WO2018017814A1 - Peptidoglycan glycosyltransferase inhibitors of sed proteins for treating bacterial infections - Google Patents

Abstract

Disclosed herein are novel compositions and methods for the inhibition of SEDs proteins. Such compositions and methods are useful, for example, for the treatment of bacterial infections. Also disclosed herein are methods of determining whether a test agent is an inhibitor of SEDs protein activity.

Description

PEPTIDOGLYCAN GLYCOSYLTRANSFERASE INHIBITORS OF SED PROTEINS FOR

TREATING BACTERIAL INFECTIONS

RELATED APPLICATIONS

This application claims the benefit of priority to U.S. Provisional Application No.

62/364,582 filed July 20, 2016, which is hereby incorporated in its entirety.

STATEMENT OF RIGHTS

This invention was made with government support under grant numbers GM073831 , GM092616, AI083365-01 , and U19 AI 109764, awarded by The National Institutes of

Health. The government has certain rights in the invention.

BACKGROUND

The rapid emergence of antimicrobial drug resi stance has been recognized as an epidemic of global proportions. Many pathogenic bacteria, particularly in hospital acquired infections, are multiply resistant to several classes of antibiotics, effectively narrowing therapeutic options.

The SEDS (shape, elongation, division, and sporulation) family of proteins is required for cell wall biogenesis during bacterial growth and division. Accordingly, SEDS proteins may be important targets for the treatment of bacterial infections. Thus, there is a great need to characterize SEDS proteins and to define their biochemical activities in order to develop novel compositions and methods for the treatment of pathological bacterial

infections.

SUMMARY

Provided herein are methods of inhibiting bacterial cell wall synthesis comprising contacting a bacteria with an agent (e.g., a small molecule) that inhibits the peptidoglycan (PG) glycotransferase activity of a SEDS protein. In some embodiments, the agent is an inhibitor}' nucleic acid, such as a RNAi molecule or an antisense oligonucleotide (ASO). In some embodiments, the agent is an antibody (e.g., an antibody specific for a SEDS protein, such as RodA). In some aspects, provided herein are methods of treating or preventing a bacterial infection in a subject comprising administering to the subject an agent that inhibits the peptidoglycan glycotransferase activity of a SEDS protein of a bacteria. In some

embodiments, the SEDS protein is RodA. In some embodiments, the bacteria is a Gram- positive bacteria. In other embodiments, the bacteria is a Gram-negative bacteria (e.g.,

Francisella tularensis or Chlamydia trachomatis) . In some embodiments, the bacteria

Mycobacterium tuberculosis. In some embodiments, the bacteria is Staphylococcus aureus, Staphylococcus epiderrnidis, Enterococcus faecal is, Streptococcus pneumonia.

Streptococcus pyogenes, Moraxella catarrhalis, Escherichia coli, Eriterobacter cloacae, Klebsiella pneumonia, Proteus mirabilis, Pseudomonas aeruginosa, Salmonella enterica, Salmonella bongori or Acinetobacter baumannii. In some embodiments, the bacteria is resistant to one or more antibiotics {e.g., moenomycins, isoniazid, rifampicin, ethambutol, pyrazinamide, aminoglycosides, ansamycins, carbacephems, carbapenems, cephalosporins, glycopeptides, lincosamides, lipopeptides, macrolides, monobactams, nitrofurans,

oxazolidonones, penicillins, polypeptide antibiotics, quinolones, fluoroquinolone, sulfonamides, tetracyclines, and anti-mycobacterial compounds ). The agent (e.g., a small molecule) may target an extracytopiasmic catalytic center of the SEDS protein. In some embodiments, the methods provided herein further comprising the step of contacting the bacteria with a second antibiotic agent (e.g., moenomycins, isoniazid, rifampicin,

ethambutol, pyrazinamide, aminoglycosides, ansamycins, carbacephems, carbapenems, cephalosporins, glycopeptides, lincosamides, lipopeptides, macrolides, monobactams, nitrofurans, oxazolidonones, penicillins, polypeptide antibiotics, quinolones,

fluoroquinolone, sulfonamides, tetracyclines, and anti-mycobacierial compounds ). In some embodiments, the bacterial infection is gastrointestinal infections, urinary tract infections, infections of skin and skin structure including wounds, cellulitis, and abscesses, ear, nose and throat infections, respiratory infections (e.g., pneumonias) or sexually transmitted bacterial infections.

In some embodiments, the agent is administered orally, intravenously, topically, parenteral!}', intramuscularly, or intraocularly.

Further provided herein are methods of determining whether an agent inhibits bacterial cell wall synthesis, the method comprising forming a test reaction mixture (i.e., comprising a SEDS protein, lipid II, a heptaprenvi alkyl chain: and a test agent), incubating the test reaction mixture under conditions conducive for the polymerization of the lipid Π by the SEDS protein, and determining the level of lipid II polymerization in the test reaction mixture; wherein an agent that reduces the amount of lipid II polymerization in the text reaction mixture compared to the amount of lipid Π polymeri zation in a control reaction mixture is an inhibitor of bacterial cell wall synthesis. In some embodiments, the SEDS protein is RodA. In some embodiments, the test agent is a small molecule. In some embodiments, the control reaction mixture is substantially identical to the test reaction mixture except that the control reaction mixture does not comprise the test agent. In some embodiments, the control reaction mixture is substantially identical to the test reaction mixture except that the control reaction mixture comprises a placebo agent instead of the test agent.

BRIEF DESCRIPTION OF THE DRAWINGS

Figure 1 is composed of six parts. A, B, C, D, E, and F. Figure 1A shows cells lacking the penicillin binding proteins (aPBPs) are capable of dividing. Part B though Part F shows cells lacking all four aPBPs exhibited GFP-Mbl dynamics that were qualitatively and

quantitatively similar to wild-type B. subtilis.

Figure 2 is an illustration of O-antigen ligase, a polytopic membrane protein

glycosyltransferase that carries out the en bloc transfer of undecaprenyl-pyrophosphate- linked O-antigen polymers to a Lipid A-core glycolipid acceptor. Also included in the illustration is PglB Oligosaccharylttansferase, O-Antigen Polymerase, and a SEDS protein. Figure 3 consists of four parts A, B, C, and D. Part A shows a ~10-fold over-production of RodA-HislO significantly alleviated the growth defect of a Rod A quadruple mutant. Figure B and C show examination of these cells by fluorescence microscopy revealed nearly- complete suppression of the cell width and elevated lysis phenotypes observed in the quadniple (Δ4) mutant. Part D shows the results of a PGT activity assay using radiolabeled synthetic lipid II isolated membranes from wild-type cells, the Δ4 mutant, and the Δ4 mutant overexpressmg RodA-Hisl O. Membranes lacking the aPBPs had less activity than WT. Figure 4 consists of five parts, A, B, C, D, and E. Part A shows FLAG-RodA,

immunopurified from, detergent-solubilized membranes and eluted with EDTA and FLAG peptide, is estimated to be 60% pure . Parts B and C show the conversion of lipid II into glycan chains in vitro, catalyzed by FLAG-RodA. Part D shows resistance of B. subtilis to moenomycin is dependent upon the extracytoplasmic function (ECF) sigma factor SigM (σ^¹). Part E shows cells lacking all four aPBPs require sigM for viability .

Figure 5 consists of four parts, A, B, C , and D. Part A and B show that directed movement was sensitive to cell wall synthesis inhibitors vancomycin and ampicillin. Parts C and D show GFP-Mbl dynamics in wild-type cells were unperturbed by moenomycin, an inhibitor of the glycosyltransferase activity of aPBPs.

Figure 6 is an illustration of the genetic linkage of bPBPs and SEDS proteins. These two protein families are represented in the RodA complex and the divisome. The bPBPs crosslink the stem, peptides on the glycan strands and the SEDS (Shape, Elongation, Division and Sporulation) family have an unknown function. The bPBPs and SEDS proteins are thought to work together as a subcomplex, and are genetically linked in many bacteria.

Figure 7 consists of four parts, A, B, C, and D. Parts A and B show a ~10-fold overproduction of RodA -His 10 significantly alleviated the growth defect of the Δ4 mutant. Part D shows examination of these cells by fluorescence microscopy, and that suppression of the ceil width and elevated lysis phenotypes observed in the Δ4 mutant.

Figure 8 is an illustration of transmembrane FLAG-RodA. W105 and D280 residues are predicted to be in the second and fourth extracellular loops of RodA .

Figure 9 shows several RodA mutants. Part A is an illustration of the RodA mutant expression system. Parts B through D show that alanine substitutions at two residues(W105A and D280A) within Rod A abolished RodA function in vivo without affecting protein levels, while other mutants. El 17A and E288A did not affect RodA function in vivo and did not affect RodA protein levels.

Figure 10 is composed of three parts, A , B, and C. Part A shows that rodA. suppressed the synthetic lethality of the AsigM Δ4 aPBP mutant. Part B and Part C show that ^-dependent expression of rod/1 does not affect moenomycin resistance.

Figure 11 shows phviogenetic data of SEDS and GT51. Phvlogenetic analysis indicates that SEDS family members are more broadly conserved than aPBPs. DETAILED DESCRIPTION

General

Disclosed herein are methods of inhibiting bacterial cell wail synthesis comprising contacting a bacteria with an agent that inhibits the peptidoglycan glycotransferase activity of a SEDS protein. Also provided herein are methods of preventing or treating a bacterial infection by administering, to the subject, an agent that inhibits the peptidoglycan glycotransferase activity of a SEDS protein,

Tims, in certain embodiments, the instant invention relates to methods for the treatment of bacterial infection through the inhibition of the peptidoglycan glycotransferase activity of a SEDS protein, in some embodiments, the composition that inhibits SEDS proteins is a small molecule. Agents that inhibit the activity of SEDS proteins include, for example, small molecules that may target an extracytoplasmic catalytic center of the SEDs protein. In addition, provided herein are methods of identifying an agent that inhibits the peptidoglycan glycotransferase activity of a SEDS protein, by forming a test reaction mixture (comprising lipid II, a heptaprenyl alky] chain, and a test agent), incubating the test reaction mixture under conditions conducive for the polymerization of the lipid II by the SEDS protein, and determining the level of lipid II polymerization in the test reaction mixture, wherein an agent that reduces the amount of lipid Π polymerization in the text reaction mixture compared to the amount of lipid II polymerization in a control reaction mixture is an inhibitor of bacterial cell wall synthesis.

