WO2017112888A1 - Antisense antibacterial compounds and methods - Google Patents

Antisense antibacterial compounds and methods Download PDF

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Publication number
WO2017112888A1
WO2017112888A1 PCT/US2016/068376 US2016068376W WO2017112888A1 WO 2017112888 A1 WO2017112888 A1 WO 2017112888A1 US 2016068376 W US2016068376 W US 2016068376W WO 2017112888 A1 WO2017112888 A1 WO 2017112888A1
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Prior art keywords
oligomer
antisense
cpp
protein
formula
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PCT/US2016/068376
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French (fr)
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David Greenberg
Bruce L. Geller
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David Greenberg
Geller Bruce L
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Application filed by David Greenberg, Geller Bruce L filed Critical David Greenberg
Priority to CA3009342A priority Critical patent/CA3009342A1/en
Priority to US16/064,306 priority patent/US11142764B2/en
Priority to JP2018553039A priority patent/JP7393121B2/en
Priority to EP16880107.4A priority patent/EP3394262A4/en
Priority to AU2016379402A priority patent/AU2016379402B2/en
Publication of WO2017112888A1 publication Critical patent/WO2017112888A1/en
Priority to US17/498,880 priority patent/US20220135973A1/en

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    • 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
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/113—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/70—Carbohydrates; Sugars; Derivatives thereof
    • A61K31/7088—Compounds having three or more nucleosides or nucleotides
    • A61K31/7115—Nucleic acids or oligonucleotides having modified bases, i.e. other than adenine, guanine, cytosine, uracil or thymine
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/70—Carbohydrates; Sugars; Derivatives thereof
    • A61K31/7088—Compounds having three or more nucleosides or nucleotides
    • A61K31/712—Nucleic acids or oligonucleotides having modified sugars, i.e. other than ribose or 2'-deoxyribose
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K47/00—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient
    • A61K47/30—Macromolecular organic or inorganic compounds, e.g. inorganic polyphosphates
    • A61K47/42—Proteins; Polypeptides; Degradation products thereof; Derivatives thereof, e.g. albumin, gelatin or zein
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K47/00—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient
    • A61K47/50—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates
    • A61K47/51—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent
    • A61K47/62—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being a protein, peptide or polyamino acid
    • A61K47/66—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being a protein, peptide or polyamino acid the modifying agent being a pre-targeting system involving a peptide or protein for targeting specific cells
    • 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
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P43/00—Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
    • 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
    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/10—Type of nucleic acid
    • C12N2310/11—Antisense
    • 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
    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/30—Chemical structure
    • C12N2310/32—Chemical structure of the sugar
    • C12N2310/323—Chemical structure of the sugar modified ring structure
    • C12N2310/3233—Morpholino-type ring
    • 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
    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/30—Chemical structure
    • C12N2310/35—Nature of the modification
    • C12N2310/351—Conjugate
    • C12N2310/3513—Protein; Peptide
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
    • Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
    • Y02A50/00—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE in human health protection, e.g. against extreme weather
    • Y02A50/30—Against vector-borne diseases, e.g. mosquito-borne, fly-borne, tick-borne or waterborne diseases whose impact is exacerbated by climate change

Definitions

  • the present disclosure includes antisense oligomers targeted against bacterial m RNAs and other macromolecules involved in a biochemical pathway and/or cellular process, and related compositions and methods of using the oligomers and compositions to treat an infected mammalian subject, for example, as primary antimicrobials or as adjunctive therapies with classic antimicrobials.
  • beta-lactam antibiotics such as penicillin and cephalosporin
  • Glycopeptide antibiotics including vancomycin and teichopianin, inhibit both
  • antibiotics include the quinolones, which inhibit bacterial DNA replication, inhibitors of bacterial RNA polymerase, such as rifampin, and inhibitors of enzymes in the pathway for production of tetrahydrofolate, including the sulfonamides.
  • antibiotics act at the level of protein synthesis. Notable among these are the aminoglycosides, such as kanamycin and gentamicin. This class of compounds targets the bacterial 30S ribosome subunit, preventing the association with the 50S subunit to form functional ribosomes. Tetracyclines, another important class of antibiotics, also target the 30S ribosome subunit, acting by preventing alignment of aminoacylated tRNAs with the corresponding mRNA codon. acroiides and lincosamides, another class of antibiotics, inhibit bacterial synthesis by binding to the 50S ribosome subunit, and inhibiting peptide elongation or preventing ribosome translocation.
  • Antibiotic resistance mechanisms can take a variety of forms.
  • resistance to aminoglycosides often involves an enzyme capable of inactivating the antibiotic, in this case by adding a phosphoryi, adenyl, or acetyl group. Active efflux of antibiotics is another way that many bacteria develop resistance.
  • efflux proteins such as the tetA, tetG, tetL, and tetK genes for tetracycline efflux
  • a bacterial target may develop resistance by altering the target of the drug.
  • PBPs penicillin binding proteins
  • Resistance to tetracycline may involve, in addition to enhanced efflux, the appearance of cytoplasmic proteins capable of competing with ribosomes for binding to the antibiotic.
  • point mutations in the target enzyme may confer resistance.
  • Klebsiella pneumoniae is found in the normal flora of the mouth, skin and intestines.
  • Klebsiella can cause infections in the urinary tract, lower biliary tract, and surgical wound sites, among other sides.
  • the range of clinical diseases includes pneumonia, thrombophlebitis, urinary tract infection, cholecystitis, diarrhea, upper respiratory tract infection, wound infection, osteomyelitis, meningitis, and bacteremia, and septicemia.
  • Klebsiella species are often resistant to multiple antibiotics. In fact, the spread of carbapenem-resistant
  • Enterobacteriaceae (including K. pneumoniae) has happened worldwide, including in the U.S. where carbapenemase-producing CRE has now been reported in most states.
  • Pseudomonas aeruginosa is a common Gram-negative bacterium that is found in soil, water, skin flora, and most man-made environments throughout the world. But it can cause serious disease in humans. For example, if Pseudomonas infections occur in critical body organs, such as the lungs, the urinary tract, and kidneys, the results can be fatal. It is also the major pathogen associated with lung infections in cystic fibrosis. CF patients typically become infected with strains of Pseudomonas aeruginosa from the environment, after which they evolve in the CF lung.
  • Acinetobacter baumannii is a ubiquitous organism that has emerged over the years to be a significant cause of hospital-acquired infections. This change in epidemiology is especially concerning given that A baumannii has become one of the most antibiotic-resistant Gram-negative pathogens that the medical community faces world-wide. The rapid increase in multi-drug resistance in A baumannii has left few therapeutic choices for the treating physician. Drugs such as coiistin are now frequently used, although colistin-resistant strains have appeared. Acinetobacter baumannii can cause a variety of clinical infections, with pneumonia being one of the most frequent.
