# Patent

## Title
Compositions and methods for the identification of inhibitors of protein synthesis

## Abstract

Compositions and methods for identifying inhibitors of RNA-target molecule interactions are provided as well as identifying inhibitors that block the role of tRNA in protein synthesis. The methods involve forming a mixture comprising a tRNA fragment molecule containing a modified nucleotide, a target molecule capable of binding to the tRNA fragment, and a test compound. The mixture is incubated under conditions that allow binding of the tRNA and the target molecule in the absence of the test compound. Assays can then be performed that detect whether or not the test compound inhibits the binding of the tRNA molecule and the target molecule. High throughput assays are also provided.

## Background
CROSS-REFERENCE TO RELATED APPLICATONS
This application is a divisional application of U.S. patent applicaton Ser. No. 11/943,924 filed on Nov. 21, 2007 and subsequently issued as U.S. Pat. No. 7,598,040 on Oct. 6, 2009, which further claims the priority of U.S. Provisional Application No. 60/866,988, filed Nov. 22, 2006 and U.S. Provisional Application No. 60/867,263, filed Nov. 27, 2006, all of which are incorporated herein by reference in their respective entireties.


FIELD
The invention generally relates to compositions and methods of identification of inhibitors of protein synthesis.
BACKGROUND
The significant progress in the understanding of the molecular basis of human disease in the last few decades has led to a significant increase in the number of potential therapeutic targets. Over the years many drugs have been developed that target various biological processes such as enzymatic reactions and signal receptors. Among these, protein synthesis inhibitors represent a large potential class of molecular targets with importance that spans across many therapeutic areas, such as antibiotics, antivirals, and anticancer treatments.
One class of under utilized therapeutic targets is the ribonucleic acids (RNAs) involved in bacterial protein synthesis. More specifically, the protein synthesis processes that use post-transcriptional modified RNA nucleotides as substrates may be ideal therapeutic targets. Post-transcriptional nucleotide modifications can be as simple as the addition of a methyl group to a standard nucleotide or complex multi-step addition of amino acid like side chains (Soli, D. and RajBhandary, U. L., tRNA: Structure, Biosynthesis, and Function, ASM Press 1995; Grosjean, H. and Benne, R., Modification and Editing of RNA., Washington, D.C., ASM Press, 1998). While 1 to 2% of all RNA bases are modified, the nucleotides in the active sites of the ribosome and the transfer RNA (tRNA) that interact with the ribosome are modified at 10-fold the rate of modification outside these active sites. One of the functions of these modifications is to enhance the selectivity and specificity of the RNA:enzyme interactions that occur during transcription and translation. One such class of enzymes that utilize tRNA containing modified nucleotide bases is the amino acyl tRNA synthetases (AaRS) which catalyze the attachment of a specific amino acid to its corresponding tRNA. The specificity of the AaRS to their respective amino acid can be influenced by many features of the tRNA molecule including the modified nucleotide bases. In the case of the Lysine tRNA synthetase (LysRS), the anticodon stem loop (ASL) of the tRNA contains 2 or 3 modified nucleotide bases depending upon the organism.
There is a need for the identification of inhibitors of protein synthesis from RNA molecules having modified nucleotide bases. To this end, there also remains a need for the development of methods for the identification of such inhibitors. Such inhibitors may be useful for the development of, for example, antimicrobial compounds for use in therapeutic applications.
SUMMARY
Compositions and methods are provided for the identification of inhibitors of protein synthesis. In one aspect, methods of identifying an inhibitor of tRNA-target molecule binding, comprise the steps of (1) forming a mixture of a first nucleic acid molecule comprising a tRNA TΨC-loop fragment, a target molecule capable of binding to the tRNA TΨC-loop fragment, and a test compound, where the tRNA TΨC-loop fragment contains at least one modified nucleotide; (2) incubating the mixture under conditions that allow binding of the tRNA TΨC-loop fragment and the target molecule in the absence of the test compound; and (3) detecting whether or not the test compound inhibits the binding of the tRNA TΨC-loop fragment and the target molecule, wherein the absence of binding of the tRNA fragment and the target molecule is indicative of the test compound being an inhibitor of tRNA-target molecule binding.
In another aspect, methods of identifying an inhibitor of tRNA-target molecule interaction, comprise the steps of (1) forming a mixture comprising a first nucleic acid molecule comprising a tRNA D-loop fragment, a target molecule capable of binding to the tRNA D-loop fragment, and a test compound, where the tRNA D-loop fragment contains at least one modified nucleotide; (2) incubating the mixture under conditions that allow binding of the tRNA D-loop fragment and the target molecule in the absence of the test compound; and (3) detecting whether or not the test compound inhibits the binding of the tRNA D-loop fragment and the target molecule, where the absence of binding of the tRNA fragment and the target molecule is indicative of the test compound being an inhibitor of tRNA-target molecule interaction.
In a further aspect, methods of diagnosing whether a subject has a bacterial infection, comprise the steps of (1) forming a mixture comprising a first nucleic acid molecule derived from a fragment of a tRNA molecule comprising at least one modified nucleotide and a biological sample from a subject, where the fragment tRNA molecule corresponds to a TΨC-loop, a D-loop, or an anticodon stem loop structure; (2) incubating the mixture under conditions that allow binding of the first nucleic acid molecule and a target molecule indicative of the presence of a bacteria in the absence of the test compound; and (3) detecting whether the first nucleic acid molecule binds to the target molecule, where the binding of the first nucleic acid molecule and the target molecule is indicative of the positive diagnosis of a bacterial infection in the biological sample.
In another aspect, microarrays are provided comprising a plurality of nucleic acid molecules having at least one modified nucleotide and a solid support to which the plurality of nucleic acid molecules are attached.
In another aspect, isolated nucleic acid molecules are provided comprising a nucleic acid fragment derived from a tRNA D-loop having at least one modified nucleotide. In still another aspect, isolated nucleic acid molecules are provided comprising a nucleic acid fragment derived from a tRNA TΨC-loop having at least one modified nucleotide.
In a further aspect, methods of identifying a target molecule that binds to a RNA molecule are provided comprising the steps of (1) forming a mixture comprising a biological sample and at least one nucleic acid molecule derived from or corresponding to a tRNA loop having at least one modified nucleotide, where the tRNA loop is selected from the group consisting of a TΨC-loop, a D-loop, and an anticodon loop; (2) incubating the mixture under conditions that allow binding of a target molecule in the biological sample to the first nucleic acid molecule; and (3) detecting whether a target molecule binds to the first nucleic acid molecule.



BRIEF DESCRIPTION OF THE DRAWINGS
FIGS. 1 A-D provide an amino acid sequence alignment of the LysRS sequences from food and water borne bacteria species included on the Category B pathogen list compared to human sequence. The LysRS sequence is highly conserved across 3 of the 7 species and has very little homology with the human sequence.
FIG. 2 provides the sequences of RNA oligomers containing various modified nucleotides used in binding experiments using a peptide mimic of phenylalanine synthetase, as well as the results of binding experiments using the phenylalanine synthetase peptide mimic.
FIG. 3 provides representative sequences for tRNA fragments containing various modified nucleotide bases. Motif 1 represents one embodiment of a tRNA anticodon-stem loop structure containing modified nucleotides. Motif 2 represents one embodiment of a tRNA TΨC loop fragment containing modified nucleotides. Motif 3 represents one embodiment of a tRNA D-loop fragment containing modified nucleotides. Motif 4 represents one embodiment of a linear tRNA-anticodon fragment containing modified nucleotides.
FIG. 4 provides, in one aspect, a schematic of a process for developing an array having nucleic acid molecules containing modified nucleotides and interrogating the array with target molecules.