Definitions

For convenience, certain terms employed in the specification, examples, and appended claims are collected here.

As used herein, the term administering" means providing a pharmaceutical agent or composition to a subject, and includes, but is not limited to, administering by a medical professional and self-administering. Such an agent can contain, for example, a small molecule that inhibits the peptidoglycan glycotransferase activity of a SEDS protein.

The term "agenf is used herein to denote a chemical compound, a small molecule, a mixture of chemical compounds and/or a biological macromolecule (such as a nucleic acid, an antibody, an antibody fragment, a protein or a peptide). Agents may be identified as having a particular activity by screening assays described herein below. The activity of such agents may render them suitable as a "therapeutic agent" which is a biologically, physiologically, or pharmacologically active substance (or substances) that acts locally or systemically in a subject.

The term '^'ammo acid" is intended to embrace all molecules, whether natural or synthetic, which include both an amino functionality and an acid functionality and capable of being included in a polymer of naturally-occurring amino acids. Exemplary amino acids include naturally-occurring amino acids; analogs, derivatives and congeners thereof; amino acid analogs having variant side chains; and all stereoisomers of any of the foregoing.

As used herein, the term ^''antibody' may refer to both an intact antibody and an antigen binding fragment thereof. Intact antibodies are glycoproteins that include at least two heavy (H) chains and two light (L) chains inter-connected by disulfide bonds. Each heavy chain includes a heavy chain variable region (abbreviated herein as VH) and a heavy chain constant region. Each light chain includes a light chain variable region (abbreviated herein as VL) and a light chain constant region. The VH and VL regions can be further subdivided into regions of hypervariability, termed complementarity determining regions (CDR), interspersed with regions that are more conserved, termed framework regions (FR). The term '"antibody" includes, for example, naturally occurring forms of antibodies, recombinant antibodies, single chain antibodies, monoclonal antibodies, polyclonal antibodies, chimeric antibodies, humanized antibodies, human antibodies, multispecific antibodies (e.g., bispecific antibodies), single-chain antibodies and antigen-binding antibody fragments. The term "antibody" also includes "antibody-like molecule", such as fragments of the antibodies (e.g., antigen-binding fragments). The term ^"'antibody" may also refer to an antibody mimetic. An antibody mimetic may refer to any compound that specifically binds to an antigen, and may be artificial peptides, proteins, nucleic acids, or small molecules.

The terms "antigen binding fragment and "antigen-binding portion" of an antibody, as used herein, refers to one or more fragments of an antibody that retain the ability to bind to an antigen. Examples of binding fragments encompassed within the term "antigen- binding fragment" of an antibody include Fab, Fab', F(ab')2, Fv, scFv, disulfide linked Fv, Fd, diabodies, single-chain antibodies, and other antibody fragments that retain at least a portion of the variable region of an intact antibody. These antibody fragments can be obtained using conventional recombinant and/or enzymatic techniques and can be screened for antigen binding in the same manner as intact antibodies.

As used herein, the term "monoclonal antibody" refers to an antibody obtained from a population of substantially homogeneous antibodies that specifically bind to the same epitope, i.e. , the individual antibodies comprising the population are identical except for possible naturally occurring mutations that may be present in minor amounts. The modifier "monoclonal" indicates the character of the antibody as being obtained from a substantially homogeneous population of antibodies, and is not to be constraed as requiring production of the antibody by any particular method.

The terms "polynucleotide^"', and "nucleic acid" are used interchangeably. They refer to a polym eric form of nucleotides of any length, either deoxyribonucleotides or ribonucleotides, or analogs thereof. Polynucleotides may have any three-dimensional structure, and may perform any function, known or unknown. The following are non- limiting examples of polynucleotides: coding or non-coding regions of a gene or gene fragment, loci (locus) defined from linkage analysis, exons, introns, messenger RNA (mRNA), transfer RNA, ribosomal RNA, ribozymes, cDNA, recombinant polynucleotides, branched polynucleotides, plasmids, vectors, isolated DNA of any sequence, isolated RNA of any sequence, nucleic acid probes, and primers. A polynucleotide may comprise modified nucleotides, such as methylated nucleotides and nucleotide analogs. If present, modifications to the nucleotide structure may be imparted before or after assembly of the polymer. The sequence of nucleotides may be interrupted by non-nucleotide components. A polynucleotide may be further modified, such as by conjugation with a labeling component. The term "recombinant" polynucleotide means a polynucleotide of genomic, cDNA, semisynthetic, or synthetic origin which either does not occur in nature or is linked to another polynucleotide in a non-natural arrangement.

As used herein, the term "parenteral" route means a route other than the oral and topical routes. A parenteral route that is suitable for use in the invention may be, for example, a ocular route.

The phrase "pharmaceutically-acceptable carrier" as used herein means a pharmaceutically-acceptable material, composition or vehicle, such as a liquid or solid filler, diluent, excipient, or solvent encapsulating material, involved in carrying or transporting the subject compound from one organ, or portion of the body, to another organ, or portion of the body

As used herein, the term "suhjecF means a human or non-human animal selected for treatment or therapy.

The phrases "therapeutically-effective amount" and '^"effective amount" as used herein means the amount of an agent which is effective for producing the desired therapeutic effect in at least a sub-population of cells in a subject at a reasonable benefit/risk ratio applicable to any medical treatment.

Treating" a disease in a subject or '^'treating" a subject having a disease refers to subjecting the subject to a pharmaceutical treatment, e.g. , the administration of a drug, such that at least one symptom of the disease is decreased or prevented from worsening.

Provided herein are methods of inhibiting bacterial cell wall synthesis comprising contacting a bacteria with an agent that inhibits the peptidoglycan glycotransferase activity of a SEDS protein. In some aspects, provided herein are methods of treating or preventing a bacterial infection in a subject comprising administering to the subject an agent that inhibits the peptidoglycan glycotransferase activity of a SEDS protein of a bacteria . In some embodiments, the SEDS protein is RodA. In some embodiments, the bacteria is Francisella hilar ensis or Chlamydia trachomatis . In one embodiment, the infection can be caused by an anaerobic or aerobic bacterium. In some embodiments, the bacteria is a Gram-positive bacterium, including, but not limited to, Staphylococcus spp., Streptococcus spp., Enterococcus spp., Bacillus spp., Listeria spp.; phylum Actinobacteria, including, but not limited to, Propionibacterium spp., Corynebacterium spp., Nocardia spp., Actinobacteria spp., and class Clostridia, including, but not limited to, Clostridium spp.

In another embodiment, the infection is caused by a Gram-negative bacterium. In some embodiments, the bacteria belongs to phylum Proteobactena

(e.g., Betaproteobacteria and Gammaproteobacteria), including Escherichia coli.

Salmonella, Shigella, other Enterobacteriaceae, Pseiidomonas, Moraxella, Salmonella, Helicobacter, Stenotrophomonas, B ellovibrio, acetic acid bacteria, Legionella or aipha- proteobacteria such as Wolbachia. In another aspect, the infection is caused by a Gram- negative bacterium selected from cyanobacteria, spirochaetes, green sulfur or green non- sulfur bacteria. In a specific aspect of this embodiment, the infection is caused by a Gram- negative bacteria selected from Enterobactericeae (e.g., E. coli, Klebsiella pneumoniae). Bacteroidetes (e.g., Bacteroid.es fragilis)., Vibrionaceae (Vibrio cholerae), Pasteurellaceae (e.g., Haemophilus influenzae), Pseudomonadaceae (e.g., Pseiidomonas aeruginosa), Neisseriaceae (e.g. Neisseria meningitidis), Rickettsiae, Moraxeilaceae (e.g., Moraxella catarrhalis), any species of Proteeae spp., Acinetobacter spp., Helicobacter spp., and Campylobacter spp. In some embodiments, the infection is caused by Gram-negative bacterium selected from the group consisting of Enterobactericeae (e.g., E. coli, Klebsiella pneumoniae }, Pseudomonas, and Acinetobacter spp. In other embodiments, the infection is caused by an organism selected from the group consisting of K pneumoniae, Salmonella, E. hirae, A. baumanii, M catarrhalis, H influenzae, P. aeruginosa, E. faecium, E. coli, S.

aureus, and E. faecal is. In another embodiment, the infection is caused by an organism selected from the group consisting of order Rickettsial.es: phylum Chlamydiae; order

Chlamydial.es; Legionella spp. (including L. pneumophila); class Mollicutes, including, but not limited to. Mycoplasma spp. (e.g. Mycoplasma pneumoniae ); Mycobacterium spp. (e.g. Mycobacterium tuberculosis); and phylum Spirochaetales (e.g. Borrelia spp. and Treponema spp).

In some embodiments, the infection is caused by a Category A Biodefense organism as described at http://www.bt.cdc.gov/agent/agentlist-category.asp, the entire teachings of which are incosporated herein by reference. Examples of Category A organisms include, but are not limited to, Bacillus anthracis (anthrax), Yersinia pestis (plague), Clostridium botulinum (botulism) or Francis ella tularemia (tularemia). In another embodiment the infection is a Bacillus anthracis infection. "Bacillus anthracis infection" includes any state, diseases, or disorders caused or which result from exposure or alleged exposure to Bacillus anthracis or another member of the Bacillus cereus group of bacteria. Additional infections that can be treated using compounds of the invention or a pharmaceutically acceptable salt thereof include, but are not limited to, anthrax, botulism, bubonic plague, and tularemia.

In another embodiment, the infection is caused by a Category B Biodefense organism as described at http:/ywww.bt.cdc.gov/agent/agentlist-categor\'.asp, the entire teachings of which are incorporated herein by reference. Examples of Category B organisms include, but are not limited to, Brucella spp. , Clostridium perfringens, Salmonella spp., Escherichia coli, Shigella spp. , Burkholderia mallei, Burkholdena pseudomallei. Chlamydia psittaci, Coxiella burnetii, Staphylococcal enterotoxin B, Rickettsia prowazekii, Vibrio cholerae, and

Cryptosporidium parvum. Additional infections that can be treated using agents disclosed herein include, but are not limited to. Brucellosis, Clostridium perfringens, food-borne illnesses, Glanders, Melioidosis, Psittacosis, Q fever, viral encephalitis, and water-borne illnesses. These are defined as Category B pathogens.

