Classifications

• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
  • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
  • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
  • C12N9/93—Ligases (6)
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
  • A61P31/04—Antibacterial agents
• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
  • C12Y—ENZYMES
  • C12Y603/00—Ligases forming carbon-nitrogen bonds (6.3)
  • C12Y603/02—Acid—amino-acid ligases (peptide synthases)(6.3.2)
  • C12Y603/02009—UDP-N-acetylmuramoyl-L-alanine-D-glutamate ligase (6.3.2.9)
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K38/00—Medicinal preparations containing peptides

Definitions

• This invention relates to the genes and enzymes involved in cell wall synthesis in bacteria, and particularly to the inhibition of such enzymes.
• the molecular target of many naturally-occurring antibiotics is the synthesis of the bacterial cell wall.
• the frequency with which these types of antibiotics arose in evolution indicates that the pathway of cell wall biosynthesis is a particularly effective point of attack against bacteria.
• Genetic studies confirm the soundness of this process as a target, as temperature-sensitive alleles of the intracellular pathway genes are lytic, and therefore lethal. Since the building blocks of the cell wall are highly conserved structures in both Gram-positive and Gram-negative bacteria, but are unique to the eubacteria, novel inhibitors of cell wall formation are expected to be both broad spectrum and safe antibiotics.
• the bacterial cell wall is a polymer — a single molecule composed of peptidoglycan — that defines the boundary and shape of the cell. Assembled by crosslinking glycan chains with short peptide bridges (Rogers, H. J., H. R. Perkins, and J. B. Ward, 1980, Biosynthesis of peptidoglycan. p. 239-297. In Microbial cell walls and membranes. Chapman & Hall Ltd. London), the completed structure is strong enough to maintain cell integrity against an osmotic pressure differential of over four atmospheres, but also flexible enough to allow the cell to move, grow and divide.
• the construction of the peptidoglycan begins in the cytoplasm with an activated sugar molecule, UDP-N-acetylglucosamine. After two reactions (catalyzed by MurA and MurB) that result in the placement of a lactyl group on the 3-OH of the glucosamine moiety, a series of ATP-dependent amino acid ligases (MurC, -D, -E, and -F) catalyze the stepwise synthesis of the pentapeptide sidechain using the newly synthesized lactyl carboxylate as the first acceptor site.
• MurA and MurB an activated sugar molecule
• a series of ATP-dependent amino acid ligases (MurC, -D, -E, and -F) catalyze the stepwise synthesis of the pentapeptide sidechain using the newly synthesized lactyl carboxylate as the first acceptor site.
• Staphlococcus aureus (Ito, E. and J. L. Strominger, 1962. Enzymatic synthesis of the peptide in bacterial uridine nucleotides: Enzymatic addition of L-alanine, D-glutamic acid, and L-lysine. J. Biol. Chem. 237: 2689-2695; Nathenson, S. G., J. L. Strominger, and E. Ito, 1964. Enzymatic synthesis of the peptide in bacterial uridine nucleotides: purification and properties of D-Glutamic acid-adding enzyme, J. Biol. Chem.
• Escherichia coli Escherichia coli. Eur. J. Biochem. 202 (3): 1169-1176
• genes encoding MurD have been cloned from several species of bacteria including E. coli (Ikeda, M., M. Wachi, F. Ishino, and M. Matsuhashi, 1990a. Nucleotide sequence involving murD and an open reading frame ORF-Y spacing murF and ftsW in Escherichia coli. Nucleic Acids Res. 18:1058; Mengin-Lecreulx, D., C Parquet, L. Desviat, J. Pla, B. Flouret, J. Ayala and J. van Heijenoort, 1989.
• MurD enzymes were purified from Gram-positive cocci (El-Sherbeini, M., Geissler, W., Pittman, J., Yuan, X., Wong, K. K. and Pompliano, D. L. 1998, Cloning and expression of Staphylococcus aureus and Streptococcus pyogenes murD genes encoding uridine diphosphate N-acetylmuramoyl-L-alanine:D-glutamate ligases. Gene, 210: 117-125).
• Polynucleotides and polypeptides of Pseudomonas aeruginosa MurD an enzyme involved in bacterial cell wall biosynthesis are provided.
• the recombinant MurD enzyme is catalytically active in ATP-dependent D-glutamate addition reactions.
• the enzyme is used in in vitro assays to screen for antibacterial compounds that target cell wall biosynthesis.
• the invention includes the purified polynucleotides, purified proteins encoded by the polynucleotides, and host cells expressing the recombinant enzyme, probes and primers, and the use of these molecules in assays.