DETAILED DESCRIPTION
The present disclosure relates to compositions and methods for the identification of compounds useful for inhibiting protein synthesis. The compositions and methods are useful for the identification of inhibitors of the interactions of RNA having one or more modified nucleotide bases with a target molecule. Thus, the disclosure generally relates to compositions and methods for the identification of inhibitors of RNA-target molecule interactions.
Prior to describing this invention in further detail, however, the following terms will first be defined.
DEFINITIONS
As used herein, an “inhibitor” refers to any compound capable of preventing, reducing, or restricting the interaction or binding of a nucleic acid molecule having at least one modified nucleotide base to a target molecule. An inhibitor may inhibit such interaction or binding, for example, by preventing, reducing or restricting binding of nucleic acid molecule to the binding site of a target molecule. In some embodiments, the inhibition is at least 20% (e.g., at least 50%, 70%, 80%, 90%, 95%, 98%, 99%, 99.5%) of the binding as compared to the binding in the absence of the inhibitor. In one aspect, an inhibitor prevents, reduces, or restricts the binding of a transfer RNA (tRNA), or fragment thereof, to a target molecule. Assays for analyzing inhibition are described herein.
As used herein, a “label” or “detectable label” is any composition that is detectable, either directly or indirectly for example, by spectroscopic, photochemical, biochemical, immunochemical, or chemical means). Useful labels include, but are not limited to, radioactive isotopes (for example, 32P, 35S, and 3H), dyes, fluorescent dyes (for example, Cy5 and Cy3), fluorophores (for example, fluorescein), electron-dense reagents, enzymes and their substrates (for example, as commonly used in enzyme-linked immunoassays, such as, alkaline phosphatase and horse radish peroxidase), biotin-streptavidin, digoxigenin, or hapten; and proteins for which antisera or monoclonal antibodies are available. Moreover, a label or detectable moiety can include an “affinity tag” that, when coupled with the target molecule and incubated with a test compound or compound library, allows for the affinity capture of the target molecule along with molecules bound to the target molecule. One skilled in the art will appreciate that an affinity tag bound to the target molecule has, by definition, a complimentary ligand coupled to a solid support that allows for its capture. For example, useful affinity tags and complimentary partners include, but are not limited to, biotin-streptavidin, complimentary nucleic acid fragments (for example, oligo dT-oligo dA, oligo T-oligo A, oligo dG-oligo dC, oligo G-oligo C), aptamers, or haptens and proteins for which antisera or monoclonal antibodies are available. The label or detectable moiety is typically bound, either covalently, through a linker or chemical bound, or through ionic, van der Waals or hydrogen bonds to the molecule to be detected.
As used herein, a “modified nucleotide” refers to any modification of a nucleotide base. Modified nucleotide bases include, but are not limited to, but not limited to, unknown modified adenosine (?A); 1-methyladenosine (m1A); 2-methyladenosine (m2A); N6-isopentenyladenosine (i6A); 2-methylthio-N6-isopentenyladenosine (ms2i6A); N6-methyladenosine (m6A); N6-threonylcarbamoyladenosine (t6A); N6-methyl-N6-threonylcarbomoyladenosine (m6t6A); 2-methylthio-N6-threonylcarbamoyladenosine (ms2t6A); 2′-O-methyladenosine (Am); I Inosine (I); 1-methylinosine Ar(m1I); 2′-O-(5-phospho)ribosyladenosine (Ar(p)); N6-(cis-hydroxyisopentenyl)adenosine (io6A); Unknown modified cytidine (?C); 2-thiocytidine (s2C); 2′-O-methylcytidine (Cm); N4-acetylcytidine (ac4C); 5-methylcytidine (m5C); 3-methylcytidine (m3C); lysidine (k2C); 5-formylcytidin (f5C); 2′-O-methyl-5-formylcytidin (f5 Cm); unknown modified guanosine (?G); 2′-O-(5-phospho)ribosylguanosine (Gr(p)); 1-methylguanosine (m1G); N2-methylguanosine (m2G); 2′-O-methylguanosine (Gm); N2N2-dimethylguanosine (m22G); N2,N2,2′-O-trimethylguanosine (m22Gm); 7-methylguanosine (m7G); archaeosine (fa7d7G); queuosine (Q); mannosyl-queuosine (manQ); galactosyl-queuosine (galQ); wybutosine (yW); peroxywybutosine (o2yW); unknown modified uridine (?U); 5-methylaminomethyluridine (mnm5U); 2-thiouridine (s2U); 2′-O-methyluridine (Um); 4-thiouridine (s4U); 5-carbamoylmethyluridine (ncm5U); 5-methoxycarbonylmethyluridine (mcm5U); 5-methylaminomethyl-2-thiouridine (mnm5s2U); 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U); uridine 5-oxyacetic acid (cmo5U); 5-methoxyuridine (mo5U); 5-carboxymethylaminomethyluridine (cmnm5U); 5-carboxymethylaminomethyl-2-thiouridine (cmnm5s2U); 3-(3-amino-3-carboxypropyl)uridine (acp3U); 5-(carboxyhydroxymethyl)uridinemethyl ester (mchm5U); 5-carboxymethylaminomethyl-2′-O-methyluridine (cmnm5Um); 5-carbamoylmethyl-2′-O-methyluridine (ncm5Um); Dihydrouridine (D); pseudouridine (Ψ); 1-methylpseudouridine (m1Ψ); 2′-O-methylpseudouridine (Ψm); ribosylthymine (m5U); 5-methyl-2-thiouridine (m5s2U); and 5,2′-O-dimethyluridine (m5Um).
As used herein, a “target molecule” refers to any biological molecule of interest or molecule that is capable of binding to a nucleic acid molecule having at least one modified nucleotide under physiological conditions. The biological molecule of interest can be any class of biological molecule, including, but not limited to, ligands, receptors, peptides, proteins, enzymes, polypeptides, nucleic acids (oligonucleotide or polynucleotide of RNA or DNA), antibodies, epitopes, hormones, oligosaccharides, or any other biological molecules. In one aspect, target protein molecules include proteins involved in protein synthesis, including proteins involved in RNA maturation and proteins involved in translation. Particular target molecules include any molecule involved in protein synthesis, such as, for example, aminoacyl tRNA synthetases, methyl transferases, pseudouridine synthases, ribosomes, retroviral reverse transcriptases, messenger RNAs, tRNA, viral RNA or fragments thereof. For example, if transcripts of genes are the interest of an experiment, the target molecules would include mRNA. Other examples include protein fragments, small molecules, etc. “Target nucleic acid” refers to a nucleic acid (often derived from a biological sample) of interest that is capable of binding, or otherwise interacting with, an RNA molecule. Target nucleic acid molecules include RNA and DNA molecules involved in binding to tRNA loop sequences having at least one modified nucleotide. A target molecule may be detected using one or more nucleic acid molecules having at least one modified nucleotide.
Methods are provided for identifying inhibitors of RNA binding to a target molecule. The methods generally involve forming a mixture of a RNA molecule having at least one modified nucleotide, a target molecule capable of binding to the RNA molecule and a test compound, and incubating the mixture under conditions that allow the binding of the RNA molecule and the target molecule in the absence of the test molecule.
The nucleic acid molecules may be derived from any ribonucleic acid, such as messenger RNA (mRNA), transfer RNA (tRNA), mitochondrial RNA (mtRNA), ribosomal RNA (rRNA), and nuclear RNA (nRNA). In another aspect, the ribonucleic acid molecules may comprise fragments of any such ribonucleic acids. For example, tRNA generally contains four stem loop structures: the TΨC-loop, the D-loop, a variable loop and the anticodon stem-loop. In addition to the four stem loop structures, the tRNA contains an acceptor arm for attachment of a particular amino acid for incorporation into a peptide chain. The nucleic acid molecule for use in the methods disclosed herein may comprise any one of the loop structures of a tRNA. For example, a tRNA TΨC-loop fragment refers to a nucleic acid sequence derived from, or corresponding to, the TΨC-loop sequence of a tRNA and includes at least part of the antiparallel stem structure of the loop. In addition, the RNA molecule may consist essentially of one of the loop structures and include additional nucleic acid sequences not derived from, or not corresponding to, the same native RNA molecule and may include detectable labels for use in the methods. The RNA molecule may also consist essentially of one of the loop structures in addition to one additional loop structure derived from, or corresponding to, the same native RNA molecule, and may contain additional nucleotides or labels. For example, the ribonucleic acid sequence may comprise an anticodon stem-loop sequence, a TΨC-loop sequence, or a D-loop sequence. A ribonucleic acid molecule may also comprise a TΨC-loop sequence in combination with an anticodon stem loop sequence. In addition, the molecule may further comprise the acceptor arm of the tRNA molecule.
The nucleic acid molecules may contain any number of modified or unmodified nucleotides. In one aspect, the ribonucleic acid molecules incorporate one, two, three, or more modified nucleotides into the nucleic acid sequence. Where two or more modified nucleotides are incorporated into a nucleic acid molecule, the modified nucleotides may be the same or may be different modified nucleotides. In another aspect, the nucleic acid molecules incorporate three or more modified nucleotides into the nucleic acid molecule.
The nucleic acid molecules containing the modified nucleotides may be linear or may form secondary or tertiary structures, such as loop structures, bulges, pseudoknots, or turns. Nucleic acid molecules may form secondary or tertiary structures for any reason, such as, for example, stem-loop structures by the inclusion of complementary nucleotides at the 5′ and 3′ terminal ends of the molecule. Nucleic acid molecules having secondary or tertiary structures may be employed in the methods discloses herein depending on the target molecule to which the nucleic acid molecule interacts.
The ribonucleic acid molecules may have any number of nucleotides, such as, for example, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, 50, 100, or more nucleotides. In one aspect, the ribonucleic acid molecule is derived from a nucleic acid sequence of a tRNA. Where the nucleic acid molecule is derived from a tRNA, the tRNA may contain modified nucleotides within the sequence corresponding to one or more of the loop structures, such as the TΨC-loop, the D-loop, or the anticodon stem loop (ASL). In one aspect, the modifications may correspond to positions 34, 37, and 39 in the anticodon stem loop of a tRNA. In another aspect, the modified nucleotides may correspond to positions 53, 54, and 57 in the TΨC-loop of a tRNA. In a further aspect, the modifications may correspond to positions 16 and 19 in the D-loop of a tRNA. In another aspect, the modifications may correspond to combinations of any of these positions in the anticodon stem loop, the TΨC-loop, or the D-loop. The position numbers used herein refer to the nucleotide position numbering of the conventional tRNA numbering as disclosed in Sprinzl, et al. Nucl. Acids. Res., 26, 148-153 (1998).