  • Escherichia coii normally inhabits the large intestine of humans as a commensal organism. However, it can also cause a variety of clinical infections, and is a leading cause of bacteremia. There has been an alarming increase in the number of antibiotic-resistant strains of E. coii isolated from patients with nosocomial and community-acquired bacteremia. It is not uncommon for strains to be resistant to multiple antibiotics.
  • Embodiments of the present disclosure relate, in part, to the discovery that the antisense targeting of bacterial genes associated with biochemical pathways, cellular processes, and/or antibiotic resistance can increase the antibiotic susceptibility of otherwise antibiotic-resistant pathogenic bacteria, and reduce the ability of certain pathogenic bacteria to grow.
  • RIMA rRNA
  • DNA replication transcription, translation initiation, lipopolysaccharide biosynthesis, nucleic acid biosynthesis, intermediary metabolism, RIMA biosynthesis, protein biosynthesis, peptidogiycan biosynthesis, cellular energy homeostasis, aromatic compound biosynthesis, and antibiotic resistance
  • RIMA rRNA
  • DNA replication transcription, translation initiation, lipopolysaccharide biosynthesis, nucleic acid biosynthesis, intermediary metabolism
  • RIMA biosynthesis protein biosynthesis
  • peptidogiycan biosynthesis cellular energy homeostasis
  • aromatic compound biosynthesis and antibiotic resistance
  • Embodiments of the present disclosure therefore include a substantially uncharged antisense morpholino oligomer, composed of morphoiino subunits and phosphorus-containing intersubunit linkages joining a morphoiino nitrogen of one subunit to a 5'-exocyclic carbon of an adjacent subunit, and having (a) about 10-40 nucleotide bases, and (b) a targeting sequence of sufficient length and complementarity to specifically hybridize to a bacterial mRNA target sequence that encodes a protein associated with a biochemical pathway and/or cellular process, or a ribosomal RNA target sequence, as described herein.
  • the oligomer is conjugated to a cell-penetrating peptide (CPP).
  • CPP cell-penetrating peptide
  • the targeting sequence is selected from Tables 1A-B.
  • the oligomer is about 10-15 or about 11-12 nucleotide bases in length and has a targeting sequence selected from Tables 1A-B.
  • an antisense oligomer of the disclosure is of formula (I):
  • each Nu is a nucleobase which taken together forms a targeting sequence
  • each R 4 is independentiy Ci-C 6 alkyl, and R E ' is selected from an electron pair and H, and R 6 is selected from OH, -N ⁇ R 7 )CH 2 C a moiety of the formula: where:
  • R'' is selected from H and C C 6 alkyl
  • R s is selected from G, -C(0)-R 9 OH, acyi, trityi, and 4-methoxytrityl, where:
  • R 9 is of the formula -(0-alkyl) y - wherein y is an integer from 3 to 10 and each of
  • the y alky! groups is independently selected from C 2 -C 6 alkyl
  • each instance of R ! is -N(R 10 ) 2 R wherein each R'° is independently C C s alkyl, and selected from an electron pair and H;
  • R" is selected from H, G, acyi, trityi, 4-methoxytrityl, benzoyl, stearoyl, and a moiety of the formula:
  • R 3 is selected from an electron pair, H, and C C 6 alkyl
  • G is a ceil penetrating peptide ("CPP") and linker moiety selected from
  • the targeting sequence specifically hybridizes to a bacterial mRNA target sequence that encodes a protein associated with a biochemical pathway and/or cellular process, or a ribosomai RNA target sequence, or a protein associated with antibiotic resistance, as described herein.
  • the target sequence comprises a translational start codon of the bacterial mRIMA and/or a sequence within about 30 bases upstream or downstream of the translational start codon of the bacterial rn RNA.
  • the protein associated with a biochemical pathway and/or cellular process is a fatty acid biosynthesis protein.
  • the fatty acid biosynthesis protein is an acyl carrier protein, in certain embodiments, the acyi carrier protein is encoded by acpp, In some embodiments, the fatty acid biosynthesis protein is an acyl carrier protein synthase. In some embodiments, the acyl carrier protein synthase is encoded b fobB.
  • the targeting sequence is set forth in SEQ ID NOS:l-3, comprises a fragment of at least 10 contiguous nucleotides of SEQ ID i ⁇ !OS: 1-3, or comprises a variant having at least 80% sequence identity to SEQ ID NOS: 1-3, where thymine bases (T) are optionally uracil bases (U).
  • the protein associated with a biochemical pathway and/or cellular process is a peptidoglycan biosynthesis protein.
  • the peptidoglycan is a protein associated with a biochemical pathway and/or cellular process. In certain embodiments, the peptidoglycan
  • biosynthesis protein is a U DP-N-acetylglucosamine 1-carboxyvinyltransferase.
  • the UDP-N-acetylglucosamine 1-carboxyvinyltransferase is encoded by murA.
  • the protein associated with a biochemical pathway and/or cellular process is a ribosomai protein.
  • the ribosomai protein is a 50S ribosomai protein L28.
  • the 50S ribosomai protein L28 is encoded by rpmB,
  • the ribosomai protein is a 30S ribosomai protein.
  • the 30S ribosomai protein is encoded by rpsJ,
  • the protein associated with a biochemical pathway and/or cellular process is a ribosomai RNA (rRNA).
  • rRNA is selected from a 16S rRNA and a 23S rRNA.
  • the protein associated with a biochemical pathway and/or cellular process is a ceil division protein, in particular embodiments, the cell division protein is a protein that assembles into a ring at the future site of the septum of bacterial ceil division.
  • the protein that assembles into a ring at the future site of the septum of bacterial ceil division is encoded byftsZ.
  • the protein associated with a biochemical pathway and/or cellular process is a DNA or chromosomal replication protein.
  • DIMA or chromosomal replication protein is a topoisomerase. in specific embodiments, the topoisomerase is encoded by gyrA.
  • DNA or chromosomal replication protein is a helicase. In some embodiments, the helicase is encoded by dnaB. In some embodiments, DNA or chromosomal replication protein is a DNA polymerase. In some embodiments, the DMA polymerase is encoded by poiB.
  • the targeting sequence is set forth in SEQ ID NQS:4-2Q, comprises a fragment of at least 10 contiguous nucleotides of SEQ ID NOS: 4-20, or comprises a variant having at least 80% sequence identity to SEQ ID NOS: 4-20, where thymine bases (T) are optionally uracil bases (U).
  • compositions comprising a pharmaceutically acceptable carrier and an antisense oligomer described herein.
  • Some pharmaceutical compositions further comprising an antimicrobial agent as described herein.
  • antimicrobial agents include tobramycin, meropenem, and colistin, and combinations thereof.
  • Some embodiments include methods of reducing expression and activity of a protein associated with a biochemical pathway and/or cellular process in a bacterium, comprising contacting the bacterium with an antisense oligomer and/or a pharmaceutical composition described herein.
