acta Crystaliogr. D50, 760-763 (1994)], which introduced about 30°C phase shifts and improved the averaged figure of merit from 0.4 to 0.8 and Rfree from 47% to 28%. An improved electron density map was then calculated.
D. Model Building and Refinement Using the three-dimensional electron density map obtained from above experiments, the polypeptide chain of the S. aureus GRS can be traced without ambiguity. Three hundred ninety-five (395) residues (most with side chains) were built for each monomer in the 3-D computer graphics program XTALVIEW [McKee, D.E. in Practical Protein Crystallography, Academic Press, San Diego (1993)]. XTALVIEW was used in building models of the GRS structure. Using the initial model, a diffraction pattern was calculated and compared to the experimental data. The difference between the calculated and experimentally determined diffraction patterns was monitored by the value of R-factors. The refinement of the structural model was carried out by adjustments of atomic positions to minimizing the R-factor, where a value of about 20% is typical for a good quality protein structure.
The GRS model was subjected to one round of Xplor [A. Brunger et al, Science, 235:458-460 (1987) refinement using the standard positional, slowcool and overall B factor refining protocols. The GRS was refined as a tightly contained dimer without any solvent molecules. The R factor of the model is 23.9% with satisfactory geometry. The rms deviations are 0.017 A for bond lengths, 2.0° for bond angles, 25.4 for dihedrals and 1.8°C for impropers. The structure contains residues 1-86, 150-161 , 164-352 and 356-463 [SEQ ID NO:l], while the other 68 residues (15%) are disordered in the crystal and not included in the model.
Example 5 - The Preparation of the Glycyl tRNA Synthetase Inhibitor, 5'-Q- Glycylsulfamoyladenosine
A solution of 2',3'-0-isopropylidene-5'-0-sulfamoyladenosine (J. Castro-Pichel et al, Tetrahedron, 1987, 43, 383) (0.50g, 1.3 mmol) in dry tetrahydrofuran (THF) (3ml) was added to a solution of N-t-butoxycarbonylglycine N-hydroxysuccinimide ester (Sigma
Chemical Co.) in dry THF( 2ml), followed by l,8-diazabicyclo[5.4.0]undec-7-ene (0.2ml, 1.3 mmol), and the mixture stirred at room temperature for 1.5h. The mixture was then partitioned between 10% aqueous citric acid (25 ml) and ethyl acetate (25ml) and the organic phase washed with saturated NaHC03, brine, dried (MgS04) and evaporated to an oil. This was chromatographed on Kieselgel 60 eluting with 0-20% methanol in dichloromethane to afford the protected product (200mg).
This material (lOOmg) was dissolved in trifluoroacetic acid (3ml). After stirring for 15 min at room temperature, water (3ml) was added and the mixture stirred at room temperature for a further hour. The solution was evaporated and the residue chromatographed on reverse-phase silica gel eluting with water. The product-containing fractions were combined and freeze-dried to afford the 5'-0- glycylsulfamoyladenosine as a white solid. (10 mg); d( ppm, D20) 3.78 (2H, CH2), 4.49- 4.52 (3H, m, 4'-H, 5'-H2), 4.54 (IH, br.s. 3'-H), 4.63 (IH, t, J = 4.84 Hz, 2'-H), 6.28 (IH, d, J = 4.72 Hz, l'-H) 8.51(1 H, s, Ar-H), 8.63(1 H, s, Ar-H); m/z (ESI) 404(MH+, 100%). Example 6 - Characterization of Inhibition by Glycylsulfamoyladenosine
The characterization of the compound as an inhibitor of the catalytic activity of GRS was performed using a procedure similar to that described in Example 2E above, except that multiple assays were performed in the presence of inhibitor concentrations ranging (in two-fold dilution steps) from 100 mM down to 0.1 mM (final concentrations). These were added from stocks prepared at 10-fold higher concentrations and added to each reaction mix. The stock of inhibitor was prepared freshly from a solid sample and dissolved in dimethylsulfoxide. The enzyme concentration used for these assays was selected so that around 50% of the tRNA available was acylated during the reaction time course. Following harvesting and counting as described above, the acylation activity (relative to controls in the absence of inhibitor) were plotted as a function of inhibitor concentration and fitted to a four-parameter logistic function (using the Grafit package; Erithacus Software Ltd.) to yield IC50, the inhibitor concentration required to inhibit half the enzyme activity.
Example 7 - Human Glycyl tRNA Synthetase
A model of the human glycyl tRNA synthetase was constructed using Quanta version 4.1 [Molecular Simulations Inc, Burlington, MA]. The human enzyme contains a number of large surface loops (see Fig. 6). A comparison of the human and Staph enzyme aminoacylation sites is shown in Figure 7. One of the most significant differences is that a glutamine in the prokaryotic enzyme is replaced by a methionine. The glutamine is believed to be capable of hydrogen bonding to the acyl phosphage moiety of glycyl adenylate.
This invention is not to be limited in scope by the specific embodiments described herein. Indeed, various modifications of the invention in addition to those described herein will become apparent to those skilled in the art from the foregoing description. Such modifications are intended to fall within the scope of the appended claims. The disclosures of the patents, patent applications and publications cited herein are incorporated by reference in their entireties.