A tRNA fragment may comprise a nucleic acid molecule derived from or corresponding to an anticodon stem loop (ASL) of a tRNA molecule. In one aspect, a tRNA fragment derived from or corresponding to an ASL comprises the nucleic acid sequence: 5′-a′b′c′d′e′NUXNNYNe′′(or Z)d′′c′′b′′a′′; where X, Y, and Z refer to modified nucleotides, a′, b′, c′, d′, e′, a′′, b′′, c′′, d′′, and e′′ refer to any nucleotide and a′, b′, c′, d′, and e′ are complementary to a′′, b′′, c′′, d′′, and e′′, respectively, and N refers to any nucleotide. In one aspect, X refers to mnm5s2U, s2U, mnm5U, and mcm5s2U; Y refers to t6A, m2A, and ms2t6A, and Z refers to Ψ.
In another aspect, the tRNA fragment comprises a nucleic acid molecule derived from or corresponding to the TΨC-loop of a tRNA molecule. In one aspect, a tRNA fragment derived from or corresponding to TΨC-loop comprises the nucleic acid sequence 5′-h′i′j′k′l′(ribothymidine)(Psi)CN(m1A)NNl′′k′′j′′i′′h′′, where h′, i′, j′, k′, l′, h′′, i′′, j′′, k′′, and l′′ refer to any nucleotide and h′, i′, j′, k′, and l′ are complementary to h′′, i′′, j′′, k′′, and l′′, respectively, and N refers to any nucleotide.
In another aspect, the tRNA fragment may comprise a nucleic acid molecule derived from or corresponding to the D-loop of a tRNA molecule. In one aspect, a tRNA fragment derived from or corresponding to a D-loop comprises the nucleic acid sequence 5′-m′n′o′p′NN(dihydrouridine)NN(dihydrouridine)NNp′′o′′n′′m′′, where m′, n′, o′, p′, m′′, n′′, o′′, and p′′ are any nucleotide and m′, n′, o′, and p′ are complementary to m′′, n′′, o′′, and p′′, respectively, and N refers to any nucleotide.
In another aspect, the tRNA fragment comprises a nucleic acid molecule derived from or corresponding to the ASL of a tRNA molecule. In one aspect, a tRNA fragment derived from or corresponding to the ASL comprises the nucleic acid sequence 5′-N1N2N3N14(mcm5s2U)N6N17(ms2t6A)N19(pseudouridine)N11N12, where N1, N2, N3, N4, N6, N7, N9, N11, and N12 refer to any nucleotide. Such ASL fragments may be linear fragments.
The tRNA fragments (or “probe tRNA fragments”) for use in the methods of the present disclosure can be a fragment derived from any tRNA. The tRNA fragment may be obtained or derived from or corresponds to a tRNAAla, tRNAArg, tRNAAsn, tRNAAsp, tRNACys, tRNAGln, tRNAGlu, tRNAGly, tRNAHis, tRNAIle, tRNALeu, tRNALys, tRNAMet, tRNAPhe, tRNAPro, tRNASer, tRNAThr, tRNATrp, tRNATyr, or tRNAVal. In one aspect, the tRNA fragment corresponds to tRNALys. In another aspect, the tRNA fragment is derived from or corresponds to the tRNALys anticodon stem loop (ASL). In another aspect, the tRNA fragment corresponds to a fragment consisting of nucleotides 32-43 of a bacterial tRNALys. In a further aspect, the tRNA fragment corresponds to a fragment consisting of nucleotides 32-43 of the human tRNALys. The position numbers used herein refer to the nucleotide position numbering of the conventional tRNA numbering as disclosed in Sprinzl, et al. Nucl. Acids. Res., 26, 148-153 (1998). In one aspect, the tRNA fragment is a fragment from a host cell tRNA, such as a mammalian host cell, including, but not limited to, human, feline, and simian host cells.
The tRNA fragment may correspond to any portion of the tRNA involved in interacting, directly or indirectly, to the target molecule. In one aspect, the tRNA fragment corresponds to the TΨC-loop, the D-loop or the anticodon stem loop (ASL) of the tRNA, or combinations thereof.
The tRNA fragment may correspond to any portion of the host cell's tRNA involved in nucleotide binding, such as the portion of the tRNA involved in the reverse transcription (RT) complex formation. For example, the tRNA may be involved in binding to a retroviral genome to initiate, prime, or facilitate reverse transcription of the retroviral genome. In one aspect, the fragment tRNA corresponds to a fragment of the anticodon stem loop of any tRNA. In one aspect, the fragment corresponds to a fragment from the anticodon stem loop of tRNA-Lys. In another aspect, the tRNA fragment corresponds to a fragment from the anticodon stem loop of human tRNA-Lys. In another aspect, the tRNA fragment corresponds to a fragment from nucleotides 32-43 of human tRNA-Lys3.
In another aspect, the tRNA fragments correspond to a portion of a bacterial host cell tRNA involved in protein synthesis in the bacterial host cell. For example, the tRNA fragment may be derived from a TΨC-loop, the D-loop or ASL from a bacterial tRNA that binds to bacterial molecules involved in protein synthesis. Bacterial molecules involved in protein synthesis include, but are not limited to aminoacyl tRNA synthetases, methyl transferases, pseudouridine synthases, tRNA sulfurtransferase, tRNA thiolase (ThiI), tRNA-guanine transglycosylase, ribosomal RNA (e.g. 5S ribosomal RNA), and transfer RNA. Each of the TΨC-loop, the D-loop or ASL may be involved in the binding of such molecules and may be important or required for protein synthesis in a bacterial host. In one aspect, test compounds that inhibit the binding of the bacterial tRNA to molecules involved in protein synthesis do not inhibit the binding a mammalian tRNAs to molecules involved in mammalian protein synthesis.
The tRNA fragment may also be any length of a fragment from a tRNA. In one aspect, the tRNA fragment comprises a fragment of between 5 to 25 continuous nucleotides of a tRNA, 7 to 20 continuous nucleotides of a tRNA, or between 10 to 20 continuous nucleotides of a tRNA. In another aspect, the fragment is a fragment of 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18 continuous nucleotides of a tRNA. In a further aspect, the fragment is a fragment of 12 continuous nucleotides of a tRNA ASL.
In some aspects, the tRNA ASL fragment may or may not be capable of forming a secondary structure. In a one aspect, the tRNA ASL fragment is not capable of forming a stem loop structure with itself. In another aspect, the fragment is a linear fragment of a tRNA that is not capable of forming a stem loop structure with itself.
The tRNA fragment may also be linked to additional nucleic acids. For example, a tRNA fragment may be linked to one or more additional nucleic acids depending on the assay method. In one aspect, the tRNA fragment may be linked to nucleotides used to attach the fragment to a solid support surface. In another aspect, the fragment tRNA is linked to additional nucleic acid molecules at one or both terminal ends of the tRNA fragment. In another aspect, the fragment tRNA is linked to additional nucleic acid molecules at both terminal ends. The additional nucleic acid sequences can be any length, preferably between 8 and 16 nucleotides, between 10 and 14 nucleotides, more preferably 12 nucleotides in length. In one aspect, the terminal sequences do not allow the tRNA fragment to form a secondary structure, such as a loop structure.
A variety of methods are known in the art for making nucleic acids having a particular sequence or that contain particular nucleic acid bases, sugars, internucleotide linkages, chemical moieties, and other compositions and characteristics. Any one or any combination of these methods can be used to make a nucleic acid, polynucleotide, or oligonucleotide for the present invention. Said methods include, but are not limited to: (1) chemical synthesis (usually, but not always, using a nucleic acid synthesizer instrument); (2) post-synthesis chemical modification or derivatization; (3) cloning of a naturally occurring or synthetic nucleic acid in a nucleic acid cloning vector (e.g., see Sambrook, et al., Molecular Cloning: A Laboratory Approach 2nd ed., Cold Spring Harbor Laboratory Press, 1989) such as, but not limited to a plasmid, bacteriophage (e.g., m13 or lamda), phagemid, cosmid, fosmid, YAC, or BAC cloning vector, including vectors for producing single-stranded DNA; (4) primer extension using an enzyme with DNA template-dependent DNA polymerase activity, such as, but not limited to, Klenow, T4, T7, rBst, Taq, Tfl, or Tth DNA polymerases, including mutated, truncated (e.g., exo-minus), or chemically-modified forms of such enzymes; (5) PCR (e.g., see Dieffenbach, C. W., and Dveksler, eds., PCR Primer: A Laboratory Manual, 1995, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.); (6) reverse transcription (including both isothermal synthesis and RT-PCR) using an enzyme with reverse transcriptase activity, such as, but not limited to, reverse transcriptases derived from avian myeloblasosis virus (AMV), Maloney murine leukemia virus (MMLV), Bacillus stearothermophilus (rBst), Thermus thermophilus (Tth); (7) in vitro transcription using an enzyme with RNA polymerase activity, such as, but not limited to, SP6, T3, or T7 RNA polymerase, Tth RNA polymerase, E. coli RNA polymerase, or another enzyme; (8) use of restriction enzymes and/or modifying enzymes, including, but not limited to exo- or endonucleases, kinases, ligases, phosphatases, methylases, glycosylases, terminal transferases, including kits containing such modifying enzymes and other reagents for making particular modifications in nucleic acids; (9) use of polynucleotide phosphorylases to make new randomized nucleic acids; (10) other compositions, such as, but not limited to, a ribozyme ligase to join RNA molecules; and/or (11) any combination of any of the above or other techniques known in the art. Oligonucleotides and polynucleotides, including chimeric (i.e., composite) molecules and oligonucleotides with non-naturally-occurring bases, sugars, and internucleotide linkages are commercially available (e.g., see the 2000 Product and Service Catalog, TriLink Biotechnologies, San Diego, Calif., USA)
The RNA molecule or the target molecule, or both the RNA molecule and the target molecule may be labeled to facilitate detection. In one aspect, the RNA molecule is labeled with a fluorophore to facilitate detection. In another aspect, the target molecule is labeled with biotin to facilitate detection. In yet another aspect, the RNA molecule is labeled with a fluorophore and the target molecule is labeled with biotin.