• An aspect of this invention is a polynucleotide having a sequence encoding a Pseudomonas aeruginosa MurD protein, or a complementary sequence.
• the encoded protein has a sequence corresponding to SEQ LD NO:2.
• the encoded protein can be a naturally occurring mutant or polymorphic form of the protein.
• the polynucleotide can be DNA, RNA or a mixture of both, and can be single or double stranded.
• the polynucelotide is comprised of natural, non- natural or modified nucleotides.
• the internucleotide linkages are linkages that occur in nature.
• the internucleotide linkages can be non-natural linkages or a mixture of natural and non-natural linkages.
• the polynucleotide has a sequence shown in SEQ ID NO:l.
• An aspect of this invention is a polynucleotide having a sequence of at least about 25 contiguous nucleotides that is specific for a naturally occurring polynucleotide encoding a Pseudomonas aeruginosa MurD protein.
• the polynucleotides of this aspect are useful as probes for the specific detection of the presence of a polynucleotide encoding a Pseudomonas aeruginosa MurD protein.
• the polynucleotides of this aspect are useful as primers for use in nucleic acid amplification based assays for the specific detection of the presence of a polynucleotide encoding a Pseudomonas aeruginosa MurD protein.
• the polynucleotides of this aspect can have additional components including, but not limited to, compounds, isotopes, proteins or sequences for the detection of the probe or primer.
• An aspect of this invention is an expression vector including a polynucleotide encoding a Pseudomonas aeruginosa MurD protein, or a complementary sequence, and regulatory regions.
• the encoded protein has a sequence corresponding to SEQ ID NO:2.
• the vector can have any of a variety of regulatory regions known and used in the art as appropriate for the types of host cells the vector can be used in.
• the vector has regulatory regions appropriate for the expression of the encoded protein in gram-negative prokaryotic host cells.
• the vector has regulatory regions appropriate for expression of the encoded protein in gram-positive host cells, yeasts, cyanobacteria or actinomycetes.
• the regulatory regions provide for inducible expression while in other preferred embodiments the regulatory regions provide for constitutive expression.
• the expression vector can be derived from a plasmid, phage, virus or a combination thereof.
• An aspect of this invention is host cell comprising an expression vector including a polynucleotide encoding a Pseudomonas aeruginosa MurD protein, or a complementary sequence, and regulatory regions.
• the encoded protein has a sequence corresponding to SEQ LD NO:2.
• the host cell is a yeast, gram-positive bacterium, cyanobacterium or actinomycete. In a most preferred embodiment, the host cell is a gram-negative bacterium.
• An aspect of this invention is a process for expressing a MurD protein of P. aeruginosa in a host cell.
• a host cell is transformed or transfected with an expression vector including a polynucleotide encoding a Pseudomonas aeruginosa MurD protein, or a complementary sequence.
• the host cell is cultured under conditions conducive to the expression of the encoded MurD protein.
• the expression is inducible or constitutive.
• the encoded protein has a sequence corresponding to SEQ ED NO:2.
• An aspect of this invention is a purified polypeptide having an amino acid sequence of SEQ LD NO:2 or the sequence of a naturally occurring mutant or polymorphic form of the protein.
• An aspect of this invention is a method of determining whether a candidate compound can inhibit the activity of a P. aeruginosa MurD polypeptide.
• a polynucleotide encoding the polypeptide is used to construct an expression vector appropriate for a particular host cell.
• the host cell is transformed or transfected with the expression vector and cultured under conditions conducive to the expression of the MurD polypeptide.
• the cell is contacted with the candidate. Finally, one measures the activity of the MurD polypeptide in the presence of the candidate. If the activity is lower relative to the activity of the protein in the absence of the candidate, then the candidate is a inhibitor of the MurD polypeptide.
• the polynucleotide encodes a protein having an amino acid sequence of SEQ ID NO:2 or a naturally occurring mutant of polymorphic form thereof. In other preferred embodiments, the polynucleotide has the sequence of SEQ LD NO: 1.
• the relative activity of MurD is determined by comparing the activity of the MurD in a host cell. In some embodiments, the host cell is disrupted and the candidate is contacted to the released cytosol. In other embodiments, the cells can be disrupted contacting with the candidate and before determining the activity of the MurD protein. Finally, according to this aspect the relative activity can determined by comparison to a previously measured or expected activity value for the MurD activity in the host under the conditions.
• the relative activity is determined by measuring the activity of the Mur D in a control cell that was not contacted with a candidate compound.
• the host cell is a pseudomonad and the protein inhibited is the MurD produced by the pseudomonad.
• An aspect of this invention is a compound that is an inhibitor of a P. aeruginosa MurD protein an assay described herein.