Claims

WHAT IS CLAIMED IS:
1. A composition comprising a Staphylococcus glycyl tRNA synthetase in crystalline form.
2. The composition according to claim 1 wherein said synthetase is a dimer.
3. The composition according to claim 1 wherein said synthetase has an active site cavity formed by the amino acids Glul74, Arg206, Glu208, Phe216, Arg217, Thr218, Phe221 , Gln223, Glul225, Asp279, Glu290, Leu291, Arg297, Glu330, Ser332 and Arg337.
4. The composition of claim 1 wherein said synthetase is a Staphylococcus aureus synthetase.
5. The composition of claim 3 wherein said synthetase is characterized by the coordinates selected from the group consisting of the coordinates of Figure 1 and Tables I, II, and III.
6. A Staphylococcus aureus glycyl tRNA synthetase crystal.
7. A heavy atom derivative of a Staphylococcus aureus glycyl tRNA synthetase crystal.
8. An isolated, properly folded synthetase molecule or fragment thereof having a conformation comprising the protein coordinates of Figure 1 and Tables I, II, and III.
9. The molecule according to claim 8 wherein said molecule is a dimer, wherein each monomer is characterized by an N-terminal domain having three a-helices and three b-strands, an active site domain, and a C-terminal domain containing a 5-stranded mixed b-sheet with three flanking helices, as illustrated in Fig. 4.
10. The molecule according to claim 8 wherein said molecule is a dimer characterized by the dimer interface of Fig. 5.
1 1. The molecule according to claim 10 which is a Staphylococcus glycyl tRNA synthetase.
12. The molecule according to claim 1 1 which is Staphylococcus aureus synthetase.
13. A peptide, peptidomimetic or synthetic molecule which interacts competitively or non-competitively with the active site of a synthetase of claim 1.
14. A method of identifying an inhibitor compound capable of binding to, and inhibiting the enzymatic activity of, a Staphylococcus glycyl tRNA synthetase, said method comprising: introducing into a suitable computer program information defining an active site conformation of a Staphylococcus glycyl tRNA synthetase molecule comprising a conformation defined by the coordinates of Figure 1 and Tables I, II, and III, wherein said program displays the three-dimensional structure thereof; creating a three dimensional structure of a test compound in said computer program; displaying and superimposing the model of said test compound on the "model of said active site; assessing whether said test compound model fits spatially into the active site; incorporating said test compound in a biological synthetase activity assay for a synthetase characterized by said active site; and determining whether said test compound inhibits enzymatic activity in said assay.
15. The method according to claim 13 wherein said synthetase molecule is a dimer, wherein each monomer is characterized by an N-terminal domain having three a- helices and three b-strands, an active site domain, and a C-terminal domain containing a 5- stranded mixed b-sheet with three flanking helices, as illustrated in Fig. 4.
16. A method of identifying an inhibitor compound capable of binding to, and inhibiting the enzymatic activity of, a Staphylococcus glycyl tRNA synthetase, said method comprising: introducing into a suitable computer program information defining an active site conformation of a glycyl tRNA synthetase molecule comprising a conformation defined by the coordinates of Figure 1 and Tables I, II, and III, wherein said program displays the three-dimensional structure thereof; creating a three dimensional structure of a test compound in said computer program; displaying and superimposing the model of said test compound on the model of said active site; assessing whether said test compound model fits spatially into the active site; incorporating said test compound in a biological synthetase activity assay for a synthetase characterized by said active site; and determining whether said test compound inhibits enzymatic activity in said assay.