  • the bacterium is in a subject, and the method comprises administering the antisense oligomer to the subject.
  • the bacterium is selected from the genera Klebsiella, Pseudomonas, Acm ' etobocter, and Escherichia.
  • the bacterium is an antibiotic-resistant strain of Klebsiella, Pseudomonas,
  • the bacterium is a multi-drug resistant (MDR) strain of Klebsiella, Pseudomonas, Aclnetobacter, or Escherichia, in specific embodiments, the bacterium is Klebsiella pneumonia, Pseudomonas aeruginosa, Aclnetobacter baumannii, or
  • Some methods comprise administering the oligomer separately or concurrently with an antimicrobial agent, optionally where administration of the oligomer increases susceptibility of the bacterium to the antimicrobial agent.
  • the antimicrobial agent is selected from one or more of a ⁇ -lactam antibiotic, an aminoglycoside antibiotic, and a polymyxin.
  • the ⁇ -lactam antibiotic is selected from at least one of carbapenems, penicillin derivatives (penams), cephalosporins (cephems), and monobactams.
  • the carbapenem is selected from one or more of meropenem, imipenem, ertapenem, doripenem, panipenem, biapenem, razupenem, tebipenem, lenapenem, and tomopenem.
  • the carbapenem is meropenem.
  • the aminoglycoside antibiotic is selected from one or more of tobramycin, gentamicin, kanamycin a, amikacin, dibekacin, sisomicin, netilmicin, neomycin B, neomycin C, neomycin E (paromomycin), and streptomycin, in specific embodiments, the aminoglycoside antibiotic is tobramycin.
  • the polymyxin is selected from one or more of colistin (polymyxin E), polysporin, neosporin, or polymyxin B. In specific embodiments, the polymyxin is colistin.
  • the ⁇ -lactam antibiotic is selected from at least one of meropenem, imipenem, ertapenem, doripenem, panipenem, biapenem, razupenem, tebipenem, lenapenem, tomopenem, cephalosporins (cephems), penicillin, penicillin derivatives (penams) and ampicillin.
  • the aminoglycoside antibiotic is selected from at least one of tobramycin, gentamicin, kanamycin a, amikacin, dibekacin, sisomicin, netilmicin, neomycin B, neomycin C, neomycin E (paromomycin), and streptomycin.
  • the tetracycline antibiotic is selected from at least one of tetracycline, chlortetracycline, oxytetracyciine, demeciocycline, lymecycline, meclocyciine, methacycline, minocycline, roiitetracyciine, and doxycyiine.
  • the ⁇ -lactam antibiotic is selected from at least one of carbapenems, penicillin derivatives (penams), cephalosporins (cephems), and monobactams.
  • the oligomer reduces the minimum inhibitory concentration (M IC) of the antimicrobial agent against the bacterium by at least about 10% relative to the antimicrobial agent alone.
  • the oligomer increases the susceptibility of the bacterium to the antimicrobial agent by at least about 10% relative to the antimicrobial agent alone.
  • the combination of oligomer and the antimicrobial agent synergisticaliy increases the susceptibility of the bacterium to the antibiotic relative to the oligomer and/or the microbial agent alone.
  • the antimicrobial agent and the antisense oligomer are administered separately, in various embodiments, the antimicrobial agent and the antisense oligomer are administered sequentially. In some embodiments, the antimicrobial agent and the antisense oligomer are administered concurrently.
  • Figure 1A shows an exemplary morphoiino oligomer structure with a phosphorodiamidate linkage.
  • Figures 1B-E show the repeating subunit segment of exemplary morphoiino oligomers, designated B through E.
  • Figures 1F-H show exemplary peptide PMO conjugates structures used in the exemplary PPMOs.
  • Figure 2 shows a minimal inhibitory concentration (iC) heatmap of PPMOs targeted against essential genes from Klebsiella pneumoniae.
  • Figure 3 shows a MIC heatmap of PPMOs targeted against ribosomal NA from Klebsiella pneumoniae, Pseudomonas aeruginosa, and Acinetobacter baumannii.
  • an element means one element or more than one element.
  • coding sequence is meant any nucleic acid sequence that contributes to the code for the polypeptide product of a gene.
  • non-coding sequence refers to any nucleic acid sequence that does not directly contribute to the code for the polypeptide product of a gene.
  • the terms "contacting a cell”, “introducing” or “delivering” include delivery of the oligomers described herein into a cell by methods routine in the art, e.g., transfection (e.g., liposome, calcium-phosphate, polyethyleneimine), electroporation (e.g., nucleofection),
  • cell penetrating peptide or "a peptide moiety which enhances cellular uptake” are used interchangeably and refer to cationic cell penetrating peptides, also called
  • the peptides have the capability of inducing ceil penetration within about or at least about 30%, 40%, 50%, 60%, 70%, 80%, 90%, or 100% of ceils of a given population and/or allow macromolecuiar translocation to or within multiple tissues in vivo upon systemic administration.
  • Particular examples of CPPs include "arginine-rich peptides.” CPPs are well-known in the art and are disclosed, for example, in U.S. Application No. 2010/0016215 and International Patent Application Publication Nos. WO 2004/097017, WO 2009/005793, and WO 2012/150960, ail of which are incorporated by reference in their entirety.
  • An electron pair refers to a valence pair of electrons that are not bonded or shared with other atoms.
  • Homology refers to the percentage number of amino acids that are identical or constitute conservative substitutions. Homology may be determined using sequence comparison programs such as GAP (Deveraux et a!., 1984, Nucleic Acids Research 12, 387-395) or BLAST, in this way sequences of a similar or substantially different length to those cited herein could be compared by insertion of gaps into the alignment, such gaps being determined, for example, by the comparison algorithm used by GAP.
  • isolated is meant material that is substantially or essentially free from components that normally accompany it in its native state.
  • an "isolated polynucleotide” or “isolated oligomer,” as used herein, may refer to a polynucleotide that has been purified or removed from the sequences that flank if in a naturally-occurring state, e.g., a DIMA fragment that is removed from the sequences that are adjacent to the fragment in the genome.
  • isolated as it relates to cells refers to the purification of cells (e.g., fibroblasts, lymphoblasts) from a source subject (e.g., a subject with a polynucleotide repeat disease).
  • a source subject e.g., a subject with a polynucleotide repeat disease.
  • isolated refers to the recovery of mRNA or protein from a source, e.g., cells.
  • module includes to “increase” or “decrease” one or more quantifiable parameters, optionally by a defined and/or statistically significant amount.
  • increasing refers generally to the ability of one or antisense compounds or compositions to produce or cause a greater physiological response (i.e., downstream effects) in a cell or a subject relative to the response caused by either no antisense compound or a control compound.
  • Relevant physiological or cellular responses in vivo or in vitro will be apparent to persons skilled in the art.