In other embodiments, the infection can be caused by one or more than one organism described herein. Examples of such infections include, but are not limited to, intra-abdominal infections (often a mixture of a gram-negative species like E. coli and an anaerobe like B. fragiiis), diabetic foot (various combinations of Streptococcus, Serratia, Staphylococcus and Enterococcus spp., anaerobes (S.E. Dowd, et al., PloS one 4142.1046-004, 2008:3:e3326, the entire teachings of which are incorporated herein by reference) and respiratory disease (especially in patients that have chronic infections like cystic fibrosis-e.g., S. aureus plus P. aeruginosa or H influenzae, atypical pathogens), wounds and abscesses (various gram- negative and gram-positive bacteria, notably MSSA/MRSA, coagulase-negative

staphylococci, enterococci, Acinetohacter, P. aeruginosa, E. coli, B. fragiiis), and bloodstream infections (13% were polymicrobial (Η. Wisplinghoff, et al.,Clin. Infect. Dis. 2004:39:311-317, the entire teachings of which are incorporated herein by reference)).

In one embodiment, the infection is caused by an organism resistant to one more antibiotics.

In another embodiment, the infection is caused by an organism resistant to tetracycline or any member of first and second generation of tetracycline antibiotics (e.g., doxycycline or minocycline). In another embodiment, the infection is caused by an organism resistant to methicillin.

In another embodiment, the infection is caused by an organism resistant to vancomycm.

In another embodiment, the infection is caused by an organism resistant to a quinolone or fluoroquinolone.

In another embodiment, the infection is caused by bacteria resistant to

tigecycline or any other tetracycline derivative. In a particular embodiment, the infection is caused by a bacteria resistant or nonsusceptible to tigecycline. In anotlier embodiment, the infection is caused by an organism resistant to macrolides, imcosamides, streptogramin antibiotics, oxazolidinones, tetracycline and/or pleuromutilins. In another embodiment, the infection is caused by an organism resistant or nonsusceptible to PTK0796 (7

dimethylamino, 9-(2,2-dimethyl-propyl)-aminomethylcycline ).

In another embodiment, the infection is caused by a multidrug-resistant pathogen (having intermediate or full resistance to any two or more antibiotics).

In some aspects, provided herein are methods that can be used to prevent or treat a bacterial infection or disease in a subject by administering to the subject, an agent that inhibits the peptidoglycan glycotransferase activity of a SEDS protein. The subject may be a mammal. In some embodiments, the subject is a human. In some embodiments, infections or diseases may include, but are not limited to, infections of skin and skin structure including wounds, cellulitis, and abscesses, ear, nose and throat infections, GI infections, urinary tract infections, genito-urinary infections, respiratory tract infections, sinuses infections, middle ear infections, systemic infections, intra-abdominal infections, pyelonephritis, pneumonia ( CABP, hospital-acquired, healthcare-associated, chronic pneumonias, such as Nocardia, Actinomyces and Blastomyces dermatitidis, as well as the granulomatous pneumonias, Mycobacterium tuberculosis and atypical mycobacteria, Histoplasma capsulatum and Coccidioides immitis, bacterial vaginosis, streptococcal sore throat, chronic bacterial prostatitis, gynecological and pelvic infections, sexually transmitted bacterial diseases, ocular and otic infections, cholera, influenza, bronchitis, acne, psoriasis, rosacea, impetigo, malaria, sexually transmitted disease including syphilis and gonorrhea, Legionnaires' disease, Lyme disease, Rocky Mountain spotted fever, Q fever, typhus, bubonic plague, gas gangrene, hospital acquired infections, leptospirosis, whooping cough, anthrax and infections caused by the agents responsible for lymphogranuloma venereum, inclusion conjunctivitis, or psittacosis.

The present invention further relates to a method of treating hospital-acquired or community-acquired bacterial infections in a human subject comprising the step of

administering to the subject a therapeutically effective amount agent that inhibits the peptidoglycan glycotransferase activity of a SEDS protein.

In some embodiments, the community-acquired bacterial pneumonia (CABP) is characterized by the presence of one or more CABP pathogens selected from Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis Staphylococcus aureus, Streptococcus pyogenes, Legionella pneumophila, Chlamydia pneumoniae, and Mycoplasma pneumoniae.

The invention also relates to a method of treating hospital -acquired bacterial pneumonia in a human subject in need of treatment comprising the step of administering to the subject a therapeutically effective amount of an agent, wherein the hospital -acquired bacterial pneumonia is characterized by the present of Streptococcus pneumoniae.

Haemophilus influenzae, Staphylococcus aureus, Escherichia coli or Klebsiella pneumonia.

The invention also relates to a method of causing a reduction in the amount of a bacterial strain selected from. MRSA and S. pneumoniae present in a human subject comprising the step of administering to the subject an agent or pharmaceutical composition disclosed herein that inhibits peptidoglycan glycotransferase activity of a SEDS protein. In one embodiment, the bacteria is methicillin-resistant Staphylococcus aureus USA 300.

The invention also relates to a method of treating complicated urinary tract infections including pyelonephritis in a human subject comprising the step of administering to the subject a therapeutically effective amount of an agent disclosed herein or a pharmaceutical composition comprising the agent, wherein the urinary pathogens can be effectively treated. In certain embodiments, the urinary pathogens are selected from: Escherichia coli and Klebsiella pneumoniae, including strains producing extended -spectrum— lactamases and/or carbapenemresisiani strains; other Enterobacteriaceae species (Proteus mirabilis, Proteus vulgaris, Citrohacter freudii, etc.) and Acinetohacter haumannii. Other urinary pathogens include a number of gram-positive species: enterococci, including vancomycin-resistant isolates, and staphylococci (including but not limited to MRSA and Staphylococcus epidermidis) are often the causative pathogen especially when an urinary catheter has been placed. Further disclosed herein are novel therapeutic methods of inhibiting bacterial wall synthesis comprising contacting a bacteria with an agent that inhibits the peptidoglycan glycotransferase activity of a SEDS protein.

In some embodiments, the present invention provides therapeutic methods of treating a bacterial disease or infection, comprising administering to a subject, (e.g., a subject in need thereof), an effective amount of an agent that inhibits SEDS expression or activity . In some embodiments the present invention provides therapeutic methods of inhibiting SEDS protein activity or treating bacterial infections.

When used for treating bacterial infections, such methods may comprise

administering agents described herein in conjunction with one or more antibiotics agents, including, for example, moenomycins, isoniazid, rifampicin, ethambutol, pyrazinamide, aminoglycosides, ansamycins, carbacephems, carbapenems, cephalosporins, glycopeptides, lincosamides, lipopeptides, macrolides, monobactams, nitrofurans, oxazolidonones, penicillins, polypeptide antibiotics, quinolones, fluoroquinolone, sulfonamides, tetracyclines, and aiiti-mycobacterial compounds. More information on ethambutol and its mechanism of action may be found in Schubert el al. (2017), American Society for Microbiology, 8: 1, hereby incorporated by reference in its entirety .

Conjunctive therapy includes sequential, simultaneous and separate, and/or coadministration of the active compounds in such a way that the therapeutic effects of the first agent administered have not entirely disappeared when the subsequent agent is administered. In certain embodiments, the second agent may be co-fonnulated with the first agent or be formulated in a separate pharmaceutical composition.

In certain embodiments, the present invention provides therapeutic methods of treating a bacterial infection or disease comprising administering to a subject, (e.g.. a subject in need thereof), an effective amount of an agent described herein. A subject in need thereof may include, for example, a subject who has been diagnosed with a bacterial disease or infection or a subject who has been treated, including subjects that have been refractory to the previous treatment.

Agents

Provided herein are methods of inhibiting bacterial cell wall synthesis by contacting a bacteria with an agent disclosed herein that inhibits the peptidoglycan glycotransferase activity of a SEDS protein. Also provided herein are methods treating or preventing a bacterial infection in a subject by administering to the subject an agent that inhibits the peptidoglycan glycotransfera.se activity of a SEDS protein of a bacteria. In some

embodiments, the agent is an inhibitor of a glycotransferase (GTase). The agent may be 654/A. 654/A is a bioactive molecule produced by actinomycete strain DEM20654. 654/A may be purified from culture extracts of actinomycete strain DEM20654, and purified by any means know in the art, such as chromatography (e.g., high performance liquid phase chromatography). 654/A activity may be tested by incubating 654/A with bacteria and quantifying bacterial growth and/or death. For example, increasing concentrations of 654/A may lead to an increase in bacterial death or a slowing of bacterial growth. In some embodiments, 654/A activity is dependent on RodA levels within a population of bacteria. For example, bacteria with increased levels of RodA may show less bacterial death when treated with 654/A when compared to a bacterial population with low levels of RodA.

Additional information about 654/A may be found in Emani et al. (2017) Nature

Microbiology, 2: 16253, hereby incorporated by reference in its entirety.

Nucleic Acid Agents

In some embodiments, an agent is an inhibitory nucleic acid, such as an RNAi molecule or an antisense oligonucleotide (ASO). In certain embodiments, interfering nucleic acid molecules that selectively target and inhibit the GTase activity or levels of a SEDS protein (e.g., RodA) are provided herein and/or used in methods described herein. An agent may inhibit the levels or activity of a SEDS protein by at least 5%, at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or 100%. An agent disclosed herein may comprise at least 5%, at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or 100%.

In some embodiments, the inhibitor}' nucleic acid is a siRNA, a shRNA, or a PNA. In some embodiments, the inhibiting nucleic acid is complementary to at least a portion of a SEDS (e.g., a RodA) niRNA sequence. In some embodiments, the inhibitory nucleic acid has at least 50%, at least 60%, at least 70%, at least 80%, at least 90% or at least 100% complementarity to a portion of SEDS (e.g., a RodA) mRNA sequence. Interfering nucleic acids generally include a sequence of cy clic subumts, each bearing a base-pairing moiety, linked by intersubunit linkages that allow the base-pairing moieties to hybridize to a target sequence in a nucleic acid (typically an RNA) by Watson-Crick base pairing, to form a nucleic acid:oligomer heteroduplex within the target sequence, interfering or inhibitory RNA molecules include, but are not limited to, antisense molecules, siRNA molecules, single- stranded siRNA molecules, and shRNA molecules.