• the compound is an inhibitor of a P. aeruginosa MurD protein produced by a host cell comprising an expression vector of this invention.
• the compound is also an inhibitor of MurD protein produced by a pathogenic strain P. aeruginosa and also inhibits the growth of said pseudomonad.
• An aspect of this invention is a pharmaceutical preparation that includes an inhibitor of P. aeruginosa MurD and a pharmaceutically acceptable carrier.
• An aspect of this invention is a method of treatment comprising administering a inhibitor of the P. aeruginosa MurD to a patient.
• the treatment can be prophylactic or therapeutic.
• the appropriate dosage for a particular patient is determined by a physician. By “about” it is meant within approximately 10-20% greater or lesser than particularly stated.
• an “inhibitor” is a compound that interacts with and inhibits or prevents a polypeptide of MurD from catalyzing the ATP-dependent addition of D-glutamate to an alanyl residue of the UDP-N-acetylmuramyl-L-alanine precursor.
• a “modulator” is a compound that interacts with an aspect of cellular biochemistry to effect an increase or decrease in the amount of a polypeptide of MurD present in, at the surface or in the periplasm of a cell, or in the surrounding serum or media. The change in amount of the MurD polypeptide can be mediated by the effect of a modulator on the expression of the protein, e.g.
• a modulator can act by accelerating or decelerating the turnover of the protein either by direct interaction with the protein or by interacting with another component(s) of cellular biochemistry which directly or indirectly effects the change.
• FIGS. 1A & IB Nucleotide sequence (SEQ LD NO: 1) and the predicted amino acid sequence (SEQ LD NO:2) of P. aeruginosa murD.
• the amino acid sequence (SEQ ID NO:2) is presented in three-letter code below the nucleotide sequence (nucleotides 51 to 1395 of SEQ ID NO: 1).
• This invention provides polynucleotides and polypeptides of a cell wall biosynthesis gene from Pseudomonas aeruginosa, referred to herein as MurD.
• the polynucleotides and polypeptides are used to further provide expression vectors, host cells comprising the vectors, probes and primers, antibodies against the MurD protein and polypeptides thereof, assays for the presence or expression of MurD and assays for the identification of modulators and inhibitors of MurD.
• the murD gene was cloned from Pseudomonas aeruginosa. Sequence analysis of the P. aeruginosa murD gene revealed an open reading frame of 448 amino acids. The deduced amino acid sequence of P. aeruginosa MurD is homologous to MurD from Escherichia coli, Haemophilus influenza, Bacillus subtilis and S. aureus . Recombinant MurD protein from P. aeruginosa was over-produced as His-tagged fusion protein in Escherichia coli host cells. The P. aeruginosa MurD enzyme was purified to apparent homogeneity.
• nucleic acids encoding murD from Pseudomonas aeruginosa are useful in the expression and production of the P. aeruginosa MurD protein.
• the nucleic acids are also useful in providing probes for detecting the presence of P. aeruginosa.
• a preferred aspect of the present invention is an isolated nucleic acid encoding a MurD protein of Pseudomonas aeruginosa.
• a preferred embodiment is a nucleic acid having the sequence disclosed in FIG. 1, SEQ ID NO:l and disclosed as follows:
• the isolated nucleic acid molecule of the present invention can include a ribonucleic or deoxyribonucleic acid molecule, which can be single (coding or noncoding strand) or double stranded, as well as synthetic nucleic acid, such as a synthesized, single stranded polynucleotide.
• the present invention also relates to recombinant vectors and recombinant hosts, both prokaryotic and eukaryotic, which contain the substantially purified nucleic acid molecules disclosed throughout this specification.
• polynucleotide is a nucleic acid of more than one nucleotide.
• a polynucleotide can be made up of multiple polynucleotide units that are referred to by description of the unit.
• a polynucleotide can comprise within its bounds a polynucleotide(s) having a coding sequence(s), a polynucleotide(s) that is a regulatory region(s) and/or other polynucleotide units commonly used in the art.
• an "expression vector” is a polynucleotide having regulatory regions operably linked to a coding region such that, when in a host cell, the regulatory regions can direct the expression of the coding sequence.
• the use of expression vectors is well known in the art. Expression vectors can be used in a variety of host cells and, therefore, the regulatory regions are preferably chosen as appropriate for the particular host cell.
• a “regulatory region” is a polynucleotide that can promote or enhance the initiation or termination of transcription or translation of a coding sequence.
• a regulatory region includes a sequence that is recognized by the RNA polymerase, ribosome, or associated transcription or translation initiation or termination factors of a host cell. Regulatory regions that direct the initiation of transcription or translation can direct constitutive or inducible expression of a coding sequence.