In another aspect, the ribonucleic acid molecules having one or more modified nucleic acids may be immobilized on a substrate to create an array. An “array” may comprise a solid support with nucleic acid probes attached to the support. Arrays may comprise a plurality of different nucleic acids that are coupled to a surface of a substrate in different, known locations. These arrays, also described as “microarrays” or colloquially “chips” have been generally described in the art, for example, in Fodor et al., Science, 251:767-777 (1991). Methods of forming high density arrays of oligonucleotides, peptides and other polymer sequences with a minimal number of synthetic steps are disclosed in, for example, U.S. Pat. Nos. 5,143,854, 5,252,743, 5,384,261, 5,405,783, 5,424,186, 5,429,807, 5,445,943, 5,510,270, 5,677,195, 5,571,639, and 6,040,138. The oligonucleotide analogue array can be synthesized on a solid substrate by a variety of methods, including, but not limited to, light-directed chemical coupling, and mechanically directed coupling. See Pirrung et al., U.S. Pat. No. 5,143,854 (see also PCT Application No. WO 90/15070) and Fodor et al., PCT Publication Nos. WO 92/10092 and WO 93/09668, U.S. Pat. Nos. 5,677,195, 5,800,992 and 6,156,501 which disclose methods of forming vast arrays of peptides, oligonucleotides and other molecules using, for example, light-directed synthesis techniques. See also, Fodor et al., Science, 251, 767-77 (1991). These procedures for synthesis of polymer arrays are now referred to as VLSIPS® procedures. Using the VLSIPS®. approach, one heterogeneous array of polymers is converted, through simultaneous coupling at a number of reaction sites, into a different heterogeneous array. See, U.S. Pat. Nos. 5,384,261 and 5,677,195.
Methods for making and using molecular probe arrays (particularly nucleic acid probe arrays) are also disclosed in, for example, U.S. Pat. Nos. 5,143,854, 5,242,974, 5,252,743, 5,324,633, 5,384,261, 5,405,783, 5,409,810, 5,412,087, 5,424,186, 5,429,807, 5,445,934, 5,451,683, 5,482,867, 5,489,678, 5,491,074, 5,510,270, 5,527,681, 5,527,681, 5,541,061, 5,550,215, 5,554,501, 5,556,752, 5,556,961, 5,571,639, 5,583,211, 5,593,839, 5,599,695, 5,607,832, 5,624,711, 5,677,195, 5,744,101, 5,744,305, 5,753,788, 5,770,456, 5,770,722, 5,831,070, 5,856,101, 5,885,837, 5,889,165, 5,919,523, 5,922,591, 5,925,517, 5,658,734, 6,022,963, 6,150,147, 6,147,205, 6,153,743, 6,140,044 and D430024. In one aspect, the ribonucleic acid molecule is a labeled with a detectable label, such as a fluorescent label. A sample containing a target molecule is contacted with the aay under appropriate conditions. The arrays are washed or otherwise processed to remove non-bound molecules. The reaction is then evaluated by detecting the distribution of the label on the chip. The distribution of label may be detected by scanning the arrays to determine florescence intensities distribution. Methods for signal detection and processing of intensity data are disclosed in, for example, U.S. Pat. Nos. 5,547,839, 5,578,832, 5,631,734, 5,800,992, 5,856,092, 5,936,324, 5,981,956, 6,025,601, 6,090,555, 6,141,096, and 5,902,723. Methods for array based assays, computer software for data analysis and applications are disclosed in, for example, U.S. Pat. Nos. 5,527,670, 5,527,676, 5,545,531, 5,622,829, 5,631,128, 5,639,423, 5,646,039, 5,650,268, 5,654,155, 5,674,742, 5,710,000, 5,733,729, 5,795,716, 5,814,450, 5,821,328, 5,824,477, 5,834,252, 5,834,758, 5,837,832, 5,843,655, 5,856,086, 5,856,104, 5,856,174, 5,858,659, 5,861,242, 5,869,244, 5,871,928, 5,874,219, 5,902,723, 5,925,525, 5,928,905, 5,935,793, 5,945,334, 5,959,098, 5,968,730, 5,968,740, 5,974,164, 5,981,174, 5,981,185, 5,985,651, 6,013,440, 6,013,449, 6,020,135, 6,027,880, 6,027,894, 6,033,850, 6,033,860, 6,037,124, 6,040,138, 6,040,193, 6,043,080, 6,045,996, 6,050,719, 6,066,454, 6,083,697, 6,114,116, 6,114,122, 6,121,048, 6,124,102, 6,130,046, 6,132,580, 6,132,996 and 6,136,269.
The use of high-density arrays allows for the development of high throughput assays for the disclosed methods. Such high throughput (HTS) assays may involve attaching or binding either the ribonucleic acid molecule or the target molecule to a solid support. A “solid support” may be any surface to which molecules may be attached through either covalent or non-covalent bonds. This includes, but is not limited to, membranes, plastics, magnetic beads, charged paper, nylon, Langmuir-Bodgett films, functionalized glass, germanium, silicon, PTFE, polystyrene, gallium arsenide, gold, and silver. Any other material known in the art that is capable of having functional groups such as amino, carboxyl, thiol or hydroxyl incorporated on its surface, is also contemplated. This includes surfaces with any topology, including, but not limited to, spherical surfaces and grooved surfaces. HTS methods generally refer to technologies that permit the rapid assaying of test compounds for therapeutic potential, for example, by inhibiting the binding of a tRNA fragment to a target nucleic acid molecule. HTS techniques may employ robotic handling of test materials, detection of positive signals, and interpretation of data. Test compounds may be identified via the detection of luminescence or absence of luminescence through the use of radioactivity or through optical assays that rely on absorbence, fluorescence or luminescence as read-outs. Gonzalez, J. E. et al., (1998) Curr. Opin. Biotech. 9:624-631.
Such microarrays containing the ribonucleic acid molecules of the present disclosure may be used in combination with any of the methods disclosed herein for the development of high-throughput assays. Nucleic acid molecules for use in developing such microarrays may be identified by first analyzing databases of various genomes and nucleotide modifications to select desired sequences. Modified nucleotides are then prepared using proper protection for automated chemical synthesis. Nucleic acid molecules are synthesized incorporating the modified nucleotides. The nucleic acid molecules are synthesized either attached to a solid support surface or in solution. Oligonucleotides prepared for solution array will have fluorescent labels attached to monitor interaction or binding with target molecules. Target molecules are prepared by appropriate methods. For solid phase arrays, the target molecule will have fluorescent labels attached, while no labeling is needed for solution based assays. The arrays are then interrogated with the target molecule solutions to identify nucleic acid molecules having the highest affinity for the target molecules.
The ribonucleic acid molecules may be used in methods of identifying an inhibitor of nucleic acid-target molecule interactions. The methods can be used to identify any inhibitor of such interactions. In one aspect, the method can be used to identify inhibitors of RNA-target molecule binding. In one aspect, the methods can be used to identify inhibitors of protein synthesis. In another aspect, the methods can be used to identify inhibitors of tRNA binding to a target nucleic acid molecule. In another aspect, the methods can be used to identify inhibitors of tRNA binding to a target aminoacyl RNA synthetase. In a further aspect, the methods can be used to identify inhibitors of tRNA binding to a target ribosome. In another aspect, the methods can be used to identify inhibitors of tRNA modification enzymes. In another aspect, the methods can be used to identify inhibitors of tRNA binding to a target viral reverse transcriptase.
In another aspect, the methods can be readily adapted for use in high-throughput assays using high-density arrays having one or more RNA probe molecules attached. Transfer RNA (tRNA) is capable of interacting with numerous biological molecules such as those involved in protein synthesis, transcription, translation, reverse transcription, and the like. Identifying inhibitors of such interactions may lead to the identification of therapeutic compounds for use in treating diseases or infections in a host cell. In one aspect, the target molecule is essential to protein synthesis. In one aspect, compounds that inhibit the binding of the bacterial tRNA to molecules involved in protein synthesis do not inhibit the binding a mammalian tRNAs to molecules involved in mammalian protein synthesis.
The inhibitors that are identified by the disclosed methods may be useful for treating any infectious disease or condition in a host cell, such as, for example, bacterial diseases, viral diseases, including retroviral diseases, protozoan diseases, and fungal diseases.
Bacterial diseases for which inhibitors can be identified by the methods disclosed herein include any bacterial disease, such as infections caused by, for example, category A, B, or C pathogens. Category A bacteria include, but are not limited to, Bacillus antracis, Clostridium botulinum, Francisella tularensis, and Yersinia pestis. Category B bacteria include, but are not limited to Burkholderia pseudomallei, Burkjolderia mallei, Clostridium perfringens, Coxiella burnetii, Brucella melitensis, Brucella abortus, Brucella canis, Staphylococcus aureus, Rickettsia prowazekii, Chlamydia psittaci, and food and water borne bacteria, such as Escherichia coli O157:H7.
Viral Diseases for which inhibitors can be identified by any of the methods disclosed herein include, for example, retroviruses (including lentivirus) and other viral diseases, such as viral encephalitis.
Retroviruses for which inhibitors can be identified by the methods disclosed herein include any viruses having RNA as their primary genetic material and use reverse transcription to produce DNA. Such viruses include, but are not limited to, Feline Immunodeficiency Virus (FIV), Simian Immunodeficiency Virus (SIV), Avian Leucosis Virus, Feline Leukemia Virus, Walleye Dermal Sarcoma Virus, Human T-Lymphotropic Virus, and Human Immunodeficiency Viruses (HIV). HIV can be any strain, form, subtype or variation in the HIV family.
The target molecules involved in protein synthesis in pathogen cells may bind to any portion of a tRNA molecule, for example the TΨC-loop, the D-loop, and/or the anticodon stem loop. For example, target molecules such as aminoacyl synthetases, methyl transferases and pseudouridine synthases may bind to the pathogen's TΨC-loop, D-loop or ASL or combinations thereof to initiate the particular protein reaction. A partial list of target molecules, their function and related pathogen are provided in Table 1.