Typically at least 17, 18, 19, 20, 21 , 22 or 23 nucleotides of the complement of the target RNA sequence are sufficient to mediate inhibition of a target transcript. Perfect complementarity is not necessary. In some embodiments, the interfering nucleic acid molecule is double-stranded RNA. The double-stranded RNA molecule may have a 2 nucleotide 3' overhang. In some embodiments, the two RNA strands are connected via a hairpin structure, forming a shRNA molecule. shRNA molecules can contain hairpins derived from microRNA molecules. For example, an RNAi vector can be constructed by cloning the interfering RNA sequence into a pCAG-miR30 construct containing the hairpin from the miR30 miRNA. RNA interference molecules may include DNA residues, as well as RNA residues.

Interfering nucleic acid molecules provided herein can contain RN A bases, non-RNA bases or a mixture of RNA bases and non-RNA bases. For example, interfering nucleic acid molecules provided herein can be primarily composed of RNA bases but also contain DNA bases or non-naturally occurring nucleotides.

The interfering nucleic acids can employ a variety of oligonucleotide chemistries. Examples of oligonucleotide chemistries include, without limitation, peptide nucleic acid (PNA), linked nucleic acid (LNA), gapmer, phosphorothioate, 2 Ό- Me -modified oligonucleotides, and morpholino chemistries, including combinations of any of the foregoing, in general, PNA and LNA chemistries can utilize shorter targeting sequences because of their relatively high target binding strength relative to 2'O-Me oligonucleotides. Phosphorothioate and 2'0-Me-modified chemistries are often combined to generate 2'O-Me- modified oligonucleotides having a phosphorothioate backbone. See, e.g., PCT Publication Nos, WO/2013/112053 and WO/2009/008725, incorporated by reference in their entireties.

Peptide nucleic acids (PNAs) are analogs of DNA in which the backbone is structurally homomorphous with a deoxyribose backbone, consisting of N-(2-aminoethyl) glycine units to which pyrimidine or purine bases are attached. PNAs containing natural pyrimidine and purine bases hybridize to complementary oligonucleotides obeying Watson- Crick base-pairing rules, and mimic DNA in terms of base pair recognition (Egholm, Buchardt et al. 1993). The backbone of PNAs is formed by peptide bonds rather than phosphodiester bonds, making them well-suited for antisense applications (see structure below). The backbone is uncharged, resulting in PNA/DNA or PNA/RNA duplexes that exhibit greater than normal thermal stability. PNAs are not recognized by nucleases or proteases.

Despite a radical structural change to the natural structure, PNAs are capable of sequence-specific binding in a helix form to DNA or RNA. Characteristics of PNAs include a high binding affinity to complementary DNA or RNA, a destabilizing effect caused by single-base mismatch, resistance to nucleases and proteases, hybridization with DNA or RNA independent of salt concentration and triplex formation with homopurine DNA.

PANAGENE. has developed its proprietary Bts PNA monomers (Bts; benzothiazole-2- sulfonyl group) and proprietary oiigomerization process. The PNA oligomerization using Bts PNA monomers is composed of repetitive cycles of deprotection, coupling and capping. PNAs can be produced synthetically using any technique known in the art. See, e.g., U.S. Pat. Nos. 6,969,766, 7,211 ,668, 7,022,851, 7, 125,994, 7, 145,006 and 7, 179,896. See also U.S. Pat. Nos. 5,539,082; 5,714,331 ; and 5,719,262 for the preparation of PN As, Further teaching of PNA compounds can be found in Nielsen et al., Science, 254: 1497-1500, 1991. Each of the foregoing is incorporated by reference in its entirety.

Interfering nucleic acids may also contain ^"locked nucleic acid" subunits (LNAs). "LNAs" are a member of a class of modifications called bridged nucleic acid (BNA). BNA is characterized by a covalent linkage that locks the conformation of the ribose ring in a C30- endo (northern) sugar pucker. For LNA, the bridge is composed of a methylene between the 2,'-0 and the 4'-C positions. LNA enhances backbone preorganization and base stacking to increase hybridization and thermal stability. In some embodiments, the agent is a gapmer (e.g., an LNA gapmer). A gapmer is a chimeric antisense oligonucleotide that contains a central block of deoxynucleotide monomers sufficiently long to induce RNase H cleavage. The central block of a gapmer is flanked by blocks of 2'-0 modified ribonucleotides or other artificially modified ribonucleotide monomers such as bridged nucleic acids (BNAs). In a gapmer, these modified nucleic acids protect the internal block from nuclease degradation.

The structures of LNAs can be found, for example, in Wengel, et al., Chemical Communications (1998) 455; Tetrahedron (1998) 54 :3607, and Accounts of Cliem. Research (1999) 32:301); Obika, et al., Tetrahedron Letters (1997) 38: 8735; ( 1998) 39:5401 , and Bioorganic Medicinal Chemistry (2008) 16:9230. Compounds provided herein may incorporate one or more LN As; in some cases, the compounds may be entirely composed of LNAs. Methods for the synthesis of individual LNA nucleoside subunits and their incorporation into oligonucleotides are described, for example, in U.S. Pat. Nos. 7,572,582, 7,569,575, 7,084, 125, 7,060,809, 7,053,207, 7,034,133, 6,794,499, and 6,670,461, each of which is incorporated by reference in its entirety. Typical intersubunit linkers include phosphodiester and phosphorothioate moieties; alternatively, non-phosphorous containing linkers may be employed. One embodiment is an LNA containing compound where each LNA subunit is separated by a DNA subumt. Certain compounds are composed of alternating LNA and DNA subunits where the intersubunit linker is phosphorothioate.

"Phosphorothioates" (or S-oligos) are a variant of normal DNA in which one of the nonbridging oxygens is replaced by a sulfur. The sulfurization of the internucleotide bond reduces the action of endo-and exonucleases including 5' to 3' and 3' to 5' DNA POL 1 exonuclease, nucleases SI and PI, RNases, serum nucleases and snake venom

phosphodiesterase. Phosphorothioates are made by two principal routes: by the action of a solution of elemental sulfur in carbon disulfide on a hydrogen phosphonate, or by the method of sulfurizing phosphite triesters with either tetraethylthiuram, disulfide (TETD) or 3H-1, 2- bensodithiol-3-one 1, 1 -dioxide (BDTD) (see, e.g., Iyer et al., J. Org. Chem. 55, 4693-4699, 1990). The latter methods avoid the problem of elemental sulfur' s insolubility in most organic solvents and the toxicity of carbon disulfide. The TETD and BDTD methods also yield higher purity phosphorothioates.

"2'O-Me oligonucleotides" molecules cany a methyl group at the 2' -OH residue of the ribose molecule. 2'-0-Me-RNAs show the same (or similar) behavior as DNA, but are protected against nuclease degradation. 2'-0-Me-RNAs can also be combined with phosphothioate oligonucleotides (PTOs) for further stabilization. 2'O-Me oligonucleotides (phosphodiester or phosphothioate) can be synthesized according to routine techniques in the art (see, e.g., Yoo et al, Nucleic Acids Res. 32:2008-16, 2004).

The interfering nucleic acids described herein may be contacted with a cell or administered to an organism (e.g., a human). Alternatively, constructs and/or vectors encoding the interfering RNA molecules may be contacted with or introduced into a cell or organism. In certain embodiments, a viral, retroviral or lentiviral vector is used. In some embodiments, the vector has a tropism for cardiac tissue. In some embodiments the vector is an adeno-associated virus.

In some embodiments, the interfering nucleic acid molecule is a siRNA molecule. Such siRNA molecules should include a region of sufficient homology to the target region, and be of sufficient length in terms of nucleotides, such that the siRNA molecule down- regulate target RNA, The term "ribonucleotide" or "nucleotide" can, in the case of a modified RNA or nucleotide surrogate, also refer to a modified nucleotide, or surrogate replacement moiety at one or more positions. It is not necessar - that there be perfect complementarity between the siRNA molecule and the target, but the correspondence must be sufficient to enable the siRNA molecule to direct sequence-specific silencing, such as by R Ai cleavage of the target RNA. In some embodiments, the sense strand need only be sufficiently complementary with the antisense strand to maintain the overall double-strand character of the molecule.

In addition, an siRNA molecule may be modified or include nucleoside surrogates. Single stranded regions of an siRNA molecule may be modified or include nucleoside surrogates, e.g., the impaired region or regions of a hairpin structure, e.g., a region which links two complementary- regions, can have modifications or nucleoside surrogates.

Modification to stabilize one or more 3'- or 5 '-terminus of an siRNA molecule, e.g., against exonucleases, or to favor the antisense siRNA agent to enter into RISC are also useful. Modifications can include C3 (or C6, C7, C12) amino linkers, thiol linkers, carboxyl linkers, non-nucleotidic spacers (C3, C6, C9, C12, abasic, Methylene glycol, hexaethylene glycol), special biotin or fluorescein reagents that come as phosphoramidites and that have another DMT-protected hydroxyl group, allowing multiple couplings during RNA synthesis.

A "small hairpin RNA" or "short hairpin RNA" or "shRNA" includes a short RNA sequence that makes a tight hairpin turn that can be used to silence gene expression via RNA interference. The shRNAs provided herein may be chemically synthesized or transcribed from a transcriptional cassette in a DNA plasmid. The shRNA hairpin structure is cleaved by the cellular machinery into siRNA, which is then bound to the RNA-induced silencing complex (RISC).

Non-limiting examples of shRN As include a double -stranded polynucleotide molecule assembled from a single-stranded molecule, where the sense and antisense regions are linked by a nucleic acid-based or non-nucleic acid-based linker; and a double-stranded polynucleotide molecule with a hairpin secondar - structure having self-complementary sense and antisense regions. In some embodiments, the sense and antisense strands of the shRNA are linked by a loop structure comprising from about 1 to about 25 nucleotides, from about 2 to about 20 nucleotides, from about 4 to about 15 nucleotides, from about 5 to about 12 nucleotides, or 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, or more nucleotides. Additional embodiments related to the shRNAs, as well as methods of designing and synthesizing such shRNAs, are described in U.S. patent application publication number 2011/0071208, the disclosure of which is herein incorporated by reference in its entirety for all purposes.