• Polynucleotides of this invention contain full length or partial length sequences of the MurD gene sequences disclosed herein.
• Polynucleotides of this invention can be single or double stranded. If single stranded, the polynucleotides can be a coding, "sense,” strand or a complementary, "antisense,” strand.
• Antisense strands can be useful as modulators of the gene by interacting with RNA encoding the MurD protein. Antisense strands are preferably less than full length strands having sequences unique or specific for RNA encoding the protein.
• the polynucleotides can include deoxyribonucleotides, ribonucleotides or mixtures of both.
• the polynucleotides can be produced by cells, in cell-free biochemical reactions or through chemical synthesis.
• Non-natural or modified nucleotides including inosine, methyl-cytosine, deaza-guanosine, etc., can be present.
• Natural phosphodiester internucleotide linkages can be appropriate.
• polynucleotides can have non-natural linkages between the nucleotides.
• Non-natural linkages are well known in the art and include, without limitation, methylphosphonates, phosphorothioates, phosphorodithionates, phosphoroamidites and phosphate ester linkages.
• Dephospho-linkages are also known, as bridges between nucleotides. Examples of these include siloxane, carbonate, carboxymethyl ester, acetamidate, carbamate, and thioether bridges.
• Plastic DNA having, for example, N-vinyl, methacryloxyethyl, methacrylamide or ethyleneimine internucleotide linkages, can be used.
• PNA Peptide Nucleic Acid
• PNA is also useful and resists degradation by nucleases. These linkages can be mixed in a polynucleotide.
• purified and isolated nucleic acid molecules can be manipulated by the skilled artisan, such as but not limited to sequencing, restriction digestion, site-directed mutagenesis, and subcloning into expression vectors for a nucleic acid fragment as well as obtaining the wholly or partially purified protein or protein fragment so as to afford the opportunity to generate polyclonal antibodies, monoclonal antibodies, or perform amino acid sequencing or peptide digestion.
• nucleic acids claimed herein can be present in whole cells or in cell lysates or in a partially or substantially purified form. It is preferred that the molecule be present at a concentration at least about five-fold to ten-fold higher than that found in nature.
• a polynucleotide is considered substantially pure if it is obtained purified from cellular components by standard methods at a concentration of at least about 100-fold higher than that found in nature.
• a polynucleotide is considered essentially pure if it is obtained at a concentration of at least about 1000-fold higher than that found in nature.
• a chemically synthesized nucleic acid sequence is considered to be substantially purified when purified from its chemical precursors by the standards stated above.
• a preferred aspect of the present invention is a substantially purified form of the MurD protein from Pseudomonas aeruginosa.
• a preferred embodiment is a protein that has the amino acid sequence which is shown in FIG. 1, in SEQ LD NO:2 and disclosed as follows:
• polynucleotide and polypeptide sequences provided herein to isolate polynucleotides encoding naturally occurring forms of MurD, one of skill in the art can determine whether such naturally occurring forms are mutant or polymorphic forms of MurD by sequence comparison. One can further determine whether the encoded protein, or fragments of any MurD protein, is biologically active by routine testing of the protein of fragment in a in vitro or in vivo assay for the biological activity of the MurD protein.
• N-terminal or C-terminal truncations, or internal additions or deletions in host cells and test for their ability to catalyze the ATP-dependent addition of D-glutamate to an alanyl residue of the UDP-N-acetylmuramyl-L-alanine precursor.
• this invention is also directed to those DNA sequences encode RNA comprising alternative codons which code for the eventual translation of the identical amino acid, as shown below:
• the present invention discloses codon redundancy which can result in different DNA molecules encoding an identical protein.
• a sequence bearing one or more replaced codons will be defined as a degenerate variation.
• mutations either in the DNA sequence or the translated protein which do not substantially alter the ultimate physical properties of the expressed protein. For example, substitution of valine for leucine, arginine for lysine, or asparagine for glutamine may not cause a change in functionality of the polypeptide.
• DNA sequences coding for a peptide can be altered so as to code for a peptide having properties that are different than those of the naturally occurring peptide.
• Methods of altering the DNA sequences include but are not limited to site directed mutagenesis. Examples of altered properties include but are not limited to changes in the affinity of an enzyme for a substrate.
• a "biologically active equivalent” or “functional derivative” of a wild-type MurD possesses a biological activity that is substantially similar to the biological activity of a wild type MurD.