TABLE 1





Target





Molecule
Function
Gene Product
Pathogen







Protein
Aminoacyl tRNA
Essential
Bacterial/Fungal



Synthetase


Protein
Methyl transferase
Essential
Bacterial/Fungal


Protein
Pseudouridine
Essential
Bacterial/Fungal



synthase


Protein
tRNA
Essential
Bacterial/Fungal



sulfurtransferase


Protein
tRNA thiolase
Essential
Bacterial/Fungal



(ThiI)


Protein
tRNA-guanine
Essential in
Bacterial/Fungal



transglycosylase
some pathogens


Nucleic Acid
5 S Ribosomal RNA
Essential
Bacterial/Fungal


(RNA)


Nucleic Acid
Transfer RNA
Essential
Bacterial/Fungal


(RNA)


Nucleic Acid
Viral RNA
Non-Essential
Lentiviruses,


(RNA)


HCV









Thus, the disclosure provides a method of identifying an inhibitor of tRNA-target molecule interactions. The method comprises forming a mixture of a nucleic acid molecule comprising a tRNA TΨC-loop fragment having at least one modified nucleotide, a target molecule that is capable of binding to the tRNA TΨC-loop fragment, and a test compound. The resulting mixture is incubated under conditions that allow binding of the tRNA TΨC-loop fragment and the target molecule in the absence of the test compound. The method further involves detecting whether the test compound inhibits the binding of the tRNA TΨC-loop fragment to the target molecule, where the absence of binding of the tRNA TΨC-loop fragment and the target molecule is indicative of the test compound being an inhibitor of tRNA-target molecule interaction. In one aspect, the detection involves the use of labels to detect the inhibition of binding of the tRNA fragment to a target molecule.
The mixture may also contain a second nucleic acid molecule that contains an anticodon stem-loop sequence. The second nucleic acid molecule may also contain one or more modified nucleotides. The second nucleic acid molecule may be linked to the first nucleic acid molecule and may facilitate binding of the TΨC-loop fragment to the target molecule in the absence of the test compound.
The nucleic acid molecule may be attached to a microarray to provide for a high-throughput assay for use in identifying such inhibitors.
In one aspect, a method of identifying an inhibitor of tRNA-target molecule interactions is also provided, where the method comprises forming a mixture of a nucleic acid molecule comprising a tRNA D-loop fragment having at least one modified nucleotide, a target molecule that is capable of binding to the tRNA D-loop fragment, and a test compound. The resulting mixture is incubated under conditions that allow binding of the tRNA D-loop fragment and the target molecule in the absence of the test compound. The method further involves detecting whether the test compound inhibits the binding of the tRNA D-loop fragment to the target molecule, where the absence of binding of the tRNA D-loop fragment and the target molecule is indicative of the test compound being an inhibitor of tRNA-target molecule interaction. In one aspect, the detection involves the use of labels to detect the inhibition of binding of the tRNA fragment to a target molecule.
In one aspect, a method of identifying an inhibitor of binding of a tRNA to a target nucleic acid molecule comprises forming a mixture containing a tRNA ASL fragment, a target nucleic acid molecule that is capable of binding to the tRNA fragment, and a test compound. The resulting mixture is incubated under conditions that allow binding of the tRNA fragment and the target nucleic acid in the absence of the test compound. The method further involves detecting whether the test compound inhibits the binding of the tRNA fragment to the target nucleic acid, where binding of the tRNA ASL fragment and the target nucleic acid molecule is indicative of the test compound being an inhibitor of binding of a tRNA to a target nucleic acid molecule. In one aspect, the detection involves the use of labels to detect the inhibition of binding of the tRNA fragment to the target nucleic acid molecule.
The disclosure also provides a method of identifying an inhibitor of tRNA-target molecule interactions, where the method comprises forming a mixture of a nucleic acid molecule comprising a tRNA D-loop fragment having at least one modified nucleotide, a tRNA ASL fragment, a target molecule that is capable of binding to the tRNA D-loop and/or ASL fragment, and a test compound. The tRNA ASL fragment may also contain one or more modified nucleotides. The resulting mixture is incubated under conditions that allow binding of the tRNA D-loop fragment and/or the ASL fragment and the target molecule in the absence of the test compound. The method further involves detecting whether the test compound inhibits the binding of the tRNA D-loop fragment and/or ASL fragment to the target molecule, where the absence of binding of the tRNA D-loop fragment and/or ASL fragment and the target molecule is indicative of the test compound being an inhibitor of tRNA-target molecule interaction. In one aspect, the detection involves the use of labels to detect the inhibition of binding of the tRNA fragment to a target molecule.
In one aspect, the tRNA D-loop fragment and the ASL fragment may be combined in a single RNA molecule, or may be used as separate nucleic acid molecules in the mixture. Where the D-loop fragment and the ASL fragment are contained in a single RNA molecule, the D-loop and the ASL may be in any arrangement, including the naturally occurring arrangement and a non-naturally occurring arrangement.
In one aspect, a method of identifying an inhibitor of tRNA-target molecule interactions comprises forming a mixture of a nucleic acid molecule comprising a tRNA TΨC-loop fragment having at least one modified nucleotide, a tRNA ASL fragment, a target molecule that is capable of binding to the tRNA TΨC-loop fragment and/or the ASL fragment, and a test compound. The resulting mixture is incubated under conditions that allow binding of the tRNA TΨC-loop fragment and/or the ASL fragment and the target molecule in the absence of the test compound. The method further involves detecting whether the test compound inhibits the binding of the tRNA TΨC-loop fragment and/or ASL fragment to the target molecule, where the absence of binding of the tRNA TΨC-loop fragment and/or ASL fragment and the target molecule is indicative of the test compound being an inhibitor of tRNA-target molecule interaction. In one aspect, the detection involves the use of labels to detect the inhibition of binding of the tRNA fragment to a target molecule.
In one aspect, the tRNA TΨC-loop fragment and the ASL fragment may be combined in a single RNA molecule, or may be used as separate nucleic acid molecules in the mixture. Where the TΨC-loop fragment and the ASL fragment are contained in a single RNA molecule, the TΨC-loop and the ASL may be in any arrangement, including the naturally occurring arrangement and a non-naturally occurring arrangement.
In one aspect, a method of identifying an inhibitor of tRNA-target molecule interactions comprises forming a mixture of a nucleic acid molecule comprising a tRNA TΨC-loop fragment having at least one modified nucleotide, a D-loop fragment, and a tRNA ASL fragment, a target molecule that is capable of binding to the tRNA TΨC-loop fragment and/or D-loop fragment and/or the ASL fragment, and a test compound. The resulting mixture is incubated under conditions that allow binding of the tRNA TΨC-loop fragment and/or D-loop fragment and/or the ASL fragment and the target molecule in the absence of the test compound. The method further involves detecting whether the test compound inhibits the binding of the tRNA TΨC-loop fragment and/or D-loop fragment and/or ASL fragment to the target molecule, where the absence of binding of the tRNA TΨC-loop fragment and/or D-loop fragment and/or ASL fragment and the target molecule is indicative of the test compound being an inhibitor of tRNA-target molecule interaction. In one aspect, the detection involves the use of labels to detect the inhibition of binding of the tRNA fragment to a target molecule. The TΨC-loop fragment, D-loop fragment and ASL may be in separate nucleic acid molecules, or may be linked on a single nucleic acid molecule, and may in any arrangement, such as the naturally occurring arrangement or non-naturally occurring arrangement.
The disclosure also provides methods for identifying inhibitors of Category B bacteria infection. Such methods comprise forming a mixture containing a tRNA fragment from a Category B Bacteria having one or more modified nucleotide bases, a target molecule from a Category B Bacteria capable of binding to the tRNA fragment, and a test compound. The resulting mixture is incubated under conditions that allow binding of the tRNA fragment and the target molecule in the absence of the test compound. The method further involves detecting whether the test compound inhibits the binding of the tRNA fragment to the target molecule. In one aspect, the detection involves the use of labels to detect the inhibition of binding of the tRNA fragment to the target molecule, where the inhibition indicates that the test compound is capable of inhibiting infection of a host cell by category B bacteria. The target molecule from a Category B Bacteria may be an aminoacyl tRNA synthetase, a methyl transferase, a pseudouridine synthase, a ribosomal RNA (e.g. 5S ribosomal RNA), or a transfer RNA.
In another aspect, the disclosure provides methods for identifying inhibitors of aminoacyl-tRNA synthetases (AaRS) for use as antimicrobial agents. In one aspect, criteria for such inhibitors also include: i) diversity between prokaryotic and eukaryotic sequences to develop inhibitors that selectively target the prokaryote; ii) conserved targets across different pathogens for development of broad spectrum antimicrobial compounds; iii) 20 potential targets as each amino acid has its own AaRS; iv) target molecules that are soluble, stable, and relatively easy to purify for use in an HTS; and v) X-ray crystal structures. In another aspect, the target molecule may be an essential gene for bacterial growth and/or propagation. For bacterial pathogens modified nucleotides at position 34 of the tRNA may be important for tRNA-AaRS binding. For example, in GluRS binding, a modified nucleotide at position 34 may be important for efficient charging of the tRNA in bacteria for binding to the synthetase.
In one aspect, the AaRS is LysRS. In addition to this being an essential enzyme, LysRS from bacteria utilizes a different modified nucleotide base and RNA sequence in the anticodon stem loop than mammals. LysRS has been isolated and purified from many species indicating that this enzyme is soluble, stable, and relatively easy to isolate. The crystal structure of LysRS has been solved for several bacteria. In addition, enzyme homology of LysRS of human to the food and water borne bacteria is less than 10% (FIGS. 1A-D, Table 2). The homology for LysRS among the bacteria may range from approximately 20% to nearly 100%. Thus, in one aspect, inhibitors identified by these methods inhibit the binding of bacterial AaRS to the bacterial tRNA, but does not inhibit the mammalian AaRS to the mammalian tRNA.
