In certain embodiments, antisense oligonucleotides (ASOs) disclosed herein may be

100% complementary to the target sequence, or may include mismatches, e.g., to improve selective targeting of allele containing the disease-associated mutation, as long as a heteroduplex formed between the oligonucleotide and target sequence is sufficiently stable to withstand the action of cellular nucleases and other modes of degradation which may occur in vivo. Hence, certain oligonucleotides may have about or at least about 70% sequence complementarity, e.g., 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence complementarity, between the oligonucleotide and the target sequence. Oligonucleotide backbones that are less susceptible to cleavage by nucleases are discussed herein. Mismatches, if present, are typically less destabilizing toward the end regions of the hybrid duplex than in the middle. The number of mismatches allowed will depend on the length of the oligonucleotide, the percentage of G:C base pairs in the duplex, and the position of the mismatch(es) in the duplex, according to well understood principles of duplex stability.

Interfering nucleic acid molecules can be prepared, for example, by chemical synthesis, in vitro transcription, or digestion of long dsRNA by Rnase HI or Dicer. These can be introduced into cells by transfection, electroporation, or other methods known in the art. See Harmon, GJ, 2002, RNA Interference, Nature 418: 244-251; Bernstein E et al., 2002, The rest is silence. RNA 7: 1509-1521: Hutvagner G et al., RNAi: Nature abhors a double- strand. Curr. Opin. Genetics & Development 12: 225-232; Brummelkamp, 2002, A system for stable expression of short interfering RNAs in mammalian cells. Science 296: 550-553; Lee NS, Dohjima T, Bauer G, Li H, Li M-J, Ehsani A, Salvaterra P, and Rossi J. (2002). Expression of small interfering RNAs targeted against HIV-1 rev transcripts in human cells. Nature Biotechnol. 20:500-505; Miyagishi M, and Taira K. (2002). U6-promoter-driven siRNAs with four uridine 3' overhangs efficiently suppress targeted gene expression in mammalian cells. Nature Biotechnol. 20:497-500; Paddison PI, Caudy AA, Bernstein E, Hannon GJ, and Conklin DS. (2002). Short hairpin RNAs (shRNAs) induce sequence- specific silencing in mammalian cells. Genes & Dev. 16:948-958; Paul CP, Good PD, Winer I, and Engelke DR. (2002). Effective expression of small interfering RNA in human cells. Nature Biotechnol. 20:505-508; Sui G, Soohoo C, Affar E-B, Gay F, Shi Y, Forrester WC, and Shi Y. (2002). A DN A vector-based RNAi technology to suppress gene expression in mammalian cells, Proc. Natl, Acad, Sci. USA 99(6):5515-5520; Yu J-Y, DeRuiter SL, and Turner DL. (2002). RNA interference by expression of short-interfering RNAs and hairpin RNAs in mammalian cells. Proc. Natl. Acad. Sci. USA 99(9):6047-6052.

In the present methods, an interfering nucleic acid molecule or an interfering nucleic acid encoding polynucleotide can be administered to the subject, for example, as naked nucleic acid, in combination with a delivery reagent, and/or as a nucleic acid comprising sequences mat express an interfering nucleic acid molecule. In some embodiment, the interfering nucleic acid is administered directly to a tumor in a subject. In some

embodiments, the nucleic acid comprising sequences that express the interfering nucleic acid molecules are delivered within vectors, e.g. plasmid, viral and bacterial vectors. Any nucleic acid delivery method known in the art can be used in the methods described herein. Suitable delivery reagents include, but are not limited to, e.g., the Minis Transit T O lipophilic reagent; lipofectin; lipofectamine; cellfectin; polycations (e.g., polylysine), atelocollagen, nanoplexes and liposomes. The use of atelocollagen as a deli very vehicle for nucleic acid molecules is described in Minakuchi et al. Nucleic Acids Res., 32(13):el09 (2004); Hanai et al. Ann NY Acad Sci ,, 1082:9-17 (2006); and Kawata et al. Mol Cancer Ther., 7(9):2904-12 (2008); each of which is incorporated herein in their entirety. Exemplary interfering nucleic acid delivery systems are provided in U.S. Patent Nos. 8,283,461 , 8,313,772, 8,501,930, 8,426,554, 8,268,798 and 8,324,366, each of which is hereby incorporated by reference in its entirety.

In some embodiments of the methods described herein, liposomes are used to deliver an inhibitor}⁷ oligonucleotide to a subject. Liposomes suitable for use in the methods described herein can be formed from standard vesicle-forming lipids, which generally include neutral or negatively charged phospholipids and a sterol, such as cholesterol. The selection of lipids is generally guided by consideration of factors such as the desired liposome size and half-life of the liposomes in the blood stream, A variety of methods are known for preparing liposomes, for example, as described in Szoka et al. ( 1980), Ann. Rev. Biophys. Bioeng. 9:467; and U.S. Pat. Nos. 4,235,871, 4,501,728, 4,837,028, and 5,019,369, the entire disclosures of which are herein incorporated by reference. The liposomes for use in the present methods can also be modified so as to avoid clearance by the mononuclear macrophage system ("MMS") and reticuloendothelial system ("RES"). Such modified liposomes have opsonization-inhibition moieties on the surface or incorporated into the liposome structure.

Small Molecule Agents

Certain embodiments of the methods and compositions disclosed herein relate to the use of small molecule agents e.g., small molecule agents that modulate the activity of a SEDS proteins (e.g., RodA). Such agents include those known in the art and those identified using the screening assays described herein. A small molecule provided herein may have at least 5%, at least 10%, at least 15%, at least 20%, at least 25%>, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or 100% specificity for a SEDS proteins (e.g., RodA).

Agents useful in the methods disclosed herein may be obtained from, any available source, including systematic libraries of natural and/or synthetic compounds. Agents may also be obtained by any of the numerous approaches in combinatorial library methods known in the art, including: biological libraries; peptoid libraries (libraries of molecules having the functionalities of peptides, but with a novel, non-peptide backbone which are resistant to enzymatic degradation but which nevertheless remain bioactive; see, e.g., Zuckermann et al, 1994, J. Med. Chem. 37:2678-85); spatially addressable parallel solid phase or solution phase libraries; synthetic library methods requiring deconvolution; the 'one-bead one-compound' library method; and synthetic library methods using affinity chromatography selection. The biological library and peptoid library approaches are limited to peptide libraries, while the oilier four approaches are applicable to peptide, non-peptide oligomer or small molecule libraries of compounds (Lam., 1997, Anticancer Drug Des. 12: 145).

Examples of methods for the synthesis of molecular libraries can be found in the art, for example in: DeWitt et al. (1993) Proc. Nail. Acad. Sci. U.S.A. 90:6909; Erb et al. (1994) Proc. Nad. Acad. Sci. USA 91 : 11422; Zuckermann et al. (1994). J. Med. Chem. 37:2678; Cho et al. (1993) Science 261 : 1303; Carrel] et al. (1994) Angew. Chem. Int. Ed. Engl.

33:2059; Careil et al. (1994) Angew. Chem. Int. Ed. Engl. 33:2061 ; and in Gallop et al. (1994) J. Med. Chem. 37: 1233.

Libraries of agents may be presented in solution (e.g., Houghten, 1992, Biotechniques 13:412-421), or on beads (Lam, 1991 , Nature 354:82-84), chips (Fodor, 1993, Nature 364:555-556), bacteria and/or spores, (Ladner, USP 5,223,409), plasmids (Cull et al, 1992, Proc Nail Acad Sci USA 89: 1865-1869) or on phage (Scott and Smith, 1990, Science 249: 386-390; Devlin, 1990, Science 249:404-406; Cwirla et al, 1990, Proc, Natl. Acad. Sci. 87:6378-6382; Felici, 1991 , ,/ Mol. Biol. 222:301-310; Ladner, supra.).

Antibody Agents

In some embodiments, the agent is an antibody. For example, the antibody may be specific for a SEDS protein (e.g., a protein sequence found in Figure 8). Antibodies may be polyclonal or monoclonal; xenogeneic, allogeneic, or syngeneic; or modified fonns thereof (e.g. humanized, chimeric, etc.). Antibodies may also be fully human. The terms

"monoclonal antibodies" and "monoclonal antibody composition", as used herein, refer to a population of antibody polypeptides that contain only one species of an antigen binding site capable of immunoreacting with a particular epitope of an antigen, whereas the term

"polyclonal antibodies" and "polyclonal antibody composition" refer to a population of antibody polypeptides that contain multiple species of antigen binding sites capable of interacting with a particular antigen. A monoclonal antibody composition typically displays a single binding affinity for a particular antigen with which it immunoreacts.

In certain embodiments, the methods and compositions provided herein relate to antibodies and antigen binding fragments thereof that bind specifically to a SEDS protein (e.g.. Rod A). In some embodiments, the antibodies inhibit the function of the protein, such as inhibiting the activity of the protein, or interfering with protein-protein interactions. Such antibodies can be polyclonal or monoclonal and can be, for example, murine, chimeric, humanized or fully human. In some embodiments, the agent may be a recombinant antibodies specific for a SEDS protein (e.g., RodA), such as chimeric or humanized monoclonal antibodies, can be made using standard recombinant DNA techniques. Such chimeric and humanized monoclonal antibodies can be produced by recombinant DNA techniques known in the art, for example using methods described in US Pat No. 4,816,567; US Pat. No. 5,565,332; Better et al. (1988) Science 240: 1041-1043; Uu et al. (1987) Proc. Natl Acad. Sci. USA 84:3439-3443; Liu et al. (1987) J. Immunol 139:3521-3526; Sun et al. (1987) Proc. Natl. Acad. Sci. 84:214-218; Nishimura a/. (1987) Cancer Res. 47:999-1005; Wood et al (1985) Nature 314:446-449; and Shaw et al (1988) J. Natl Cancer Inst.

80: 1553-1559); Morrison, S. L. (1985) Science 229: 1202-1207; Oi et al (1986)

Biotechniques 4:214; Winter U.S. Patent 5,225,539; Jones et al. (1986) Nature 321:552-525;

- zl - VVeerrhhooeeyyaann eerr a//.. ((11998888)) SScciieennccee 223399:: 11553344;; aanndd BBeeiiddlleerr eett aall.. ((11998888)) ,,// IImmmmuunnooll. 114411 ::44005533-- 44006600..