• the term “functional derivative” is intended to include the “fragments,” “mutants,” “variants,” “degenerate variants,” “analogs,” “orthologues,” and “homologues” and “chemical derivatives” of a wild type MurD protein that can catalyze the ATP-dependent addition of D- glutamate to an alanyl residue of the UDP-N-acetylmuramyl-L-alanine precursor.
• fragment refers to any polypeptide subset of wild-type MurD.
• mutant is meant to refer to a molecule that may be substantially similar to the wild- type form but possesses distinguishing biological characteristics. Such altered characteristics include but are in no way limited to altered substrate binding, altered substrate affinity and altered sensitivity to chemical compounds affecting biological activity of the MurD or MurD functional derivative.
• variant refers to a molecule substantially similar in structure and function to either the entire wild-type protein or to a fragment thereof. A molecule is "substantially similar” to a wild-type MurD-like protein if both molecules have substantially similar structures or if both molecules possess similar biological activity.
• analog refers to a molecule substantially similar in function to either the full-length MurD protein or to a biologically active fragment thereof.
• a "polymorphic" MurD is a MurD that is naturally found in the population of Pseudomonads at large.
• a polymorphic form of MurD can be encoded by a different nucleotide sequence from the particular murD gene disclosed herein as SEQ LD NO: 1.
• SEQ LD NO: 1 SEQ LD NO: 1
• a polymorphic murD gene can encode the same or different amino acid sequence as that disclosed herein.
• some polymorphic forms MurD will exhibit biological characteristics that distinguish the form from wild-type MurD activity, in which case the polymorphic form is also a mutant.
• a protein or fragment thereof is considered purified or isolated when it is obtained at least partially free from it's natural environment in a composition or purity not found in nature. It is preferred that the molecule be present at a concentration at least about five-fold to ten-fold higher than that found in nature. A protein or fragment thereof is considered substantially pure if it is obtained at a concentration of at least about 100-fold higher than that found in nature. A protein or fragment thereof is considered essentially pure if it is obtained at a concentration of at least about 1000-fold higher than that found in nature. We most prefer proteins that have been purified to homogeneity, that is, at least 10,000 -100,000 fold.
• Polynucleotide probes comprising full length or partial sequences of SEQ LD NO: 1 can be used to determine whether a cell or sample contains P. aeruginosa MurD DNA or RNA.
• the effect of modulators that effect the transcription of the murD gene can be studied via the use of these probes.
• a preferred probe is a single stranded antisense probe having at least the full length of the coding sequence of MurD. It is also preferred to use probes that have less than the full length sequence, and contain sequences specific for P. aeruginosa murD DNA or RNA.
• the identification of a sequence(s) for use as a specific probe is well known in the art and involves choosing a sequence(s) that is unique to the target sequence, or is specific thereto.
• polynucleotides that are probes have at least about 25 nucleotides, more preferably about 30 to 35 nucleotides.
• the longer probes are believed to be more specific for P. aeruginosa murD gene(s) and RNAs and can be used under more stringent hybridization conditions. Longer probes can be used but can be more difficult to prepare synthetically, or can result in lower yields from a synthesis. Examples of sequences that are useful as probes or primers for P. aeruginosa murD gene(s) are Primer A (sense)
• polynucleotides having sequences that are unique or specific for P. aeruginosa murD can be used as primers in amplification reaction assays. These assays can be used in tissue typing as described herein. Additionally, amplification reactions employing primers derived from P. aeruginosa murD sequences can be used to obtain amplified P. aeruginosa murD DNA using the murD DNA of the cells as an initial template. The murD DNA so obtained can be a mutant or polymorphic form of P.
• aeruginosa murD that differs from SEQ LD NO:l by one or more nucleotides of the MurD open reading frame or sequences flanking the ORF. The differences can be associated with a non-defective naturally occurring form or with a defective form of MurD.
• polynucleotides of this invention can be used in identification of various polymorphic P. aeruginosa murD genes or the detection of an organism having a P. aeruginosa murD gene.
• Many types of amplification reactions are known in the art and include, without limitation, Polymerase Chain Reaction, Reverse Transcriptase Polymerase Chain Reaction, Strand Displacement Amplification and Self-Sustained Sequence Reaction. Any of these or like reactions can be used with primers derived from SEQ ID NO: 1.
• a variety of expression vectors can be used to express recombinant MurD in host cells.
• Expression vectors are defined herein as nucleic acid sequences that include regulatory sequences for the transcription of cloned DNA and the translation of their mRNAs in an appropriate host.
• Such vectors can be used to express a bacterial gene in a variety of hosts such as bacteria, bluegreen algae, plant cells, insect cells and animal cells. Specifically designed vectors allow the shuttling of genes between hosts such as bacteria-yeast or bacteria-animal cells.