  • an “increased” or “enhanced” amount is typically a “statistically significant” amount, and may include an increase that is 1.1, 1.2, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 30, 40, 50 or more times (e.g., 500, 1000 times) (including all integers and ranges between and above 1), e.g., 1.5, 1.6, 1.7. 1.8) the amount produced by no antisense compound (the absence of an agent) or a control compound.
  • the term “reduce” or “inhibit” may relate generally to the ability of one or more antisense compounds or compositions to "decrease" a relevant physiological or cellular response, such as a symptom of a disease or condition described herein, as measured according to routine techniques in the diagnostic art.
  • a “decrease" in a response may be "statistically significant” as compared to the response produced by no antisense compound or a control composition, and may include a 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% decrease, including ail integers and ranges in between.
  • an “antisense oligomer,” “oligomer,” or “oligomer” refers to a linear sequence of nucleotides, or nucleotide analogs, which allows the nucleobase to hybridize to a target sequence in an RNA by Watson-Crick base pairing, to form an oiigomer:RNA heteroduplex within the target sequence.
  • compound may be used interchangeably to refer to an oligomer.
  • the cyclic subunits may be based on ribose or another pentose sugar or, in certain embodiments, a morpholino group (see description of morpholino oligomers below).
  • oligomer also encompasses an oligomer having one or more additional moieties conjugated to the oligomer, e.g., at its 3'- or 5'-end, such as a polyethylene glycol moiety or other hydrophilic polymer, e.g., one having 10-100 monomeric subunits, which may be useful in enhancing solubility, or a moiety such as a lipid or peptide moiety that is effective to enhance the uptake of the compound into target bacterial cells and/or enhance the activity of the compound within the cell, e.g., enhance its binding to a target polynucleotide.
  • additional moieties conjugated to the oligomer e.g., at its 3'- or 5'-end
  • a polyethylene glycol moiety or other hydrophilic polymer e.g., one having 10-100 monomeric subunits, which may be useful in enhancing solubility, or a moiety such as a lipid or peptide moiety that is effective to
  • nuclease-resistant oligomers refers to one whose backbone is substantially resistant to nuclease cleavage, in non-hybridized or hybridized form; by common extracellular and intracellular nucleases in the body or in a bacterial cell (for example, by exonucleases such as 3'-exonucleases, endonucieases, RNase H); that is, the oligomer shows little or no nuclease cleavage under normal nuclease conditions to which the oligomer is exposed.
  • a “nuclease-resistant heteroduplex” refers to a heteroduplex formed by the binding of an antisense oligomer to its complementary target, such that the heteroduplex is substantially resistant to in vivo degradation by intracellular and extracellular nucleases, which are capable of cutting double-stranded RNA/RNA or RNA/DNA complexes.
  • a “heteroduplex” refers to a duplex between an antisense oligomer and the
  • nucleobase (Nu), “base pairing moiety” or “base” are used interchangeably.
  • a purine or pyrimidine base found in native DMA or RNA (uracil, thymine, adenine, cytosine, and guanine), as well as analogs of the naturally occurring purines and pyrimidines, that confer improved properties, such as binding affinity to the oligomer.
  • Exemplary analogs include hypoxanthine (the base component of the nucleoside inosine); 2, 6-diaminopurine; 5-methyl cytosine; C5-propynyl-modifed pyrimidines; 9-(aminoethoxy)phenoxazine (G-ciamp) and the like.
  • a nucleobase covalently linked to a ribose, sugar analog or morpholino comprises a nucleoside.
  • Nucleotides are composed of a nucleoside together with one phosphate group. The phosphate groups covalently link adjacent nucleotides to one another to form an oligomer.
  • An oligomer "specifically hybridizes" to a target sequence if the oligomer hybridizes to the target under physiological conditions, with a Tm substantially greater than 40°C or 45°C, preferably at least 50°C, and typically 60°C-80°C or higher.
  • Tm substantially greater than 40°C or 45°C, preferably at least 50°C, and typically 60°C-80°C or higher.
  • Such hybridization preferably corresponds to stringent hybridization conditions.
  • the Tm is the temperature at which 50% of a target sequence hybridizes to a complementary polynucleotide.
  • Such hybridization may occur with "near" or “substantial” complementarity of the antisense oligomer to the target sequence, as well as with exact complementarity.
  • sufficient length includes an antisense oligomer that is complementary to at least about 8, more typically about 8-10, 8-11, 8-12, 8-13, 8-14, 8-15, 8-16, 8-17, 8-18, 8-19, 8-20, 8-30, 8-40, or 10-11, 10-12, 10-13, 10-14, 10-15, 10-16, 10-17, 10-18, 10-19, 10-20, 10-30, 10-40 (including all integers and ranges in between) contiguous or non-contiguous nucleobases in a region of a bacterial mRNA target sequence or a bacterial rR!MA target sequence.
  • An antisense oligomer of sufficient length has at least a minimal number of nucleotides to be capable of specifically hybridizing to a region of the bacterial mRNA or rRNA target.
  • an oligomer of sufficient length is from 8 to 30 nucleotides in length, for example, about 10-20 nucleotides in length.
  • sequence identity or, for example, comprising a “sequence 50% identical to,” as used herein, refer to the extent that sequences are identical on a nucleotide-by-nucleotide basis or an amino acid-by-amino acid basis over a window of comparison.
  • a "percentage of sequence identity” may be calculated by comparing two optimally aligned sequences over the window of comparison, determining the number of positions at which the identical nucleic acid base (e.g., A, T, C, G, I) or the identical amino acid residue (e.g., Ala, Pro, Ser, Thr, Gly, Val, Leu, lie, Phe, Tyr, Trp, Lys, Arg, His, Asp, Glu, Asn, Gin, Cys and Met) occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison (i.e., the window size), and multiplying the result by 100 to yield the percentage of sequence identity.
  • the identical nucleic acid base e.g., A, T, C, G, I
  • the identical amino acid residue e.g., Ala, Pro, Ser, Thr, Gly, Val, Leu, lie, Phe, Tyr, Trp, Lys, Arg,
  • Optimal alignment of sequences for aligning a comparison window may be conducted by computerized implementations of algorithms (GAP, BESTFIT, FAST A, and TFASTA in the Wisconsin Genetics Software Package Release 7.0, Genetics Computer Group, 575 Science Drive Madison, Wis., USA) or by inspection and the best alignment (i.e., resulting in the highest percentage homology over the comparison window) generated by any of the various methods selected.
  • a “subject” or a “subject in need thereof” includes a mammalian subject such as a human subject.
  • TAG triethylene glycol moieties conjugated to the oligomer, e.g., at its 3'- or 5' -end.
  • T of the compound of formula (I), ( ⁇ ), or (III) is of the formula:
  • pip-PDA refers to a 5' terminal piperazine-phosphorodiamidate moiety that connects a G group, where the G group comprises a cel!-penetrating peptide (CPP) and linker moiety further discussed below, to the 5'end of the oligomer by way of an amide bond between the G group linker and the piperazinyl nitrogen.