In certain embodiments the instant invention relates to a composition, e.g., a pharmaceutical composition, containing at least one agent (e.g., a small molecule) that inhibits the peptidoglycan glycotransferase activity of a SEDS protein described herein formulated together with a pharmaceutically acceptable carrier. In one embodiment, the composition includes a combination of multiple (e.g., two or more) agents of the invention.

Agents and pharmaceutical compositions comprising the agents discloser herein are delivered in effective amounts. The term ^"'effective amount" refers to the amount necessary or sufficient to realize a desired biologic effect. Combined with the teachings provided herein, by choosing among the various active compounds and weighing factors such as potency, relative bioavailability, patient body weight, severity of adverse side-effects and preferred mode of administration, an effective prophylactic or therapeutic treatment regimen can be planned which does not cause substantial toxicity and yet is effective to treat the particular subject. The effective amount for any particular application can vary depending on such factors as the disease or condition being treated, the particular inhibitor being administered, the size of the subject, or the severity of the disease or condition . It is preferred generally that a maximum dose be used, that is, the highest safe dose according to some medical judgment. Multiple doses per day may be contemplated to achieve appropriate systemic levels of compounds. Appropriate systemic levels can be determined by, for example, measurement of the patient's peak or sustained plasma level of the drug.

In certain embodiments, an effective amount of agent to be employed therapeutically will depend, for example, upon the therapeutic objectives, the route of administration, and the condition of the patient. Accordingly, it will be necessary for the therapist to titer the dosage and modify the route of administration as required to obtain the optimal therapeutic effect.

The pharmaceutical compositions of the present invention may be delivered by any suitable route of administration, including orally, intravenously (e.g., in a bolus or through infusion), topically, parenterally, intramuscularly, or intraocularly, nasally, as by, for example, a spray, rectaliy, intravaginaHy, parenterally, intracistemally and topically, as by powders, ointments or drops, including buccally and sublingual!}⁷. In certain embodiments the pharmaceutical compositions are delivered generally (e.g., via oral or parenteral administration).

In any one of the aspects or embodiments described herein, the intravenous infusion can be constant or intermittent. The agent may be administered in more or more dosages. For repeated administrations over several days or longer, the treatment is sustained until a desired suppression of disease symptoms occurs or reduction of bacteria load is achieved. However, other dosage regimens may be useful. The progress of this therapy is easily monitored by conventional techniques and assays.

Pharmaceutical compositions and agents disclosed herein can be administered in combination therapy, i.e., combined with other agents. For example, the pharmaceutical composition of the invention may also include additional antibiotic agents disclosed herein. Antibiotics include, but are not limited to aminoglycosides, ansamycins, carbacephems, carbapenems, cephalosporins, glycopeptides, lincosamides, Irpopeptides, macrolides, monobactams, nitrofurans, oxazolidonones, penicillins, polypeptide antibiotics, quinolones, fluoroquinolone, sulfonamides, tetracyclines, and anti-mycobacterial compounds, and combinations thereof.

As described in detail below, the pharmaceutical compositions of the present invention may be specially formulated for administration in solid or liquid form, including those adapted for the following: (1) oral administration, for example, drenches (aqueous or non-aqueous solutions or suspensions), tablets, e.g. , those targeted for buccal, sublingual, and systemic absorption, boluses, powders, granules, pastes for application to the tongue; or (2) parenteral administration, for example, by subcutaneous, intramuscular, intravenous or epidural injection as, for example, a sterile solution or suspension, or sustained-release formulation.

Methods of preparing these formulations or compositions include the step of bringing into association an agent described herein with the carrier and, optionally, one or more accessory ingredients. In general, the formulations are prepared by uniformly and intimately bringing into association an agent described herein with liquid carriers, or finely divided solid earners, or both, and then, if necessary, shaping the product.

Pharmaceutical compositions of this invention suitable for parenteral administration comprise one or more agents described herein in combination with one or more pharmaceutically-acceptable sterile isotonic aqueous or nonaqueous solutions, dispersions, suspensions or emulsions, or sterile powders which may be reconstituted into sterile injectable solutions or dispersions just prior to use, which may contain sugars, alcohols, antioxidants, buffers, bacteriostats, solutes which render the formulation isotonic with the blood of the intended recipient or suspending or thickening agents.

Examples of suitable aqueous and nonaqueous carriers which may be employed in the pharmaceutical compositions of the invention include water, ethanol, polyols (such as glycerol, propylene glycol, polyethylene glycol, and the like), and suitable mixtures thereof, vegetable oils, such as olive oil, and injectable organic esters, such as ethyl oleate. Proper fluidity can be maintained, for example, by the use of coating materials, such as lecithin, by the maintenance of the required particle size in the case of dispersions, and by the use of surfactants.

In another aspect, the disclosure features an aerosol composition comprising any one or more of the inhibitors described herein, e.g., for use in treating or preventing a bacterial infection, such as an active or latent bacterial infection described herein. The inhibitor is formulated in a composition suitable for aerosolization. The inhibitor may be formulated in combination with an additional active agent, and the combination formulation is suitable for aerosolization. Alternatively, the inhibitor and an additional active agent may be formulated separately, such that they will be combined after aerosolization occurs or after being administered to a subject.

In another aspect, the disclosure features a nebulization composition comprising one or more of any of the inhibitors described herein, e.g., for use in treating or preventing a bacterial infection, such as an active or latent bacterial infection described herein. The inhibitor can be formulated in a composition suitable for nebulization . Similarly, the inhibitor may be formulated in combination with an additional active agent, and the combination formulation is suitable for nebulization. Alternatively, the inhibitor and an additional active agent may be formulated separately, such that they will be combined after nebulization occurs or after being administered to a subject.

In another aspect, the disclosure provides a biopharmaceutical package comprising one or more of any of the inhibitors described herein, e.g., for use in treating or preventing a bacterial infection, such as an active or latent bacterial infection described herein. The biopharmaceutical package may further comprise an active agent in addition to the inhibitor(s). The biopharmaceutical package may also comprise instructions for use.

In yet another aspect, the disclosure provides a composition {e.g., a sterile aqueous or powdered (lyophilized) composition) comprising one or more of any of the inhibitors described herein, e.g., for use i inhibiting bacterial growth . For example, the composition can be a cleaning solution, or additive for a cleaning solution, used to decontaminate surfaces, e.g., surgical tools or tables. In another example, the compositions can be suitable as soaking solutions or perfusion solutions for transplant organs or implants to be transplanted or implanted in a subject.

In some embodiments, the compositions are formulated as an eye drop. In some embodiments, the compositions are formulated as an ointment, lotion, gel, cream, aerosol, spray, or salve. In some embodiments, the compositions comprise one or more antibiotics for use in treating bacterial infections.

In another aspect, the disclosure features a sterile bandage or dressing for use in treating a wound or other cutaneous infection. The bandage or dressing comprises (or is impregnated with) a carbonic anhydrase inhibitor in an amount effective to inhibit the growth or viability of bacterial ceils. In some embodiments, the bandage or dressing can be for surgical use and can contact cutaneous surfaces as well as internal surfaces.

A physician or veterinarian having ordinary skill in the art can readily determine and prescribe the effective amount of the pharmaceutical composition required. For example, the physician or veterinarian could prescribe and/or administer doses of the compounds of the invention employed in the pharmaceutical composition at levels lower than that required in order to achieve the desired therapeutic effect and gradually increase the dosage until the desired effect is achieved.

Certain embodiments of the present invention relate to methods of inhibiting cell wall synthesis comprising contacting bacteria with an agent that inhibits the peptidoglycan glycotransferase activity of a SEDS protein. These methods include administering an agent that decreases the peptidoglycan glycotransferase activity of a SEDS protein. Agents which may be used to inhibit the activity of SEDS proteins (e.g. RodA) may be a small molecule. In some aspects, provided herein are methods to determine whether an agent inhibits the activity of a SEDS protein by measuring the level of lipid II polymerization in the presence of a SEDS protein.

Agents useful in the methods of the present invention may be obtained from any available source, including sy stematic libraries of natural and/or synthetic compounds. Agents may also be obtained by any of the numerous approaches in combinatorial library methods known in the art, including: spatially addressable parallel solid phase or solution phase libraries; synthetic library methods requiring decon volution; the One-bead one- compound' library method; and synthetic library methods using affinity chromatography selection. These approaches are applicable to small molecule libraries of compounds (Lam, 997, Anticancer Drug Des. 12: 145).

Examples of methods for the synthesis of molecular libraries can be found in the art, for example in: DeWitt f a/. (1993) Proc, Natl. Acad. Sci. U.S.A. 90:6909; Erb et al.

(1994) Proc. Natl Acad. Sci. USA 91 : 11422; Zuckermann et al. (1994). J. Med. Chem. 37:2678; Cho et al. (1993) Science 261 : 1303; Carrel! et al. (1994) Angew. Chem. Int. Ed. Engl. 33:2059; Carell et al. (\99A) Angew. Chem. Int. Ed. Engl. 33:2061; and in Gallop et al. ( 1994) J. Med. Chem. 37 : 1233.

Libraries of agents may be presented in solution (e.g. , Houghten, 1992, Biotechniques 13:412-421), or on beads (Lam, 1991 , Nature 354:82-84), chips (Fodor, 1993, Nature 364:555-556), bacteria and/or spores, (Ladner, USP 5,223,409), plasmids (Cull et al, 1992, Proc Natl Acad Sci USA 89: 1865-1869) or on phage (Scott and Smith, 1990, Science 249:386-390; Devlin, 1990, Science 249:404-406; Cwirla et al, 1990, Proc. Natl. Acad. Sci. 87:6378-6382; Felici, 1991, J. Mol. Biol. 222:301-310; Ladner, supra.).

Agents useful in the methods of the present invention may be identified, for example, using assays for screening candidate or test compounds which modulate the activity of SEDS proteins. For example, candidate or test compounds can be screened for the ability to decrease the polymerization rate of lipid I in the presence of a SEDS protein.