• An appropriately constructed expression vector should contain: an origin of replication for autonomous replication in host cells, selectable markers, a limited number of useful restriction enzyme sites, a potential for high copy number, and regulatory sequences.
• a promoter is defined as a regulatory sequence that directs RNA polymerase to bind to DNA and initiate RNA synthesis.
• a strong promoter is one which causes mRNAs to be initiated at high frequency.
• Expression vectors can include, but are not limited to, cloning vectors, modified cloning vectors, specifically designed plasmids or viruses.
• bacterial expression vectors can be used to express recombinant MurD in bacterial cells.
• Commercially available bacterial expression vectors which are suitable for recombinant MurD expression include, but are not limited to pQE (Qiagen), pETl la or pET15b (Novagen), lambda gtl 1 (Invitrogen), and pKK223-3 (Pharmacia).
• MurD DNA in cell-free transcription- translation systems, or murD RNA in cell-free translation systems.
• Cell-free synthesis of MurD can be in batch or continuous formats known in the art.
• a variety of host cells can be employed with expression vectors to synthesize MurD protein. These can include E. coli, Bacillus, and Salmonella. Insect and yeast cells can also be appropriate.
• MurD polypeptides can be recovered.
• Several protein purification procedures are available and suitable for use.
• MurD protein and polypeptides can be purified from cell lysates and extracts, or from culture medium, by various combinations of, or individual application of methods including ultrafiltration, acid extraction, alcohol precipitation, salt fractionation, ionic exchange chromatography, phosphocellulose chromatography, lecithin chromatography, affinity (e.g., antibody or His-Ni) chromatography, size exclusion chromatography, hydroxylapatite adsorption chromatography and chromatography based on hydrophobic or hydrophillic interactions.
• protein denaturation and refolding steps can be employed.
• High performance liquid chromatography (HPLC) and reversed phase HPLC can also be useful. Dialysis can be used to adjust the final buffer composition.
• the MurD protein itself is useful in assays to identify compounds that modulate the activity of the protein — including compounds that inhibit the activity of the protein.
• the MurD protein is also useful for the generation of antibodies against the protein, structural studies of the protein, and structure/function relationships of the protein.
• Modulators and Inhibitors of MurD The present invention is also directed to methods for screening for compounds which modulate or inhibit a MurD protein.
• Compounds which modulate or inhibit MurD can be DNA, RNA, peptides, proteins, or non-proteinaceous organic or inorganic compounds or other types of molecules.
• Compounds that modulate the expression of DNA or RNA encoding MurD or are inhibitors of the biological function of MurD can be detected by a variety of assays.
• the assay can be a simple "yes/no" assay to determine whether there is a change in expression or function.
• the assay can be made quantitative by comparing the expression or function of a test sample with the levels of expression or function in a standard sample, that is, a control.
• a compound that is a modulator can be detected by measuring the amount of the MurD produced in the presence of the compound.
• An compound that is an inhibitor can be detected by measuring the specific activity of the MurD protein in the presence and absence of the compound.
• kits suitable for the detection and anaysis of MurD Such a kit would comprise a compartmentalized carrier suitable to hold in close confinement at least one container.
• the carrier would further comprise reagents such as recombinant MurD or anti- MurD antibodies suitable for detecting MurD.
• the carrier can also contain a means for detection such as labeled antigen or enzyme substrates or the like.
• compositions comprising a modulator or inhibitor of MurD can be formulated according to known methods such as by the admixture of a pharmaceutically acceptable carrier. Examples of such carriers and methods of formulation can be found in Remington's Pharmaceutical Sciences. To form a pharmaceutically acceptable composition suitable for effective administration, such compositions will contain an effective amount of the inhibitor.
• compositions of the invention are administered to an individual in amounts sufficient to treat, prevent or diagnose disorders.
• the effective amount can vary according to a variety of factors such as the individual's condition, weight, sex and age. Other factors include the mode of administration. The appropriate amount can be determined by a skilled physician
• compositions can be provided to the individual by a variety of routes such as subcutaneous, topical, oral and intramuscular.
• the term "chemical derivative" describes a molecule that contains additional chemical moieties which are not normally a part of the base molecule. Such moieties can improve the solubility, half-life, absorption, etc. of the base molecule. Alternatively the moieties can attenuate undesirable side effects of the base molecule or decrease the toxicity of the base molecule. Examples of such moieties are described in a variety of texts, such as Remington's Pharmaceutical Sciences.
• the present invention also provides a means to obtain suitable topical, oral, systemic and parenteral pharmaceutical formulations for use in the methods of treatment of the present invention.