  • CPP cel!-penetrating peptide
  • linker moiety further discussed below
  • target sequence refers to a portion of the target RNA, for example, a bacterial mR!MA or rRNA, against which the antisense oligomer is directed, that is, the sequence to which the oligomer will hybridize by Watson-Crick base pairing of a complementary sequence, in certain embodiments, the target sequence may be a contiguous region of the translation initiation region of a bacterial mRIMA or a ribosomal RNA.
  • targeting sequence refers to the sequence in an oligomer that is complementary or substantially complementary to the target sequence in the RNA, e.g., the bacterial mRNA, the bacterial rRNA.
  • the entire sequence, or only a portion, of the antisense compound may be complementary to the target sequence.
  • RNA e.g., the bacterial mRNA, the bacterial rRNA.
  • the entire sequence, or only a portion, of the antisense compound may be complementary to the target sequence.
  • an oligomer of about 10-30 bases about 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, or 29 of the bases may be targeting sequences that are complementary to the target region.
  • the targeting sequence is formed of contiguous bases, but may alternatively be formed of non-contiguous sequences that when placed together, e.g., from opposite ends of the oligomer, constitute sequence that spans the target sequence.
  • a “targeting sequence” may have "near or "substantia! complementarity to the target sequence and still function for the purpose of the present disclosure, that is, still be
  • the oligomer analog compounds employed in the present disclosure have at most one mismatch with the target sequence out of 10 nucleotides, and preferably at most one mismatch out of 20.
  • the antisense oligomers employed have at least 90% sequence homology, and preferably at least 95% sequence homology, with the exemplary targeting sequences as designated herein.
  • the term “quantifying”, “quantification” or other related words refer to determining the quantity, mass, or concentration in a unit volume, of a nucleic acid, polynucleotide, oligomer, peptide, polypeptide, or protein.
  • treatment of a subject (e.g. a mammal, such as a human) or a cell is any type of intervention used in an attempt to alter the natural course of the individual or cell.
  • Treatment includes, but is not limited to, administration of a pharmaceutical composition, and may ⁇ be performed either prophyiactically or subsequent to the initiation of a pathologic event or contact with an etioiogic agent. Also included are “prophylactic” treatments, which can be directed to reducing the rate of progression of the disease or condition being treated, delaying the onset of that disease or condition, or reducing the severity of its onset. “Treatment” or “prophylaxis” does not necessarily indicate complete eradication, cure, or prevention of the disease or condition, or associated symptoms thereof. if. Bacterial Targeting Sequences
  • Certain embodiments relate to antisense oligomers, and related compositions and methods, which are of sufficient length and complementarity to specifically hybridize to a bacterial rnRNA target sequence that encodes a gene in a biochemical pathway and/or cellular process, or a ribosomai RNA target sequence.
  • General examples include: murein biosynthesis, cell division, global gene regulatory mechanisms, fatty acid biosynthesis, ribosomai proteins, ribosomai RNA (rRNA), DNA/chromosomal replication, transcription, translation initiation, lipopolysaccharide biosynthesis, nucleic acid biosynthesis, intermediary metabolism, RNA biosynthesis, protein biosynthesis, peptidoglycan biosynthesis, cellular energy homeostasis, aromatic compound biosynthesis, and antibiotic resistance.
  • genes in biochemical pathways and cellular processes include: rpsJ and rpmB (ribosomai proteins); IpxC, waaC, waaG, waaA, waaF, IpxA, and ipxB
  • iriurA (formerly known as murZ), mraY, murC, murB, murE, rnurF, and murG (peptidoglycan biosynthesis); fahG, acpP, accA, fabB, accB, and fabZ (fatty acid biosynthesis); adk (cellular energy homeostasis); infA (transcription antitermination and/or protein synthesis); /tsZ (cell division); rpoD (R!MA synthesis); aroC (aromatic compound biosynthesis); gyrA, dnaB, pol B (chromosomal and DMA replication).
  • antibiotic resistance genes examples include hiaJ, cml, and adeA.
  • the rRNA target sequence or mRNA target sequence that encodes the gene is from Kiebsielio, e.g., Klebsiella pneumoniae.
  • the rRNA target sequence or the mRNA target sequence that encodes the gene is from Pseudomonas, e.g., Pseudomonas aeruginosa.
  • the rRNA target sequence or the m RNA target sequence that encodes the gene is from Acinetobacter, e.g., Acinetobacter baumannii.
  • the rRIMA target sequence or the m RNA target sequence that encodes the gene is from Escherichia, e.g., E. coii.
  • the bacterial target is a gene or protein that is associated with biosynthesis of fatty acids.
  • proteins associated with fatty acid biosynthesis include: acyl carrier protein (ACP), such as AcpP, that plays an essential role in stabilizing and shuttling the intermediate fatty acid chain to each of the enzymes in the fatty acid synthase complex; acyl carrier protein synthase (AcpS), an enzyme that transfers the 4'-phosphopantetheine prosthetic group to apo-ACP to form the functional holo-ACP; acetyl-CoA carboxylase, an enzyme composed of four proteins that catalyzes the conversion of acetyl-CoA to malonyl-CoA in the first committed step of fatty acid biosynthesis: AccA (carboxyltransferase alpha subunit catalyzing the transfer of the carboxyl group from biotin to acetyl-CoA to form malonyl-CoA), AccB (biotin carboxyl carrier
  • ACP
  • the acpP gene is from Klebsiella, e.g., Klebsiella pneumoniae.
  • the acpP gene is from Pseudomonas, e.g., Pseudomonas aeruginosa.
  • the acpP gene is from Acinetobacter, e.g., Acinetobacter baumannii.
  • the acpP gene is from Escherichia, e.g., E. coii. Certain embodiment relate to antisense oligomers, and related compositions and methods, which are of sufficient length and complementarity to specifically hybridize to an mRNA target sequence of a bacterial fabB gene.
  • the fabB gene is from Klebsiella, e.g., Klebsiella pneumoniae. In some embodiments, the fabB gene is from Pseudomonas, e.g.,
  • the fabB gene is from Acinetobacter, e.g., Acinetobacter baumannii. In some embodiments, the fabB gene is from Escherichia, e.g., E. coli.
  • the bacterial cell wall peptidoglycan is an essential cellular component involved in the maintenance of shape and protection from osmotic shock lysis.
  • peptidoglycan is assembled from a basic building block composed of N-acetyigiucosamine (Glc!NiAc) and N-acetyimuramic acid with an attached pentapeptide.
  • the bacterial target is a gene or protein that is associated with peptidoglycan biosynthesis.
  • a particular example of a gene associated with peptidoglycan biosynthesis include murA (formerly known as murZ ⁇ , which encodes a UDP-N- acetylglucosamine 1-carboxyvinyltransferase, which catalyzes the first committed step of peptidoglycan biosynthesis.