TABLE 2







Shi
E C
Sal
Yer
Lis
Cam
Vib
H S
























Shigella
1.00
0.99
0.95
0.86
0.5
0.46
0.19
0.08


flexneri


Escherichia
0.99
1.00
0.95
0.86
0.5
0.46
0.19
0.08


coli


Salmonella
0.95
0.95
1.00
0.85
0.5
0.45
0.18
0.08


enterica


Yersinia
0.86
0.86
0.85
1.00
0.48
0.47
0.19
0.07


enterocolitica


Listeria
0.5
0.5
0.5
0.48
1.00
0.45
0.2
0.09


monocytogenes


Campylobacter
0.46
0.46
0.45
0.47
0.45
1.00
0.19
0.07


jejuni


Vibrio
0.19
0.19
0.18
0.19
0.2
0.19
1.00
0.07


cholerae


Homo sapiens
0.08
0.08
0.08
0.07
0.09
0.07
0.07
1.00









In another aspect, the methods may involve the detection of the binding of the test compound to the tRNA fragment, the target molecule, or both the tRNA fragment and the target molecule. In one aspect, the binding of the test compound is indicative of the test compound being an inhibitor of bacterial propagation, bacterial infection, protein synthesis, or tRNA binding.
In another aspect, methods for diagnosing (or assisting in diagnosing) whether a subject has an infectious disease are also provided. Such methods may be used to diagnose (or assist in diagnosis) of any infectious disease, including, but not limited to bacterial diseases, viral diseases, and fungal diseases.
Thus, in one aspect, a method for diagnosing (or assisting in diagnosing) whether a subject has a bacterial infection is provided. The method comprises forming a mixture comprising a first RNA molecule having at least one modified nucleotide and a biological sample obtained from a subject. The mixture is then incubated under conditions that allow the interaction, or binding, of the first RNA molecule and a target molecule in the biological sample, then detecting whether or not the first RNA molecule binds to the target molecule in the biological sample. Binding of the first RNA molecule and the target molecule is indicative of the positive diagnosis of a bacterial infection. The lack of binding of the RNA molecule and the target molecule is indicative of the negative diagnosis of a bacterial infection.
In another aspect, a method for identifying target molecules that bind to nucleic acid molecules having one or more modified nucleotides is provided. The methods generally comprise forming a mixture of a biological sample from a subject and at least one nucleic acid molecule derived from, or corresponding to, a tRNA loop having at least one modified nucleotide. The mixture is incubated under conditions that allow binding of a target molecule in the biological sample to the first nucleic acid molecule. After the incubation, target molecules that bind to the nucleic acid molecule can be detected. A washing step may also be used to remove unbound molecules and facilitate the detection of the bound molecules. The tRNA loop molecules that can be used in the mixture include those selected from the group consisting of a TΨC-loop, a D-loop, and an anticodon loop, and combinations thereof.
The tRNA loop molecules may be derived from or correspond to tRNA sequences from any organism. For example, tRNA loop molecules for use in the methods may be derived from, or correspond to, tRNA sequences from bacterial, fungal, or viral pathogens, and may incorporate modified nucleotides based on the particular pathogen.
The nucleic acid molecules may be arranged on an array to allow for the development of high throughput assays for the detection of molecules that bind to nucleic acid molecules having a modified nucleotide. Such arrays may contain multiple nucleic acid molecules derived from tRNA TΨC-loop fragments, D-loop fragments, and anticodon loop fragments, to allow for the simultaneous screening of one or more different nucleic acid sequences having one or more different modified nucleotides. The one or more different nucleic acid sequences may be derived from or correspond to sequences from a single pathogen or a group of pathogens to identify target compounds for which broad spectrum inhibitors may be identified. In addition, the nucleic acid molecules may be detectably labeled to further facilitate detection of the binding of a target molecule to a tRNA molecule.
Such methods may be useful in the development of diagnostic methods to detect whether a subject is infected with a particular pathogen. In addition, molecules that are identified as binding to the tRNA loop molecules by such methods can be used in inhibition assays as disclosed herein to identify compounds useful for the inhibition of pathogen infection in a subject. Such compounds may be useful as therapeutic compounds or in the development of therapeutic compounds for the treatment of pathogen infections.
The methods for detecting binding of the target molecule to the tRNA or the inhibition of such binding or the diagnostic methods may be performed using any method for such detection, for example, the AlphaScreen® assay (Packard Instrument Company, Meriden, Conn.). AlphaScreen® technology is an “Amplified Luminescent Proximity Homogeneous Assay” method utilizing latex microbeads (250 nm diameter) containing a photosensitizer (donor beads), or chemiluminescent groups and fluorescent acceptor molecules (acceptor beads). Upon illumination with laser light at 680 nm, the photosensitizer in the donor bead converts ambient oxygen to singlet-state oxygen. The excited singlet-state oxygen molecules diffuse approximately 250 nm (one bead diameter) before rapidly decaying. If the acceptor bead is in close proximity to the donor bead (i.e., by virtue of the interaction of the target molecule and RNA molecule), the singlet-state oxygen molecules react with chemiluminescent groups in the acceptor beads, which immediately transfer energy to fluorescent acceptors in the same bead. These fluorescent acceptors shift the emission wavelength to 520-620 nm, resulting in a detectable signal. Antagonists of the interaction of the target molecule with the RNA molecule will thus inhibit the shift in emission wavelength, whereas agonists of this interaction would enhance it.
The disclosed methods may be performed by mixing the component nucleotides (e.g. the RNA molecule), the target molecule and the test compound in any order, or simultaneously. For example, a target molecule may be first combined with a test compound to form a first mixture, and then an RNA molecule may be added to form a second mixture. In another example, a target molecule, an RNA molecule and the test compound may all be mixed at the same time before incubation. In one aspect, the mixture is incubated under conditions that allow binding of the RNA molecule and the target molecule in the absence of the test compound.
The inhibition of binding of the RNA molecule and the target molecule by the test Compound may be detected using any method available for the detection of inhibition. In one aspect, the determining step may be performed using methods including, but not limited to, gel shift assays, chemical and enzymatic footprinting, circular dichroism and NMR spectroscopy, equilibrium dialysis, or in any of the binding detection mechanisms commonly employed with combinatorial libraries of probes or test compounds. The inhibition of binding indicates that the test compound may be useful for inhibiting the interaction between an RNA molecule and a target molecule.
Any compound may be tested using the methods of the present invention to identify compounds capable of inhibiting interactions between an RNA and a target molecule. Test compounds that may be screened with methods of the present invention include, but are not limited to, polypeptides, beta-turn mimetics, polysaccharides, phospholipids, hormones, prostaglandins, steroids, aromatic compounds, heterocyclic compounds, benzodiazepines, oligomeric N-substituted glycines, oligocarbamates, polypeptides, saccharides, fatty acids, steroids, purines, pyrimidines, derivatives, structural analogs or combinations thereof. Some test compounds are synthetic molecules while others are natural molecules.
Test compounds may be obtained from a wide variety of sources including libraries of synthetic or natural compounds. Combinatorial libraries can be produced for many types of compound that can be synthesized in a step-by-step fashion. Large combinatorial libraries of compounds can be constructed by the encoded synthetic libraries (ESL) method described in WO 95/12608, WO 93/06121, WO 94/08051, WO 95/35503 and WO 95/30642. Peptide libraries can also be generated by phage display methods (see, e.g., Devlin, WO 91/18980). Libraries of natural compounds in the form of bacterial, fungal, plant and animal extracts can be obtained from commercial sources or collected in the field. Known pharmacological agents can be subject to directed or random chemical modifications, such as acylation, alkylation, esterification, amidification to produce structural analogs.
Combinatorial libraries of peptides or other compounds can be fully randomized, with no sequence preferences or constants at any position. Alternatively, the library can be biased, i.e., some positions within the sequence are either held constant, or are selected from a limited number of possibilities. For example, in some cases, the nucleotides or amino acid residues are randomized within a defined class, for example, of hydrophobic amino acids, hydrophilic residues, sterically biased (either small or large) residues, towards the creation of cysteines, for cross-linking, prolines for SH-3 domains, serines, threonines, tyrosines or histidines for phosphorylation sites, or to purines.
In another aspect, the test compounds may be naturally occurring proteins or their fragments. Such test compounds may be obtained from a natural source, e.g., a cell or tissue lysate. Libraries of polypeptide agents may also be prepared, e.g., from a cDNA library commercially available or generated with routine methods. The test compounds can also be peptides, e.g., peptides of from about 5 to about 30 amino acids, with from about 5 to about 20 amino acids being preferred and from about 7 to about 15 being particularly preferred. The peptides can be digests of naturally occurring proteins, random peptides, or “biased” random peptides. In some methods, the test compounds are polypeptides or proteins.
In another aspect, the test compounds may be nucleic acids. Nucleic acid test compounds may be naturally occurring nucleic acids, random nucleic acids, or “biased” random nucleic acids. For example, digests of prokaryotic or eukaryotic genomes may be similarly used as described above for proteins.
In some preferred methods, the test compounds are small molecules, e.g., molecules with a molecular weight of not more than about 500 or 1,000. Preferably, high throughput assays are adapted and used to screen for such small molecules. In some methods, combinatorial libraries of small molecule test compounds as described above can be readily employed to screen for small molecule modulators of retroviral propagation. A number of assays are available for such screening, e.g., as described in Schultz et al., Bioorg Med Chem Lett 8:2409-2414, 1998; Weller et al., Mol Divers. 3:61-70, 1997; Fernandes et al., Curr Opin Chem Biol 2:597-603, 1998; and Sittampalam et al., Curr Opin Chem Biol 1:384-91, 1997.
The invention also comprises kits and compositions (e.g., reaction mixtures, etc.) for a method of the invention. A kit is a combination of individual compositions useful or sufficient for carrying out one or more steps of a method of the invention, wherein the compositions are optimized for use together in the method. A composition comprises an individual component for at least one step of a method of the invention. The present disclosure further provides a kit for screening for an inhibitor of interactions between an RNA molecule and a target molecule, comprising: an RNA fragment and a reagent for detection of binding to a target molecule, such as a detectable label. In some embodiments, the kit also comprises one or more target molecule(s) that are capable of binding to the RNA fragment. In some embodiments, the kit further comprises additional reagents for conducting the screening methods. In some embodiments, the kit further comprises a plurality of inhibitors of retroviral reverse transcription. In some embodiments, the reagent comprises a dye that undergoes fluorescence enhancement upon binding to nucleic acids (e.g., the dye is RIBOGREEN, SYBR Gold, SYBR Green I, or SYBER Green II). In some embodiments, the kit further comprises control reagents (e.g., sample polymerases and/or inhibitors for positive controls, polymerase and/or inhibitor minus samples for negative controls, etc.). In some embodiments, the kit further comprises instructions for carryout out the methods. In some embodiments, the instructions are embodied in computer software that assists the user in obtaining, analyzing, displaying, and/or storing results of the method. The software may further comprise instructions for managing sample information, integrating with scientific equipment (e.g., detection equipment), etc.
Also provided are kits for identifying inhibitors bacterial infection. In one aspect, the kits include, a tRNA fragment and a detectable label for detecting the interaction of the tRNA fragment and a target molecule from a biological sample. The kits of the present invention may also include target molecules, and/or reagents for performing the assays. The kits may also include labeling components for detecting whether a test compound inhibits the binding of the fragment tRNA and the target molecule.
Also provided are kits for diagnosing whether a subject is infected with an infectious disease. Such kits comprise: an RNA fragment and a reagent for detection of binding to a target molecule from a biological sample (such as a detectable label).
The invention will be further explained by the following illustrative examples that are intended to be non-limiting.
EXAMPLES
Example 1
Synthesis of RNA Sequences Having Modified Nucleotides
The first step in producing the fragment RNA molecule sequences is the synthesis of the modified nucleotides, also known as phosphoramidites (Agris et. al Biochimie. (1995) 77(1-2):125-34). The modified nucleotides are then used during the synthesis of the RNA oligomers (Ogilvie et. al. Proc Natl Acad Sci USA. (1988) 85:5764-8). Synthetic approaches overcome the substantial barrier of obtaining sufficient amounts of natural products for the functional characterization studies. In addition to providing the fully modified RNA for characterization of the fragment tRNA:target molecule binding, the synthetic approach allows for the preparation of intermediate steps/forms of the modified material that can further elucidate the individual contribution of each modification step in enhanced tRNA binding.
Modified base nucleic acid molecules were prepared using a combination of methods for the synthesis, incorporation, and purification of all the modified nucleotides. Modified base phosphoramidites were prepared using known methods, such as those disclosed in Ogilive et. al., Proc. Natl. Acad. Sci., U.S.A., 85:5764-5768 (1988). S (mnm5s2U) was prepared following the previously published procedures of Vorbruggen et. al., Angew. Chem., 14: 225-256 (1975). 6 (t6A) and $ (cmnm5s2U) were synthesized following the procedures described below. Pseudouridine is commercially available and was incorporated into the RNA oligomers using the methods described below. Functional groups on the modified nucleotide bases were protected using phosphoramidite chemistry (Ogilvie et. al., 1988). Using this chemistry, over 20 different modified nucleotides have been incorporated into a range of oligonucleotides ranging in length from 3 to 36 nucleotides (Nobles, et. al., Nuc. Acids Res., 30: 4751-4760 (2002)). The addition of a protecting group to each modified base and ribose is described below. The protecting group was subsequently removed after synthesis of the RNA oligomer. While 2 position thio-groups can be oxidized in standard RNA synthesis protocols this barrier has been overcome by using the tert-butyl hydroperoxide (10% solution in acetonitrile) oxidizing agent (Kumar and Davis, Nuc. Acids Res., 25(6): 1272-1280 (1997)).
Compound 1—mnm5s2U Phosphoramidite
Base protection of mnm5s2U [5-(N-trifiluoroacetyl)methylaminomethy 2-thiouridine]: The 2,2,2-trichloroethoxycarbonyl protecting groups were used to protect exo-amino function of the nucleotide. The nucleotide is treated with excess of trifluoroacetic anhydride in pyridine solution, followed by selective removal of trifluoroacetyl groups from sugar moiety with 10% sodium bicarbonate giving the base protected product (Malkiewicz, Tetrahedron Letters, 24: 5387-5390 (1983)).
Protection of the ribose and phosphitylation follow the general scheme:
Base Protection of mnm5s2U




Preparation of the N6—(N-threonylcarbonyl)adenosine for automated synthesis follows a slightly different approach than that for the other phosphoramidites. First, the ribose functions of adenosine are protected following the methods outlined above. Next, the ribose protected adenosine was reacted with 3 equivalents of phenoxycarbonyltetrazole in anhydrous dioxane for 18 hr at 37° C. to produce phenyl carbamates at the six position. This was followed by aminolysis with 3 equivalents of crystalline L-threonine p-nitrobenzyl ester in anhydrous dioxane, for 18 hr at 37° C., producing the N6-(N-threonylcarbonyl)adenosine. The t6A carboxylate was then protected by a trimethylsilylethyl group, in a manner similar to that used to protect the ribose function. Finally the phosphoramidite was phosphitylated following the protocol described below.
Modification of Adenosine to t6A




Preparation of the 3—cmnm5s2U nucleotide follows published methods (Reese and Sanghvi, J. Chem. Soc. Chem. Commun., 62-63 (1984)). Briefly, 2 thiouridine was heated with 5 molar equivalents each of pyrrolidine and formaldehyde in aqueous solution for 1 h, under reflux to produce 2′,3′-O-isopropylidene-5-pyrrolidinomethyl-2-thiouridine. This base was treated with 10 mol. equivalents of methyl iodide in acetonitrile at room temperature. After 16 hours, the products were concentrated under reduced pressure to give the putative niethiodide which was then dissolved in acetonitrile and allowed to react with 3 molar equivalents of glycine t-butyl ester at room temperature for 16 h. This product was then purified and protection of the ribose and phosphitylation follow the general scheme:
Preparation and Base Protection of cmnm5s2U