• the compositions containing compounds identified according to this invention as the active ingredient can be administered in a wide variety of therapeutic dosage forms in conventional vehicles for administration.
• the compounds can be administered in such oral dosage forms as tablets, capsules (each including timed release and sustained release formulations), pills, powders, granules, elixirs, tinctures, solutions, suspensions, syrups and emulsions, or by injection.
• compounds of the present invention can be administered in a single daily dose, or the total daily dosage can be administered in divided doses of two, three or four times daily.
• compounds for the present invention can be administered in intranasal form via topical use of suitable intranasal vehicles, or via transdermal routes, using those forms of transdermal skin patches well known to those of ordinary skill in that art.
• the dosage administration will, of course, be continuous rather than intermittent throughout the dosage regimen.
• the active agents can be administered concurrently, or they each can be administered at separately staggered times.
• the dosage regimen utilizing the compounds of the present invention is selected in accordance with a variety of factors including type, species, age, weight, sex and medical condition of the patient; the severity of the condition to be treated; the route of administration; the renal, hepatic and cardiovascular function of the patient; and the particular compound thereof employed.
• a physician or veterinarian of ordinary skill can readily determine and prescribe the effective amount of the drug required to prevent, counter or arrest the progress of the condition.
• Optimal precision in achieving concentrations of drug within the range that yields efficacy without toxicity requires a regimen based on the kinetics of the drug's availability to target sites. This involves a consideration of the distribution, equilibrium, and elimination of a drug.
• Genomic DNA from P. aeruginosa was prepared from 100 ml late stationary phase culture in Brain Heart Infusion broth (Difco, Detroit, MI). Cells were washed with 0.2 M sodium acetate, suspended in 10 ml of TEG (100 mM Tris, pH 7, containing 10 mM EDTA and 25% glucose) and lysed by incubation with 200 ⁇ g of N-acetylmuramidase (Sigma) for lh at 37°C. Chromosomal DNA was purified from the cell lysate using a Qiagen (Santa Clarita, CA) genomic DNA preparation kit and following the manufacturers protocol.
• TEG 100 mM Tris, pH 7, containing 10 mM EDTA and 25% glucose
• the cell lysate was treated with protease K at 50°C for 45 min, loaded onto an equilibrated Qiagen genomic tip, entered into the resin by centrifugation at 3000 rpm for 2 min. Following washing the genomic tip, the genomic DNA was eluted in distilled water and kept at 4°C. Approximately 50 ng genomic DNA was used as a template in PCR reactions to clone murD.
• oligonucleotide primers (Gibco/BRL, Bethesda, MD) complementary to sequences at the 5' and the 3' ends of P. aeruginosa murD were used to clone this gene using KLENTAQ ADVANTAGETM polymerase (Clontech, Palo Alto, CA).
• the primer nucleotide sequences were as follows: 5 ' -TCTCG AG ATG AGCCTGATCGCCTC-3 ' (SEQ ID NO:3) (a Xhol linker plus nucleotides 51-67 of SEQ LD NO: 1) and 5 ' -TTGG ATCCTC ACGCT AGCTCCTCT AC-3 ' (SEQ ID NO:4) (a BamHI linker plus the complement of nucleotides 1378-1395 of SEQ LD NO: 1).
• SEQ ID NO:3 a Xhol linker plus nucleotides 51-67 of SEQ LD NO: 1
• 5 ' -TTGG ATCCTC ACGCT AGCTCCTCT AC-3 ' SEQ ID NO:4
• aeruginosa murD was verified by nucleotide sequence, digested with Xhol and BamHI, and cloned between the Xhol and BamHI sites of pET-15b, creating plasmid pPaeMurD. This plasmid was used for expression of the murD gene in E. coli. The plasmid pPaeMurD has been deposited with the American Type
• the nucleotide sequence of murD determined in both orientations, and the deduced amino acid sequence of the MurD protein is depicted in FIG. 1.
• aeruginosa MurD protein GlySerAspGlyLysThrThr (codons 116 to 122, SEQ ID NO:2). While region I is an ATP -binding domain (Ikeda, et al, 1990), the functions of the other homologous regions is unknown. All four homologous regions are conserved in the P. aeruginosa MurD.
• murD was cloned into the expression vector pET-15b (Novagen) as described above to create plasmid pPaeMurD.
• the pET-15b vector incorporates the 6xHistidine-tag into the protein construct to allow rapid purification of MurD by affinity chromatography.
• the pET (Plasmids for Expression by T7 RNA polymerase) plasmids are derived from pBR322 and designed for protein over-production in E. coli.