  • murA originally known as murZ ⁇ , which encodes a UDP-N- acetylglucosamine 1-carboxyvinyltransferase, which catalyzes the first committed step of peptidoglycan biosynthesis.
  • the enzyme catalyzes the transfer of enoipyruvate from
  • the murA gene is from Klebsiella, e.g., Klebsiella pneumoniae. In some embodiments, the murA gene is from Pseudomonas, e.g., Pseudomonas aeruginosa, in some embodiments, the murA gene is from Acinetobacter, e.g., Acinetobacter baumanii. In some embodiments, the murA gene is from
  • Escherichia e.g., E. coli.
  • the ribosome is crucial for translation of mRNA molecules into proteins.
  • the bacterial target is a gene or protein that is associated with ribosomal proteins.
  • a particular example of a gene associated with ribosomal proteins is rp B, a 50S ribosomal protein L28 essential for ribosome assembly and translation.
  • Another example of a gene associated with ribosomal proteins is rpsJ, a 30S ribosomal protein.
  • the rpmB or rpsJ gene is from Klebsiella, e.g., Klebsiella pneumoniae.
  • the rpmB or rpsJ gene is from Pseudomonas, e.g., Pseudomonas aeruginosa. In some embodiments, the rpmB or rpsJ gene is from Acinetobacter, e.g., Acinetobacter baumanii. In some embodiments, the rpmB or rpsJ gene is from Escherichia, e.g., f. coli.
  • the bacterial target is a ribosomal RNA (rRNA).
  • rRNA ribosomal RNA
  • examples of rRIMA include 5S, 16S, and 23S rRNA.
  • the rRNA e.g., 55, 16S, 23S
  • Klebsiella e.g., Klebsiella pneumoniae
  • the rRNA e.g., 5S, 16S, 23S is from
  • the rRNA e.g., 5S, 16S, 23S
  • the rRNA is from Acinetobacter, e.g., Acinetobacter baumanii.
  • the rRNA is from Escherichia, e.g., E. coli.
  • the bacterial target is a gene or protein that is associated with cellular energy homeostasis.
  • a particular example of a gene associated with cellular energy homeostasis includes an adenylate kinase (adk) gene, which encodes a phosphotransferase enzyme that catalyzes the inferconversion of adenine nucleotides.
  • adk adenylate kinase
  • the bacterial target is a gene or protein that is associated with transcription antitermination and/or protein biosynthesis.
  • a particular example of a gene associated with transcription antitermination and/or protein biosynthesis includes translation initiation factor IF1.
  • IF1 encoded by infA, is a protein containing an Sl-iike domain that may play a role in binding and melting nucleic acid secondary structure and transcription antitermination. Other functions may also include increasing the rate of 70S ribosome dissociation and subunit association and
  • the bacterial target is a gene or protein that is associated with cell division.
  • a particular example of a gene associated with cell division includes a /tsZ gene, which encodes a protein that assembles into a ring at the future site of the septum of bacterial ceil division. This is a prokaryotic homoiogue to the eukaryotic protein tubulin.
  • the ftsZ gene is from Klebsiella, e.g., Klebsiella pneumoniae.
  • the/fsZ gene is from Pseudomonas, e.g., Pseudomonas aeruginosa.
  • the /tsZ gene is from
  • the /tsZ gene is from
  • Escherichia e.g., f. coil.
  • the bacterial target is a gene or protein that is associated with DMA or chromosomal replication.
  • a gene associated with DNA or chromosomal replication is gyrA, which encodes a topoisomerase.
  • dnaB which encodes a helicase.
  • polB which encodes a DNA polymerase
  • the gyrA or dnaB or polB gene is from Klebsiella, e.g., Klebsiella pneumoniae.
  • the gyrA or dnaB or polB gene is from Pseudomonas, e.g., Pseudomonas aeruginosa.
  • the gyrA or dnaB or polB gene is from Acinetobacter, e.g., Acinetobacter baumanii.
  • the gyrA or dnaB or polB gene is from Escherichia, e.g., E. coii.
  • the bacterial target is a gene or protein that is associated with lipopolysaccharide biosynthesis.
  • a gene associated with lipopolysaccharide biosynthesis is IpxC, which encodes an N-acety!g!ucosamine deacetylase.
  • the IpxC, gene is from Klebsiella, e.g., Klebsiella pneumoniae.
  • the IpxC gene is from Pseudomonas, e.g., Pseudomonas aeruginosa.
  • the IpxC gene is from Acinetobacter, e.g., Acinetobacter baumanii.
  • the IpxC gene is from
  • Escherichia e.g., f. coii.
  • the bacterial target is a gene or protein that is associated with RNA synthesis.
  • a particular example of a gene associated with RNA synthesis includes an rpoD gene, which encodes a sigma D (sigma 70) factor of RNA polymerase that allows binding of the polymerase to gene promoters and is important for transcribing most genes in growing cells. Genes recognized by this sigma factor have promoter consensus sequences centered at 10 and 35 nucleotides before the start of transcription.
  • the rpoD gene is from Klebsiella, e.g., Klebsiella pneumoniae.
  • the rpoD gene is from Pseudomonas, e.g., Pseudomonas aeruginosa, in some embodiments, the rpoD gene is from Acinetobacter, e.g., Acinetobacter baumanii. In some embodiments, the rpoD gene is from Escherichia, e.g., E. coli.
  • the biosynthesis of aromatic compounds is important for the growth and survival of bacterial cells.
  • the shikimate pathway is a biosynthetic route in microorganisms that lead to the synthesis of chorismic acid, a central precursor for other aromatic compounds, in some
  • the bacterial target is a gene or protein that is associated with aromatic compound biosynthesis.
  • a particular example of a gene associated with aromatic compound biosynthesis includes an aroC gene, which encodes chorismate synthase (5-enolpyruvylshikimate-3-phosphate phosphoiyase), the final enzyme in the shikimate pathway that catalyzes the conversion of 5- enolpyruvylshikimate-3-phosphate to chorismic acid.
  • the gene or protein is associated with resistance of the bacteria to at least one antimicrobial agent, i.e., an antibiotic resistance gene.
  • an antibiotic resistance gene i.e., an antibiotic resistance gene.
  • General examples of antibiotic resistance genes include beta-lactamases, which can enzymatically deactivate certain antimicrobial agents, and proteins that increase the permeability or active efflux (pumping-out) of an
  • antibiotic resistance genes include TE beta-lactamase (blaT), chloramphenicol resistance gene ⁇ cm! ⁇ , and resistance-nodulation-ceii division (RN D)-type multidrug efflux pump subunit AdeA (adeA).
  • the target sequence contains all or a portion (e.g., 1 or 2 nucleotides) of a transiationai start codon of the bacterial m RNA. In some embodiments, the target sequence contains a sequence that is about or within about 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, 26, 27, 28, 29, 30 bases upstream or downstream of a transiationai start codon of the bacterial m RNA target sequence, including common and alternative start codons (e.g., AUG, GUG, U UG, AUU, CUG).