General procedure for ribose protection and phosphitylation prior to RNA oligomer synthesis: After base protection the scheme for the synthesis of 5′-O-(4,4′-dimethoxytrityl)-2′-O-tertbutyldimethylsilyi-modified ribonucleoside-3′-O-(2-cyanoethyl-N-diisopropyl)-phosphoramidites is the same for all modified nucleotides. The protected nucleoside was dried by co-evaporation twice with pyridine and dissolved in pyridine. Tert-butyldimethylchlorosilane and imidazole were added and reacted for 4 hours at room temperature. The excess silyl chloride was decomposed with water and dichloromethane. The aqueous layer was extracted twice with dichloromethane and combined with the organic layer. The solvent was evaporated by vacuum yielding a gum which was dissolved in ether and precipitated by pouring slowly into petroleum ether (40-60° C.) with stirring. The precipitate was collected and washed twice with petroleum ether. At this point the crude product contains three components; the 2′,3′ disilylated, 2′ silylated (major product) and 3′ silylated. The pure 2′ protected isomer were obtained by silica gel column chromatography. This product is then ready for phosphitylation.
The N-protected-5′-O-dimethoxytrityl-2′-O-tert-butyldimethylsilyl-ribonucleosides was dried by two co-evaporations with anhydrous pyridine and THF. The residue was dissolved in anhydrous THF under argon. Dimethylaminopyridine, N,N,N-ethyldiisopropylamine and cyano-ethoxydiisopropy amino-chlorophosphine were added through a rubber septum. After 2 hours the reaction mixture was quenched with ethyl acetate and washed with 5% sodium bicarbonate followed by water. Aqueous washes were back extracted with ethyl acetate. Combined organic layers were dried over sodium sulphate. Solvent was evaporated yielding a viscous oil. The product was co-evaporated twice with toluene and the pale yellow phosphoramidite products were purified by flash silica gel chromatography.
Generalized Sugar Protection and Phosphinylation of Modified Nucleotides




The protecting group is subsequently removed after synthesis of the RNA oligomer. The addition of a protecting group to each modified base and ribose is described. While 2 position thio-groups can be oxidized in standard RNA synthesis protocols this has been overcome by using the tert-butyl hydroperoxide (10% solution in acetonitrile) oxidizing agent (Kumar and Davis, 1997).
The modified bases were incorporated into the 17 residue tRNA oligomers based on 7 food and water borne bacteria from the Category B priority pathogen list (Table 2, S=mnm5s2U; 6=t6A; $=cmnm5s2U; P=pseudouridine) along with a random 17mer oligomer to be used as a negative control. In those cases where the actual oligomer sequence was not fully determined (S or $ in Table 3) both sequences were synthesized and tested. Each oligomer was tagged with a fluorescent dye for use in the assays and diagnostic. In addition, a subset of the oligomers were synthesized with a thiol group on the 3′ end and a different dye for attachment to the microarray chips. For the microtiter plate format each oligomer was tagged with fluorescent dye on the 3′ end. Purity of the oligomers was confirmed by gel electrophoresis and proper incorporation of the modified nucleotide bases was confirmed by mass spectrometry.







TABLE 3





(SEQ ID NOS 9-17), respectively in order of


appearance):
















E. Coli
G U U G A C U S    U U 6 A P C A A U


 


Salmonella
G U U G A C U S    U U 6 A P C A A U


 


Shigella
G U U G A C U S    U U 6 A P C A A U


 


Camptobacteria
U C U C C C U Sor$ U U 6 A G G A G G


 


Vibrio
G U U G G C U Sor$ U U 6 A C C A A U


 


Listeria 1
U C U G A C U Sor$ U U 6 A P C A G A


 


Listeria 2
G C U G A C U C    U U 6 A P C A G C


 


Yersinia 1
C U U G A C U S    U U 6 A P C A A U


 


Yersinia 2
C U U G A C U C    U U 6 A P C A A U









Example 2
Inhibitor Screening Assay
A set of experiments was conducted to identify an RNA oligomer substrate to be used in an assay to identify substrates for use in identifying inhibitors of tRNA binding to a phenylalanine synthetase from yeast. A peptide was first identified for use as a phenylalanine synthetase mimic. The peptide was labeled with a fluorescent peptide for use in detection in binding assays.
A series of RNA oligomer substrates were also synthesized containing modified nucleotides (FIG. 2). A 17mer RNA oligomer containing the modified nucleotide bases Cm, Gm, and m5C was identified as having a greater affinity for a fluorescent peptide that mimics phenylalanine synthetase than the native RNA oligomer or the unmodified RNA oligomer with no modified nucleotide bases (FIG. 2).
To determine binding affinity, an assay of ASL for yeast tRNAphe was prepared varying only in the number of post-transcriptional nucleotide base modifications. This array was probed using a peptide from a phage display library that bound to an ASL containing 3 modifications. The affect of modification on the affinity of a peptide to an RNA substrate-sequence (Sequence A in FIG. 2: 5′-CCAGACUGAAGAUCUGG) (SEQ ID NO: 18) is the primary unmodified yeast ASLPhe. Sequence B in FIG. 2 (5′-CCAGACmUGm AAGAUm5CUGG) (SEQ ID NO: 19) is a template ASL sequence indicating the locations of the modified nucleotides for the various combinations of modified nucleotide bases in the mimics of the anticodon stem loop. Sequence C in FIG. 2 (5′-CCAGACmUGmAAm1GAΨm5CUGG) (SEQ ID NO: 20) is the sequence of the native yeast tRNAphe. Sequence D in FIG. 2 (5′-GGUCUAGAA GmUCmAGACC) (SEQ ID NO: 21) is a secondary structure for the doubly modified Phe ASL sequence that's has a propensity to form a duplex. When the affinity of the peptide to the ASLs was determined it was found that the modifications affected the affinity by more than 3 orders of magnitude (FIG. 2). This assay also demonstrates the significance of the effect of the modified nucleotides on binding between the enzyme and its RNA substrate. Such an assay may be used to identify inhibitors of tRNAphe binding to phenylalanine synthetase.
Example 3
Lysine Synthetase Inhibitor Assay
A set of assays can be developed to target LysRS that is unique to each of the Category B Bacteria and can be based on microtiter plate technology. In addition, assays can be developed to utilize microarray technology for the development of a multidimensional HTS assay that incorporates a subset of 7 of the individual HTS assays onto a single microarray chip. A diagnostic assay can also use the microarray technology, but in a format tailored to diagnostic applications. The microtiter based and microarray based HTS assays can then be used to screen compound libraries for active compounds that can be developed as a narrow-spectrum organism specific antibiotics and as a broad-spectrum antibiotic.
RNA oligomers are produced incorporating modified nucleotide bases, mnm5s2U, cmnm5s2U, t6A, and P. The modified bases are incorporated into the 17 residue tRNA oligomers in Table 3 along with a random 17mer oligomer to be used as a negative control. In those cases where the actual oligomer sequence has not been fully determined (S or $ in Table 3) both sequences are synthesized and tested. Each oligomer is tagged with a fluorescent dye for use in the assays and diagnostic. In addition, a subset of the oligomers is synthesized with a thiol group on the 3′ end and a different dye for attachment to the microarray chips. For the microtiter plate format each oligomer is tagged with fluorescent dye on the 3′ end. The RNA oligomers are synthesized and purified following protocols developed specifically for these modified reagents (Agris et. al., Biochimie, 77(1-2):125-134 (1995), Murphy et. al., Nat. Struct. Mol. Biol., (12):1186-1191 (2004)). Purification of the oligomers is performed by HPLC as described (Agris et. al., Acta Biochim Pol., 46(1):163-172 (1999)). Purity of the oligomers is confirmed by gel electrophoresis and proper incorporation of the modified nucleotide bases is confirmed by mass spectrometry.
LysRS corresponding to each of the 7 organisms will be over expressed in and isolated from E. coli using previously described methods (Madore et. al., FEBS Journal, 266:1125-1135 (1999)). A BAC clone containing the LysRS gene can be obtained. The LysRS is encoded from nucleotides from each of the organisms and is available on a BAC clone (Table). From the BAC a subclone can be used to generate an expression vector for production of the Lysine Synthetase enzyme. The production of active LysRS enzyme can be performed using published protocols (e.g. Madore et. al.).







TABLE 4







LysRS genome for each organism is available as a BAC clone.









Organism
Genome location
Source





Salmonella enterica
19802-21330
Washington University




Genome Sequencing Center.




St. Louis, Mo


Campylobacter jejuni
365440-367864
Sanger Inst. Hinxton,




Cambridge, UK


Listeria
35510-37065
Institut Pasteur Paris,


monocytogenes
chromosome I,
France Vibrio


cholerae
section 239
The Institute for Genomic



residues 7399-
Research Rockville,



10352
Maryland


Escherichia coli
3838117-3841613
Laboratory of Genetics,


O157: H7 IP32953

University of Wisconsin-




Madison, Madison




Wisconsin.