The basic principle of the assay systems used to identify compounds that modulate the activity of SEDS proteins involves preparing a reaction mixture containing a SEDS protein, lipid Π, and a heptaprenyl alkyl chain under conditions and for a time sufficient to allow lipid 11 polymerization in the presence of SEDS proteins. In order to test an agent for inhibitory activity, the reaction mixture is prepared in the presence and absence of the test compound. The test compound can be initially included in the reaction mixture, or can be added at a time subsequent to the addition of SEDS and lipid II. Control reaction mixtures are incubated without the test compound or with a placebo. The polymerization of lipid II is then detected. Polymerization in the control reaction, but less or no such polymerization in the reaction mixture containing the test compound, indicates that the compound is an inhibitor of SEDS proteins.

The assay for compounds that inhibit the peptidoglycan glycotransferase activity of SEDS proteins and therefore modulate the polymerization of lipid II may be conducted in a homogeneous format. In homogeneous assays, the entire reaction is carried out in a liquid phase. In eitlier approach, the order of addition of reactants can be varied to obtain different information about the compounds being tested. For example, test compounds that interfere with the interaction between SEDS protein and lipid II (e.g., by competition) can be identified by conducting the reaction in the presence of the test substance, i.e., by adding the test substance to the reaction mixture prior to or simultaneously with SEDS protein and lipid II. This is typically a reaction, analogous to those mentioned above, which is conducted in a liquid phase in the presence or absence of the test compound. The order of addition of reactants to the liquid phase can yield information about which test compounds modulate lipid II polymerization.

In such a homogeneous assay, the reaction products may be separated from, unreacted assay components by any of a number of standard techniques, including but not limited to: differential centrifugation, chromatography, electrophoresis and immunoprecipitation. Standard chromatographic techniques may also be utilized to separate products of interest {e.g.. polymerized lipid II). For example, a detergent such as sodium dodecyl sulfate (SDS) can be used to dissolve cell membranes and keep membrane proteins in solution during purification; however, because SDS causes denaturation, milder detergents such as Triton X- 100 or CHAPS can be used to retain the protein's native conformation during complete purification. Similarly, the relatively different charge properties of unpolymerized or polymerized lipid II may be exploited to differentially separate the lipid II from the remaining individual reactants, for example through the use of ion-exchange

chromatography resins. Such resins and chromatographic techniques are well known to one skilled in the art (see, e.g., Heegaard, 1998, JMol. Recognii. 11 : 141-148; Hage and Tweed, 1997, J. Chromatogr. B. Biomed. Sci. Αρρί, 699:499-525). Gel electrophoresis may also be employed to separate molecules from unbound species (see, e.g.. Ausubel et al (eds.), In: Current Protocols in Molecular Biology, J. Wiley & Sons, New York. 1999). Another technique that may be used is paper chromatography. Paper chromatography is one method for testing the purity of compounds and identifying substances. In paper chromatography , substances are distributed between a stationary phase and a mobile phase. When a substrate is placed on the paper, different products with a unique chemical structure will have a slightly different polarity, giving each product/ molecule a different solubility in the solvent. The unequal solubility can cause the various molecules to leave solution at different places as the solvent continues to move up the paper. Immunoprecipitation is another common technique utilized for the isolation of a proteins from solution (see, e.g., Ausubel et al (eds.), In: Current Protocols in Molecular Biology, J. Wiley & Sons, New York. 1999). In this technique, all proteins binding to an antibody specific to one of the binding molecules are precipitated from solution by conjugating the antibody to a polymer bead that may be readily collected by centrifugation. The bound assay components are released from the beads, and a second immunoprecipitation step is performed, this time utilizing antibodies specific for the correspondingly different interacting assay component. Variations in lipid II

polymerization in both the presence and the absence of a test compound can be compared, thus offering information about the ability of the compound to modulate interactions between SEDS protein and lipid II.

EXEMPLIFICATION

The invention now being generally described will be more readily understood by reference to the following examples, which are included merely for purposes of illustration of certain aspects and embodiments of the present invention, and are not intended to limit the in ention in any way.

A handful of bacteria, including the pathogens Francisella tularensis and Chlamydia trachomatis, possess a cell wall but do not encode Class A PBPs (aBPBs). Among these taxa are organisms recently discovered to make PG or encode an essential lipid II biosynthetic pathway. In all cases, these organisms contain at least one SEDS family member and a Class B PBP (bPBP). Finally, phylogenetic analysis indicates that SEDS family members are more broadly conserved than aPBPs (Figure 1 1 ). Based on these findings, SEDS-bPBP pairs may^¬ be the core PG synthases in the cell wall elongation and division machineries.

Example 1: The Rod complex is functional in the absence of all known peptidoglycan polymerases.

To investigate whether the cell wall elongation machinery is functional in the absence of tlie aPBPs, a GFP-labeled component (Mbl) of the Rod complex was monitored by time- lapse fluorescence microscopy. The Rod complex moves in a directed and circumferential manner around the long axis of the cell, and this movement depends on active cell wall synthesis, and thus reflects Rod complex-dependent PG polymerization. Cells lacking all four aPBPs exiiibited GFP-Mbl dynamics that were qualitatively and quantitatively similar to wild-type (Figure lb-e). Furthermore, the directed movement was sensitive to cell wall synthesis inhibitors vancomycin and ampicillin (Figure If, Figure 5). Thus, Rod complexes - dependent PG synthesis is largely unaffected in the absence of all known PGTs, Consistent with these findings, GFP-Mbi dynamics in wild-type cells were unperturbed by moenomycm, an inhibitor of the glycosyltransferase activity of aPBPs (Figure 5c-d). It was concluded that an unidentified and central PGT functions in the context of the Rod complex. Furthermore, since cells lacking the aPBPs are capable of dividing (Figure la), an unidentified PGT is also likely to function in the divisome.

Example 2: The SEDS proteins bear similarity to glycosyltransf erases.

Two protein families are represented in Rod complex and the divisome: the bPBPs which crosslink the stem peptides on tlie glycan strands and the SEDS (Shape, Elongation, Division and Sporalation) family of unknown function. The bPBPs and SEDS proteins are thought to work together as a subcomplex, and are genetically linked in many bacteria (Figure 6). In B. subtilis, the bPBP-SEDS pair present in the Rod complex is PBP2A (or PBPH) and RodA, respectively, while PBP2B and FtsW are components of the divisome.

Using the remote homology detection algorithm. HHpred, it was discovered that the SEDS proteins exhibit weak similarity to O-antigen ligases involved in synthesis of lipopolysaccharide (LPS) in Gram-negative bacteria. Although the homology did not extend to sequence motifs conserved between the two families, tlie secondary structure and positional amino acid distribution produced a high confidence match (Probability 98.4%, E- value 0.0071). O-antigen ligase is a polytopic membrane protein glycosyltransferase that carries out the en bloc transfer of undecaprenyl-pyrophosphate-linked O-antigen polymers to a Lipid A-core glycolipid acceptor (Figure 2). Like the SEDS proteins, O-antigen ligases contain 10-12 transmembrane segments and a large extracytoplasmic loop that is required for activity. Moreover, peptidoglycan precursors are similarly linked to an undecaprenyl- pyrophosphate carrier (Figure 2). O-antigen ligase represents one of many multipass membrane protein glycosyltransferases that use lipid-linked precursor substrates. These include proteins involved in the synthesis of LPS and other surface polymers, as well as O- and N-linked protein glycosylation (Figure 2). On tlie basis of these observations, it was hypothesized that tlie SEDS proteins RodA and FtsW are the unidentified PGTs in tlie Rod complex and the divisome, respectively.

Example 3: RodA overexpression partially suppresses the quadruple aPBP 'mutant.

To investigate whether RodA can catalyze PGT activity, RodA from the B. subtilis strain lacking all four aPBPs (Δ4) was purified to avoid contaminating activities. A functional rodA-hisw fusion under the control of a strong IPTG-inducible promoter was introduced into the quadruple aPBP mutant, it was discovered that ~ 10-fold over-production of RodA-HislO significantly alleviated the growth defect of the quadruple mutant (Figure 3a and Figure 7a-b). Furthermore, examination of these cells by fluorescence microscopy revealed nearly complete suppression of the cell width and elevated lysis phenotypes observed in the Δ4 mutant (Figure3b-c and Figure 7d-e).

Isolated membranes from wild-type cells, the Δ4 mutant, and the Δ4 mutant overexpressing RodA-HislO were assayed for PGT activity using radiolabeled synthetic lipid IT. As expected, membranes lacking the aPBPs had less activity than WT (Figure 3d). However, PGT activity significantly increased in the membranes in which RodA was over- produced. Furthermore, RodA and RodA-dependent PGT activity could be solubilized by the zwitterionic detergent CHAPS (Figure 3d and Figure 7c). These experiments suggest that RodA is a PGT or stimulates an unidentified PGT.

Example 4: RodA has peptidoglycan glycos transferase activity in vitro.

To improve RodA purification, an E. con expression system modeled after those used to purify G protein- coupled receptors was constructed, in which a SUMO-FLAG-RodA fusion and the SUMO protease Ulpl were co-expressed. SUMO cleavage generates an amino-terminal aspartic acid in the FLAG tag that is recognized by the Ml anti-FLAG monoclonal antibody allowing for rapid and specific immuno-affinity purification. To reduce possible contamination from E. coli aPBPs and other proteins containing GT51 domains, three (ponB, pbpC, mtgA) of the four genes were deleted that encode them from the expression strain. The only remaining family member was PBP A, whose presence during RodA purification could be tracked by immunoblot. FLAG-RodA was immunopurified from detergent-solubilized membranes and eluted with EDTA and FLAG peptide. The protein, estimated to be 60% pure (Figure 4a), catalyzed the conversion of lipid II into glycan chains in vitro (Figure 4b-c). Importantly, the PGT activity was resistant to moenomcyin at concentrations that inhibit PBP1A as well as SgtB, a PGT from Staphylococcus aureus (Figure 4b), suggesting the activity was not due to aPBP contamination. To test whether RodA was responsible for glycan strand polymerization, non-functional mutants were assayed. Essential residues in RodA were screened by mutagenesis followed by high- throughput sequencing (MutSeq). Among the residues identified in the screen, two residues were chosen (W105 and D280) predicted to be in the second and fourth extracellular loops of RodA (Figure 8). Alanine substitutions at either position abolished RodA function in vivo without affecting protein levels (Figure 3a and Figure 9). Purified FLAG-RodA (W105A) and separately (D280A) (Figure 4a) failed to polymerize glycan strands (Figure 4b and c). Importantly, immunoblot and mass spectrometry analyses indicate that theij jlevels of

PBP1A and other E. coli contaminating proteins were similar in ail three purifications (Figure 4a). This data, is consistent with a model in which RodA is the PG polymerase in the RodA complex.