  • common and alternative start codons e.g., AUG, GUG, U UG, AUU, CUG.
  • the 5'-end of the target sequence is the adenine, uracil, or guanine nucleotide (respectively) in an AUG start codon of the bacterial mRNA.
  • the 5'-end of the target sequence is the guanine, uracil, or guanine nucleotide (respectively) in a GUG start codon of the bacterial mRNA.
  • the 5' -end of the target sequence is the uracil, uracil, or guanine nucleotide (respectively) in a UUG start codon of the bacterial mRNA.
  • the 5'-end or 3- end of the target sequence begins at residue 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, 26, 27, 28, 29, or 30 downstream of the last (third) nucleotide of a translational start codon of the bacterial mRNA.
  • the 5' -end or 3-end of the target sequence begins at residue 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, 26, 27, 28, 29, or 30 upstream of the first nucleotide of a translational start codon of the bacterial mRNA.
  • antisense targeting sequences are designed to hybridize to a region of one or more of the target genes described herein.
  • Selected antisense targeting sequences can be made shorter, e.g., about 8, 9, 10, 11, 12. 13, 14. or 15 bases, or longer, e.g., about 20, 30, or 40 bases, and include a small number of mismatches, as long as the sequence is sufficiently complementary to reduce transcription or translation upon hybridization to the target sequence, and optionally forms with the RNA a heteroduplex having a Tm of 45°C or greater.
  • the degree of complementarity between the target sequence and antisense targeting sequence is sufficient to form a stable duplex.
  • the region of complementarity of the antisense oligomers with the target RNA sequence may be as short as 8-9 bases, 8-10 bases, 8- 11 bases, 8-12 bases, 10-11 bases, 10-12 bases, but can be 12-15 bases or more, e.g., 10-40 bases, 12-30 bases, 12-25 bases, 15-25 bases, 12-20 bases, or 15-20 bases, including ail integers in between these ranges.
  • An antisense oligomer of about 10-15 bases is generally long enough to have a unique complementary sequence, in certain embodiments, a minimum length of complementary bases may be required to achieve the requisite binding Tm, as discussed herein.
  • oligomers as long as 40 bases may be suitable, where at least a minimum number of bases, e.g., 10-12 bases, are complementary to the target sequence.
  • facilitated or active uptake in cells is optimized at oligomer lengths of less than about 30 or less than about 20 bases.
  • antisense oligomers that consist of about 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, or 40 bases, in which at least about 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, or 40 contiguous or non-contiguous bases are complementary to a target gene described herein.
  • antisense oligomers may be 100% complementary to the target sequence, or may include mismatches, e.g., to accommodate variants, as long as a heteroduplex formed between the oligomer and target sequence is sufficiently stable to withstand the action of cellular nucleases and other modes of degradation which may occur in vivo, and reduce expression of the targeted mRNA.
  • certain oligomers 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 oligomer and the target sequence.
  • Oligomer 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 oligomer, 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.
  • an antisense oligomer is not necessarily 100% complementary to the target sequence, it is effective to stably and specifically bind to the target sequence, for example, such that translation of the target RNA is reduced.
  • the stability of the duplex formed between an oligomer and a target sequence is a function of the binding Tm and the susceptibility of the duplex to cellular enzymatic cleavage.
  • the Tm of an oligomer with respect to complementary-sequence RNA may be measured by conventional methods, such as those described by Names et al., Nucleic Acid Hybridization, IRL Press, 1985, ⁇ . 107-108 or as described in iyada C. G. and Wallace R. B., 1987, Oligomer Hybridization Techniques, Methods Enzymol. Vol. 154 pp. 94-107.
  • antisense oligomers may have a binding Tm, with respect to a complementary-sequence RNA, of greater than body temperature and preferably greater than about 45°C or 50°C. Trn's in the range 60-80°C. or greater are also included.
  • the Tm of an oligomer, with respect to a complementary-based RNA hybrid can be increased by increasing the ratio of C:G paired bases in the duplex, and/or by increasing the length (in base pairs) of the heterodupiex.
  • Tables 1A-B below show exemplary targeting sequences (in a 5'-to-3' orientation) of the antisense oligomers described herein.
  • Certain antisense oligomers thus comprise, consist, or consist essentially of a targeting sequence in Tables 1A-B (e.g., SEQ ID MOS: 1-20) or a variant or contiguous or non-contiguous portion(s) thereof.
  • certain antisense oligomers comprise about or at least about 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, or 27 contiguous or non-contiguous nucleotides of any of the targeting sequences in Tables 1A-B (e.g., SEQ ID NOS:1-20).
  • intervening nucleotides can be deleted or substituted with a different nucleotide, or intervening nucleotides can be added.
  • variants include oligomers having about or at least about 70% sequence identity or homology, 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 identity or homology, over the entire length of any of the targeting sequences in Tables 1A-B (e.g., SEQ ID NQS: 1-20).
  • Tables 1A-B e.g., SEQ ID NQS: 1-20.
  • antisense oligomers and variants thereof can be assayed according to routine techniques in the art (see, e.g., the Examples).
  • ⁇ Antisense Oligomer Compounds
  • the antisense oligomers typically comprises a base sequence of sufficient length and complementarity to specifically hybridize to a bacterial rnRNA target sequence that encodes a protein associated with a biochemical pathway and/or cellular process and thereby reduce expression (e.g., translation) of the protein, or a ribosoma! RNA target sequence and thereby inhibit its interaction with other macromolecules.
  • This requirement is optionally met when the oligomer compound has the ability to be actively taken up by bacterial ceils, and once taken up, form a stable duplex (or heterodupiex) with the target mRNA or target rRNA, optionally with a Tm greater than about 40°C or 45°C.
  • the backbone of the antisense oligomer is substantially uncharged, and is optionally recognized as a substrate for active or facilitated transport across a ceil wall and/or cell membrane.
  • the ability of the oligomer to form a stable duplex with the target RiMA may also relate to other features of the backbone, including the length and degree of complementarity of the antisense oligomer with respect to the target, the ratio of G:C to A:T base matches, and the positions of any mismatched bases.
  • the ability of the antisense oligomer to resist cellular nucleases may promote survival and ultimate delivery of the agent to the ceil. Exemplary antisense oligomer targeting sequences are listed in Tables 1A-B (supra).
  • the antisense oligomer is a morpholino-based oligomer, for example, a phosphorodiamidate morpholino oligomer (PMO).
  • Morpholino-based oligomers refer to an oligomer comprising morpholino subunits supporting a nucieobase and, instead of a ribose, contains a morpholine ring.
  • Exemplary internucleoside linkages include, for example,
  • Each morpholino subunit comprises a purine or pyrimidine nucieobase effective to bind, by base - specific hydrogen bonding, to a base in an oligomer.