• the vector pET-15b contains the ampicillin resistance gene, ColEl origin of replication in addition to T7 phage promoter and terminator.
• the T7 promoter is recognized by the phage T7 RNA polymerase but not by the E. coli RNA polymerase.
• a host E coli strain such as BL21(DE3)pLysS is engineered to contain integrated copies of T7 RNA polymerase under the control of lacUV5 that is inducible by LPTG. Production of a recombinant protein in the E. coli strain BL21(DE3)pLysS occurs after expression of T7RNA polymerase is induced.
• the pPaeMurD plasmid was introduced into the host strain BL21
• Cultures containing either the recombinant plasmid pPaeMurD or the control plasmid vector, pET-15b were grown at 30°C and induced with IPTG.
• Cells transformed with pPaeMurD contained an inducible protein of approximately 51 kDa, corresponding to the expected size of P. aeruginosa MurD protein as shown by SDS- PAGE. There were no comparable detectable protein bands after induction of cells transformed with the control plasmid vector, pET-15b. Purification of recombinant MurD enzyme.
• the cell pellet from 100 ml of induced culture prepared as described above was resuspended in 10 ml BT buffer (50 mM bis-tris-propane, pH 8.0, containing 100 mM potassium chloride and 1% glycerol) at 4°C. Cells were lysed either by freeze-thaw or by French Press. After centrifugation, the supernatant was mixed with 15 ml of freshly prepared TALONTM (Clontech) resin and incubated for 30 min at room temp. The resin was washed twice by centrifugation with 25 ml of BT buffer at room temperature.
• the resin was loaded into a column and washed with 20 ml of BT, pH 7.0, containing 5 mM imidazole. Protein was eluted with 20 ml of BT buffer pH 8.0, containing 100 mM imidazole. Fractions (0.5 ml) were collected and analyzed by SDS-Gel electrophoresis. This resulted in a partially purified preparation of P. aeruginosa MurD protein that could be used in activity assays. The protein may be purified further, if desired, using methods known in the art. Assay for activity of MurD enzyme.
• the ATP-dependent MurD activity was assayed by monitoring the formation of product ADP using the pyruvate kinase and lactate dehydrogenase coupled enzyme assay. The reaction was monitored spectrophotometrically. Typically, the assay contained 100 mM BIS-TRIS-propane, pH 8.0,
• the mixture was incubated at 25°C for 5 min and the reaction initiated by the addition of 1-10 ⁇ g of MurD.
• These conditions are one example of an assay useful for evaluating the activity of MurD.
• Other assays can be used, or amounts of buffers, substrate and enzyme can be changed, as desired, to alter the rate of production of ADP.
• P. aeruginosa MurD was partially purified as described above. Assays have been conducted using 120 and 350 ⁇ M UDP-N-acetylmuramyl-L-alanine. However, it has been observed that at the higher level of 350 ⁇ M UDP-N-acetyl-muramyl-L-alanine, substrate inhibition of the E. coli MurD occurs. At the lower level, the specific activity of the E. coli enzyme can be in the area of 8 units/mg. It is unclear whether the P. aeruginosa enzyme is similarly inhibited.
• Example 4 One assay for the measurement of the activity of MurD is provided in Example 4. That assay, and other assays for MurD activity can be adapted for screening assays to detect inhibitors of MurD. For example, for inhibition assays, inhibitors in DMSO are added at the desired concentration to the assay mixture. In a separate, control reaction, only DMSO is added to the assay mixture. The reactions are initiated by the addition of enzyme (MurD). Rates are calculated as described above. Relative activities are calculated from the equation 1 :
• Inhibition constant (IC50) values are determined from a range of inhibitor concentrations and calculated from equation 2.
• relative activity 1/(1 + [I]/ICso) (2)
• inhibitors of MurD that result in relative activities of the MurD enzyme of at least less than 75%, more preferably, 25-50% or 10-25%.
• a patient presenting with an indication of infection with a microorganism susceptible to inhibitors of MurD can be treated by administration of inhibitors of MurD.
• Physicians skilled in the art are familiar with administering therapeutically effective amounts of inhibitors or modulators of microbial enzymes. Such skilled persons can readily determine an appropriate dosing scheme to achieve a desired therapeutic effect.
• Therapy can also be prophylactic.
• a patient at risk for developing a bacterial infection, including infection with P. aeruginosa can be treated by administration of inhibitors of MurD.
• Physicians skilled in the art are familiar with administering therapeutically effective amounts of inhibitors or modulators of microbial enzymes. Such skilled persons can readily determine an appropriate dosing scheme to achieve a desired therapeutic effect.

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