Example 5: RodA induction provides intrinsic resistance to moenom cin.

B, siibtilis is intrinsically resistant to moenomycin, and this resistance is dependent upon the extracytoplasmic function (ECF) sigma factor SigM (σ^Μ) (Figure 4d). Consistent with the idea that aPBPs are specifically targeted by moenomycin, cells lacking all four aPBPs require sigM for viability (Figure 4e). Among the genes that are induced by σ^Μ in response to envelope stress is rodA⁷³. In light of data, that RodA is a moenomycin-resistant PGT (Fig. 4b and c), it was investigated if RodA upregulation was responsible for this natural resistance. Indeed, overexpression of rodA restored moenomy cin resistance to a sigM null mutant (Figure 4d). Furthermore, it suppressed the synthetic lethality of the AsigM Δ4 aPBP mutant (Figure 10a). To directly test whether o^M-dependent expression of rodA provides moenomycin resistance, the σ^Μ recognition sequences (both -10 and -35 elements) was mutated in the rodA promoter. In the absence of drug, the promoter mutant was indistinguishable from wild-type with respect to growth rate and morphology (Figure lOb-c). However, the mutant was sensitive to moenomycin and synthetically lethal with the quadruple aPBP deletion (Figure 4d and e). Thus, increased expression of rodA mediated by σ^Μ is both necessary and sufficient to confer intrinsic resistance to moenomycin and viability to cells lacking the aPBPs.

Example 6: Exemplary Assay to identify inhibitors of SEDS Proteins

PGT activity in B. subtilis membranes, detergent-sol ubilized membrane proteins, and immuno-pursfied proteins from E. coli membranes or protein samples were incubated with 4 μΜ ^!4C-labeled synthetic lipid Π with a heptaprenyl alkyl chain for 1 h. The reaction buffer consisted of 20% DMSO, 50 niM HEPES pH 7.0, 20 mM MgCh, 20 mM CaCh. For B. subtilis membranes and detergent-solubilized membrane proteins, the final protein concentration was 0.05 mg/ml . Purified proteins were used at a final concentration of 0,2 μΜ. Moenomycin and mutanolysin (Sigrna-Aldrich) were used at 0.6 μΜ and 100 μg ml, respectively. Synthetic lipid II was synthesized. Reactions were quenched by the addition of an equal volume of 10% Triton-X-100. Substrate and products were resolved by paper chromatography. Tire reactions were spotted onto 20 cm paper strips and chromatography was carried out for 8 h using a mobile phase of isobutyric acid : 1 M NH4OH (5 :3). Strips were cut 2.5 cm from the origin and each section was analyzed by scintillation counting (Ecolite scintillation cocktail). Counts at the origin-proximal section represent polymeric glycan products, while counts on the distal part of the strip represent unpolymerized lipid II (or short oligomers). For SDS-PAGE-based analysis, reaction products were quenched by boiling for 2 min, dried by speedvac and resuspended in 10 μΐ Laemmli buffer and resolved on a 20x20cm 12% polyacryl amide gel. The gel was dried and exposed to a phosphor screen for I wk.

Incorporation by Reference

All publications, patents, and patent applications mentioned herein are hereby- incorporated by reference in their entirety as if each individual publication, patent or patent application was specifically and individually indicated to be incorporated by reference. In case of conflict, the present application, including any definitions herein, will control.

Equivalents

Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, many equivalents to the specific embodiments of the invention described herein. Such equivalents are intended to be encompassed by the following claims.

Claims

What is claimed is:

1. A method of inhibiting bacterial cell wall synthesis comprising contacting a bacteria with an agent that inhibits the peptidoglycan glycotransferase activity of a SEDS protein.

2. The method of claim 1, wherein the SEDS protein is RodA.

3. The method of claim 1 or claim 2, wherein the bacteria is a Gram-positive bacteria.

4. The method of claim 1 or claim 2, wherein the bacteria is a Gram-negative bacteria.

5. The method of claim 4, wherein the bacteria is Francisella tularensis or Chlamydia trachomatis .

6. The method of claim 1 or claim 2, wherein the bacteria is selected from a group consisting of Mycobacterium tuberculosis, Staphylococcus aureus, Staphylococcus epidermidis, Enterococcus faecal is, Streptococcus pneumonia, Streptococcus pyogenes, Moraxella catarrhalis, Escherichia coli, Enterobacter cloacae, Klebsiella pneumonia, Proteus mirabilis, Pseudomonas aeruginosa, Salmonella enterica, Salmonella bongori or Acinetobacter baumannii.

7. The method of any one of claims 1 to 6, wherein the bacteria is resistant to one or more antibiotics selected from the group consisting of moenomycins, isoniazid, rifampicin, ethambutol, pyrazinamide, aminoglycosides, ansamycins, carbacephems, carbapenems, cephalosporins, glycopeptides, lincosamides, lipopeptides, macrolides, monobactams, nitrofurans, oxazolidonones, penicillins, polypeptide antibiotics, quinolones,

fluoroquinolone, sulfonamides, tetracyclines, and anti-mycobacterial compounds.

8. The method of any one of claims 1 to 7, wherein the agent targets an

extracytoplasmic catalytic center of the SEDs protein.

9. The method of any one of claims 1 to 8, wherein the agent is a small molecule.

10. The method of any one of claims 1 to 8, wherein the agent is an inhibitory nucleic acid.

11. The method of any one of claims 1 to 8, wherein the agent is an antibody.

12. The method of any one of claims 1 to 11, further comprising the step of contacting the bacteria with a second antibiotic agent.

13. The method of claim 12, wherein the second antibiotic agent is selected from the group consisting of moenomycins, isoniazid, rifampicin, ethambutol, pyrazinamide, aminoglycosides, ansamycins, carbacephems, carbapenems, cephalosporins, glycopeptides, lincosamides, lipopeptides, macrolides, monobactams, nitrofurans, oxazolidonones, penicillins, polypeptide antibiotics, quinolones, fluoroquinolone, sulfonamides, tetracyclines, and anti-mycobacterial compounds.

14. A method treating or preventing a bacterial infection in a subject comprising administering to the subject an agent that inhibits the peptidoglycan glycotransferase activity of a SEDS protein of a bacteria.

15. The method of claim 14, wherein the SEDS protein is RodA.

16. The method of claim 14 or claim 15, wherein the bacteria is a Gram-positive bacteria.

17. The method of claim 14 or claim 15, wherein the bacteria is a Gram-negative bacteria.

18. The method of claim 14, wherein the bacteria is Francisella tularensis or Chlamydia trachomatis .

19. The method of claim 14, wherein the bacteria is Mycobacterium tuberculosis.

20. The method of claim 14 or claim 15, wherein the bacteria is selected from a group consisting of Staphylococcus aureus, Staphylococcus epidermidis, Enterococcus faecal is, Streptococcus pneumonia, Streptococcus pyogenes, Moraxella catarrhalis, Escherichia coli, Eriterobacter cloacae, Klebsiella pneumonia, Proteus mirahilis, Pseudornonas aeruginosa, Salmonella enterica. Salmonella bongori or Acinetobacter baumannii.

21. The method of any one of claims 14 to 20, wherein the bacteria is resistant to one or more antibiotics selected from the group consisting of moenomycins, isoniazid, rifampicin, ethambutol, pyrazinamide, aminoglycosides, ansamycins, carbacephems, carbapenerns, cephalosporins, glycopeptides, lincosamides, lipopeptides, macrolides, monobactams, nitrofurans, oxazolidonones, penicillins, polypeptide antibiotics, quinolones,

fluoroquinolone, sulfonamides, tetracyclines, and anti-mycobacterial compounds.

22. The method of any one of claims 14 to 21, wherein the agent targets an

extracytoplasmic catalytic center of the SEDs protein.

23. The method of any one of claims 14 to 22, wherein the agent is a small molecule.

24. The method of any one of claims 14 to 22, wherein the agent is an inhibitory nucleic acid.

25. The method of any one of claims 14 to 22, wherein the agent is an antibody.

26. The method of any one of claims 14 to 25, further comprising the step of

administering to the subject a second antibiotic agent.

27. The method of claim 26, wherein the second antibiotic agent is selected from, the group consisting of moenomycins, isoniazid, rifampicin, ethambutol, pyrazinamide, aminoglycosides, ansamycins, carbacephems, carbapenems, cephalosporins, glycopeptides, lincosamides, lipopeptides, macrolides, monobactams, nitrofurans, oxazolidonones, penicillins, polypeptide antibiotics, quinoiones, fluoroquinolone, sulfonamides, tetracyclines, and anti-mycobacterial compounds.

28. The method of any one of claims 14 to 27, wherein the bacterial infection is selected from the group consisting of diarrhea, urinary tract infections, infections of skin and skin structure including wounds, cellulitis, and abscesses, ear, nose and throat infections, pneumonias , or sexually transmitted bacterial infections.

29. The method of any one of claims 14 to 28, wherein the agent is administered orally, intravenously, topically orally, intravenously, topically, parenteraiiy, intramuscularly, or intraocularly.

30. A method of determining whether an agent inhibits bacterial cell wall synthesis, the method comprising:

(a) forming a test reaction mixture comprising:

(i) a SEDS protein;

(ii) lipid II;

(lii) a heptaprenyl aikyl chain: and

(iv) a test agent;

(b) incubating the test reaction mixture under conditions conducive for the polymerization of the lipid II by the SEDS protein; and

(c) determining the level of lipid II polymerization in the test reaction mixture;

wherein an agent that reduces the amount of lipid Π polymerization in the text reaction mixture compared to the amount of lipid II polymerization in a control reaction mixture is an inhibitor of bacterial cell wall synthesis.

31. The method of claim 30, wherein the SEDS protein is RodA.

32. The method of claim 30 or 31 , wherein the test agent is a small molecule.

33. The method of any one of claims 30 to 32, wherein the control reaction mixture is substantially identical to the test reaction mixture except that the control reaction mixture does not comprise the test agent.

34. The method of any one of claims 30 to 32, wherein the control reaction mixture is substantially identical to the test reaction mixture except that the control reaction mixture compri ses a placebo agent instead of the test agent.