17. The method according to claim 16 wherein said synthetase molecule is a dimer, wherein each monomer is characterized by an N-terminal domain having three a- helices and three b-strands, an active site domain, and a C-terminal domain containing a 5- stranded mixed b-sheet with three flanking helices, as illustrated in Fig. 4.
18. A peptide, peptidomimetic or synthetic molecule identified by the method of claim 13 or 15.
19. The molecule according to claim 17, which is glycylsulfamoyladenosine.
20. A method for solving a crystal form comprising using the structural coordinates of a Staphylococcus glycyl tRNA synthetase crystal or portions thereof, to solve a crystal form of a mutant, homologue or co-complex of said synthetase by molecular rearrangement.
21. A method of drug design comprising the step of using the structural coordinates of a Staphylococcus glycyl tRNA synthetase crystal to computationally evaluate a chemical entity for associating with the active site of a Staphylococcus glycyl tRNA synthetase.
22. The method according to claim 21, wherein said entity is a competitive or non-competitive inhibitor of a Staphylococcus aureus synthetase.
23. The method of drug design according to claim 21 comprising the step of using the structure coordinates of Staphylococcus aureus glycyl tRNA synthetase to identify an intermediate in a chemical reaction between said synthetase and a compound with is a substrate or inhibitor of said synthetase.
24. The method according to claim 21 wherein said structure coordinates comprise the coordinates of Figure 1 and Tables I, II, and III.
25. The method according to claim 22 wherein said structure coordinates comprise the coordinates of Figure 1 and Tables I, II, and III.
26 The method according to claim 23 wherein said structure coordinates comprise the coordinates of Figure 1 and Tables I, II, and III.
27. A composition comprising a human glycyl tRNA synthetase in crystalline form, as illustrated in Figures 6 and 7.
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Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1997026340A1 (en) * 1996-01-19 1997-07-24 Smithkline Beecham Plc STAPHYLOCOCCUS AUREUS GLYCYL-tRNA SYNTHETASE
US6037117A (en) * 1997-01-31 2000-03-14 Smithkline Beecham Corporation Methods using the Staphylococcus aureus glycyl tRNA synthetase crystalline structure

Patent Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1997026340A1 (en) * 1996-01-19 1997-07-24 Smithkline Beecham Plc STAPHYLOCOCCUS AUREUS GLYCYL-tRNA SYNTHETASE
US6037117A (en) * 1997-01-31 2000-03-14 Smithkline Beecham Corporation Methods using the Staphylococcus aureus glycyl tRNA synthetase crystalline structure

Non-Patent Citations (1)

* Cited by examiner, † Cited by third party
Title
NIYOMPORN ET AL.: "Biosynthesis of the peptidoglycan of bacterial cell walls. IX. Purification and properties of glycyl ribonucleic acid synthetase from Staphylococcus aureus", JOURNAL OF BIOLOGICAL CHEMISTRY,, vol. 243, no. 4, 1968, pages 773 - 778, XP000900608 *

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