Yersinia
3718692-3722057
Institut Pasteur Paris,


pseudotuberculosis

France


Shigella flexneri 2a str.
2958664-962160
Laboratory of Genetics,


2457T

University of Wisconsin-




Madison, Madison




Wisconsin









Assays can then be performed to monitor the inhibition of ASLLys binding to LysRS. Such assays take advantage of the fact that modified tRNALys is a 100 fold better substrate for binding to LysRS than a tRNALys containing no modified bases (Sylver et. al., Biochemistry 32(15):3836-3841 (1995)). Monitoring of the ASLLys LysRS complex formation can be determined using time-resolved fluorescent detection (Millar, Curr. Opin. Struct. Biol., 6:637-642 (1996)). Time-resolved fluorescence detection allows for monitoring complex formation and inhibition in solution. Affinity of each of three or four oligomers for each LysRS: modified ASLLys; unmodified ASLLys; and, the negative random control can be determined by monitoring the change in fluorescence.
The enzyme and tRNA interactions can be monitored using time resolved fluorescence spectroscopy to effectively monitor the binding of tRNA to the synthetase (Lam, Biochemistry, 14:2775-2780 (1975)). tRNA synthetase binding can be characterized by monitoring the quenching of tryptophan residues in the protein. While several of the target organism synthetases contain a tryptophan that could be used to monitor tRNA binding, for uniformity the LysRSs is labeled using fluorescein isothiocyanate, FITC (Pierce, Rockford Ill.), as described, for example, by Commans, J. Mol. Biol., 253:100-113 (1995). The association of tRNA for its cognate synthetase is strong (Ka=1×106) and specific with non-cognate tRNA Ka 1 to four orders of magnitude lower. While measuring total fluorescence is sufficient to monitor complex formation, integration of time resolved fluorescence detection allows for monitoring both free and bound species in the interaction (Jager, Curr. Pharma. Biotech., 4:463-476 (2003)). Time resolved measurements monitor an intrinsic molecular property which results in high statistical accuracy and may make fluorescence lifetime analysis (FLA) more appropriate for HTS applications (Jager). Titrations studies 100 nM of enzyme solution can be used to monitor complex formation (Commans 1995). To determine the amount of ASL to add per reaction a titration of the ASL can be made. The starting solution conditions for the assay can be 5 mM MgCl2 and 2 μM spermidine, pH 6.8. Affinity of tRNALys for the synthetase a titration of 0 to 4 μM should be sufficient to achieve complete complex formation. Initially a 96 well format can be used in method development that will be expanded to a 386 format once the assay parameters have been determined.
Two alternatives are available for time resolved fluorescence. First, is the use of alternative fluorescent dyes such as Cy3 or Cy5 which can easily be attached to each oligomer. Alternatively, an enzyme linked assay format is available where the purified LysRS can be chemically modified to add biotin which will bind to the surface of streptavidin coated well using a Mts-Atf-Biotin Label Transfer Reagent from Pierce, Rockford Ill. This will allow for the binding of the protein to the surface of each well. With the LysRS bound to surface, complex formation can be monitored.
Using the more sensitive assay protocol from above, the assay reagents and conditions can be varied and the optimum reaction mixture will be determined based on Z-factor analysis. After the optimum conditions are determined, the robustness of the assay will be verified by modifying various reagent concentrations or assay conditions by .+−0.10% and determining Z-factor scores. These scores will be plotted and used to determine which assay conditions are most relevant to control. In parallel, positive control compounds can be tested and selected. The positive control compounds can be used during the routine use of the assay to verify that the assay is functioning properly. As part of the assay optimization experiments, the specificity and selectivity of each enzyme can be confirmed by determining the affinity for other closely related substrates (oligomers prepared for the other LysRS).
The assays can then be used with a small number of molecular inhibitors contained in a test library supplemented with known inhibitors of LysRS along with other known positive controls to confirm the use of the assay. The test compounds, known AaRS inhibitors and positive control compounds can be aliquoted into 96-well plates at a predetermined concentration corresponding to 40 μg of compound per well. The remaining assay components can be added and the reaction allowed to proceed to completion. The reaction results can be quantified and the IC50 calculated. A dilution series of compounds with an IC50 less than 1×10−5 M can be analyzed with this assay to confirm that the compound is active and to more accurately determine the IC50. Those compounds that are active in this assay can be classified as ‘hits’ and further assayed for biological testing to determine antimicrobial activity.
For determining activity of the compounds, the following bacterial species can be tested against each sample:
Escherichia coli American Type Culture Collection (ATCC) 25922 as a surrogate marker for diarrheagenic E. coli. 
Shigella sonnei (clinical isolate) as the most common species causing shigellosis in developed countries.
Salmonella serotype Enteritidis (clinical isolate) as a common and expanding global cause of salmonellosis.
Yersinia enterocolitica (clinical isolate) as a common cause of intestinal yersiniosis.
Vibro cholerae (clinical isolate) as the most important species in the genus Vibrio causing diarrhea.
Campylobacter jejuni (clinical isolate) which continues to be the most common enteric pathogen isolated from patients with diarrhea.
Listeria monocytogenes (clinical isolate) as the most common cause of invasive listeriosis.
As a minimum inhibitory concentration (MIC), an achievable potency of less than or equal to 32 μg/ml tested against any of the above pathogens would be considered an active compound worthy of an extended secondary screen study.
Samples can be tested using the reference broth microdilution methods recommended by the Clinical and Laboratory Standards Institute (CLSI; formerly the National Committee for Clinical Laboratory Standards [NCCLS]) M7-A7 and M45-A documents. A 96 well microtiter tray assay can be used to test a single concentration of 32 μg/ml against each pathogen. A working concentration of 64 μg/ml can be made using appropriate solvents and diluents. A calibrated pipette is used to transfer 50 μL of each sample into one well of each of three 96-well microtitre plates. A direct colony suspension is used to make a standard inoculum (equivalent to a 0.5 MacFarland standard) of each bacteria in Mueller-Hinton broth (MHB). A 50 μL aliquot of a diluted bacterial suspension in MHB (supplemented with lysed horse blood for C. jejuni) is added to each sample to achieve a final bacterial concentration of 3-5×105 CFU/ml, thus diluting the sample 1:2 to a final test concentration of 32 μg/ml. Each batch of samples includes two internal quality control antimicrobial agents with a know potency range and that target protein synthesis. A positive growth control with only growth support media and an ethanol control at concentrations equivalent to that in the samples is also tested for each pathogen concurrently. After the broth microdilution plates are inoculated and incubated in an ambient air environment at 35° C. for 20-24 hours for the enteric bacilli and L. monocytogenes. C. jejuni is incubated for 48 hours at 37° C. in a microaerobic atmosphere, using gas-generated sachets in a sealed hard plastic container. After appropriate incubation times, the plates are removed from incubation and each well inspected for growth. If a well is clear of growth (non-turbid), an MIC of .ltoreq.32 μg/ml would be determined and the investigational agent therefore identified as being active
A secondary screen of “active” samples includes an extended dilution series (eight to 12 log2 dilution steps) to determine “on-scale” MIC values for a potential antimicrobial agent including evaluation of breadth of spectrum against a larger collection (140 strains) of FWB pathogens listed above (20 isolates each). These isolates are recent clinical strains representing wild-type and strains with documented critical resistance phenotypes; testing methodologies to be those described above.
A multidimensional microarray HTS based on the above assay can then be developed. The multidimensional microarray HTS can be used to screen for inhibitors of each enzyme simultaneously; thus, providing a means to identify narrow spectrum inhibitors (inhibits one enzyme) or broad spectrum inhibitors (inhibits several to all of the enzymes). Each of the specific oligomers can be attached in a small grid on the microarray. After all of the oligomers are attached each enzyme is added and allowed to bind to its respective oligomer to form a substrate-enzyme complex as confirmed in the specificity and selectivity testing. A single inhibitor is then added to each grid and the active compounds will dissociate the substrate-enzyme complex as determined by measuring fluorescence.
Alternatively, rather than fluorescently labeling the bacterial proteins, a fluorophore can be attached within the RNA substrate. While the most common method to fluorescently label an oligomer is to attach it either on the 3′ or 5′ end; for these microarray applications attaching the fluorophore within the oligonucleotide may simplify and/or facilitate detection. A pyrrolo fluorescent cytidine analog may be used in the generation of the RNA oligonucleotides (Glen Research Sterling, Va.). This cytidine analog base pairs with other nucleotides as a normal nucleotide. Also, this fully substituted oligonucleotide has the same Tm as the control oligonucleotide.
A review of all the LysRS substrates, Table 3, finds that they all contain a cytosine in the loop at position 32 and also in the stem portion of the ASL. To determine to optimum position for placement of the cytidine analog, test oligomers can be made with both positions labeled for the E. coli substrate. The association constant and intensity of signal quenching can be determined for both test oligomers. Results of these experiments will determine the optimal substrate(s) for the chip. For the remaining oligomers, the selectivity and specificity of each oligomer containing the modified nucleotide bases to their respective enzymes is confirmed in solution during the development of the HTS assays and can be verified when attached to the microarray chip. The organism specific RNA oligomers are attached to the glass microarray chip using gold-thiol methods. The thiol group is commercially available in the phosphoramidite formulation used in oligomer synthesis and is incorporated in the same chemical step fashion as individual amidites (i.e. A, U, G, C) during synthesis of the oligomers.
Each individual oligomer along with a positive and negative control will be attached to a substrate followed by addition of the enzymes. Each grid is mechanically isolated. Inhibitors are added to each grid followed by fluorescent detection to determine which enzyme-substrate combinations are dissociated; thus, identifying active inhibitors.
A rapid diagnostic assay can also be developed using the same microarray and the organism specific RNA oligomers used for the HTS screening assays. To use the assay, a subsample of the specimen extract is applied to the microarray after which the microarray is rinsed and analyzed with fluorescence detection. If a particular spot fluoresces then the sample is positive for the organism corresponding to that spot. The arrangement of the oligomer substrates on the microarray can be arranged depending on the particular application of the diagnostic assay.
Culture media containing each organism is extracted to release the proteins from the organisms. A subsample of this extract is applied to each grid on the microarray containing RNA oligomers. The microarray is rinsed with distilled water and analyzed with a standard laboratory fluorometer. Those spots corresponding to the specific organism should fluoresce. This process can be repeated for each organism to confirm selectivity and specificity. Finally, sensitivity testing can be conducted by repeating these assays using cultures with decreasing numbers of plaque forming units and/or extract dilutions.

## Claims

1. A microarray comprising a plurality of nucleic acid molecules having at least one modified nucleotide and a solid support to which the plurality of nucleic acid molecules are attached,
wherein the nucleic acid molecules are tRNA fragments having between 5 and 25 continuous nucleotides of tRNA molecules, and
wherein the nucleic acid molecules comprise fragments of tRNA molecules consisting essentially of TΨC-loops, D-loops, and anticodon stem loops.

2. The microarray of claim 1, wherein the nucleic acid molecules are tRNA fragments having between 5 and 25 continuous nucleotides of tRNAAla, tRNAArg, tRNAAsn, tRNAAsp, tRNACys, tRNAGln, tRNAGlu, tRNAGly, tRNAHis, tRNAIle, tRNALeu, tRNALys, tRNAMet, tRNAPhe, tRNAPro, tRNAser, tRNAThr, tRNATrp, tRNATyr, and tRNAVal.

3. The microarray of claim 1, wherein the nucleic acid molecules include a detectable label.

4. An isolated nucleic acid molecule comprising a nucleic acid fragment having between 5 and 25 continuous nucleotides of a tRNA D-loop having at least one modified nucleotide.

5. The isolated nucleic acid molecule of claim 4, wherein said nucleic acid fragment is a fragment of 16 nucleotides.

6. The isolated nucleic acid molecule of claim 4, wherein the at least one modified nucleotide is dihydrouridine.

7. The isolated nucleic acid molecule of claim 4, wherein the nucleic acid fragment is capable of forming a stem-loop structure.

8. The isolated nucleic acid molecule of claim 4, wherein the nucleic acid molecule comprises a nucleic acid molecule having the sequence 5′-m′n′ o′p′NN(dihydrouridine) NN(dihydrouridine)NNp′′o′′n′′m′′, wherein m′, n′, o′, p′ refer to any nucleotide and are complementary to m′′, n′′ o′′ and p′′, and N refers to any nucleotide.

9. An isolated nucleic acid molecule comprising a nucleic acid fragment having between 5 and 25 continuous nucleotides of a tRNA TΨC-loop having at least one modified nucleotide.

10. The isolated nucleic acid molecule of claim 9, wherein said nucleic acid fragment is a fragment of 17 nucleotides.

11. The isolated nucleic acid molecule of claim 9, wherein the nucleic acid fragment has at least two different modified nucleotides.

12. The isolated nucleic acid molecule of claim 9, wherein the at least one modified nucleotide is selected from the group consisting of Psi, ribothymidine, and m1A.

13. The isolated nucleic acid molecule of claim 9, wherein the nucleic acid fragment is capable of forming a stem-loop structure.

14. The isolated nucleic acid molecule of claim 13, wherein the nucleic acid molecule comprises a nucleic acid molecule having the sequence 5′-h′IT k′l′ (ribothymidine)(Psi) CN(m1A)NNl′′k′′j′′I′′h′′, wherein h′, i′, j′, k′, and l′ refer to any nucleotide and are complementary to h′′, i′′, j′′, k′′, and l′′, and N refers to any nucleotide.