  • IVlorphoiino-based oligomers are detailed, for example, in U.S. Patent Mos. 5,698,685; 5,217,866; 5, 142,047; 5,034,506; 5, 166,315; 5, 185,444; 5,521,063; 5, 506,337 and pending US Patent Application Mos. 12/271,036; 12/271,040; and PCT Publication No. WO/2009/064471 and WO/2012/043730 and Summerton et al. 1997, Antisense and Nucleic Acid Drug Development, 7, 187-195, which are hereby incorporated by reference in their entirety.
  • the phosphate groups are commonl referred to as forming the "internucleoside linkages" of the oligomer.
  • the naturally occurring internucleoside linkage of R1MA and DNA is a 3' to 5' phosphodiester linkage.
  • a "phosphoramidate” group comprises phosphorus having three attached oxygen atoms and one attached nitrogen atom, while a
  • phosphorodiamidate group comprises phosphorus having two attached oxygen atoms and two attached nitrogen atoms.
  • one nitrogen is always pendant to the linkage chain.
  • the second nitrogen, in a phosphorodiamidate linkage is typically the ring nitrogen in a morpholine ring structure.
  • the morpholino subunits are joined by phosphorous-containing intersubunit linkages in accordance with the structure: w or sulfur, preferably oxygen; Pj is a purine or pyrimidine base-pairing moiety effective to bind, by base-specific hydrogen bonding, to a base in a polynucleotide, and X is -NRR' where R and R' are the same or different and are either H or alkyl. In particular embodiments, X is -NRR', where R and R' are the same or different and are either H or methyl.
  • antisense oligomer that comprise a sequence of nucleotides of the formula in Figures 1A-1E.
  • B is a purine or pyrimidine base-pairing moiety effective to bind, by base-specific hydrogen bonding, to a base in a polynucleotide.
  • Yi or Y 2 may be oxygen, sulfur, nitrogen, or carbon, preferably oxygen.
  • the X moiety pendant from the phosphorus may be fluorine, an alkyl or substituted alkyl, an alkoxy or substituted aikoxy, a thioalkoxy or substituted thioalkoxy, or unsubstituted, monosubstituted, or disubstituted nitrogen, including cyclic structures, such as morphoiines or piperidines.
  • Alkyl, aikoxy and thioalkoxy include 1-6 carbon atoms.
  • the Z moieties may be sulfur or oxygen, and are preferably oxygen.
  • various embodiments of the disclosure include a substantially uncharged antisense morpholino oligomer, composed of morpholino subunits and phosphorus-containing intersubunit linkages joining a morpholino nitrogen of one subunit to a 5'-exocyclic carbon of an adjacent subunit, and having (a) about 10-40 nucleotide bases, and (b) a targeting sequence of sufficient length and complementarity to specifically hybridize to a bacterial mRNA target sequence that encodes a protein associated with a biochemical pathway and/or cellular process, or a ribosomal RiMA target sequence, as described herein.
  • the oligomer is conjugated to a cell-penetrating peptide (CPP).
  • an antisense oligomer of the disclosure includes a compound of formula
  • each i ⁇ !u is a nucleobase which taken together forms a targeting sequence
  • X is an integer from 9 to 38;
  • T is selected from OH and a moiet of the formula:
  • each R 4 is independently Ci-C 6 alkyl, and R 5 is selected from an electron pair and H, and R 6 is selected from OH, -N(R')CH 2 C a moiety of the formula:
  • R' is selected from H and C C s alkyl
  • R 8 is selected from G, -C ⁇ Q)-R 9 OH, acyl, trityl, and 4-methoxytrityl, where:
  • R 9 is of the formula -(0-alkyl) y - wherein y is an integer from 3 to 10 and each of the y alky! groups is independently selected from C 2 -C 6 alkyi; each instance of R ! is -N(R 10 ) 2 R wherein each R ll ⁇ is independently C C s alky!, and
  • R 2 is selected from H, G, acy!, trityl, 4-methoxytrityl, benzoyl, stearoyl, and a moiety of the formula:
  • R 3 is selected from an electron pair, H, and C r C 6 alkyi
  • G is a cell penetrating peptide (“CPP”) and linker moiety selected from
  • G is of the formula:
  • the targeting sequence specifically hybridizes to a bacterial rnRMA target sequence that encodes a protein associated with a biochemical pathway and/or cellular process, or a rRNA target sequence.
  • X is from 9 to 18. In certain embodiments, X is 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29 or 30.
  • T is selected from :
  • R is selected from H, G, acyl, trityi, 4-methoxytrityi, benzoyl, and stearoyl.
  • T is selected from :
  • T is of the formula:
  • R 2 is G
  • T is of the formula:
  • T is of the formula:
  • R 2 is G or T is of the formula:
  • R " is selected from H, acyl, trityi, 4-methoxytrityi, benzoyl, and stearoyl.
  • R 2 is selected from H or G, and R 3 is selected from an electron pair or H, in a particular embodiment, R 2 is G. In some embodiments, R 2 is H or acyl. In some embodiments, each R L is -IM(CH 3 ) 2 . in some embodiments, at least one instance of R 1 is -N(CH 3 ) 2 . In certain embodiments, each instance of is -N(CH 3 ) 2 .
  • an antisense oligomer of the disclosure includes a compound of formula (II):
  • each Nu is a nucleobase which taken together forms a targeting sequence
  • X is an integer from 9 to 28;
  • T is selected from:
  • R z is selected from H, G, acyl, trityi, 4-methoxytrityi, benzoyl, and stearoyi; and R 3 is selected from an electron pair, H, and C :l -C 6 aikyi,
  • G is a cell penetrating peptide ("CPP") and linker moiety selected from -C(0)(CH 2 ) 5 NH-CPP, -C(0)(CH 2 ) 2 NH-CPP, -C(0) ⁇ CH 2 ) 2 MHC(0)(CH 2 ) 5 NH-CPP,
  • CPP cell penetrating peptide
  • T is TEG as defined above, R' " is G, and R 3 is an electron pair or H.
  • R" is selected from H, acyl, trityi, 4-methoxytrityi, benzoyl, and stearoyl and T is of the formula:
  • R 2 is G or T is of the formula:
  • an antlsense oligomer of the disclosure includes a compound of formul
  • each Nu is a nucleobase which taken together forms a targeting sequence
  • X is an integer from 9 to 28;
  • T is selected from :
  • each instance of R 1 is -N(R i0 ) 2 R a wherein each R 10 is independently C C 6 a!kyi, and R l is selected from an electron pair and H;
  • R 2 is selected from an electron pair, H, and C C 6 alkyi; and G is a cell penetrating peptide ("CPP") and linker moiety selected
  • G is of the formula:
  • At least one instance of R ! is -M(CH 3 ⁇ 2 . In certain embodiments, each instance of R 1 is -M(CH 3 ⁇ 2 .
  • an ant isense oligomer of the disclosure includes a compound of formula
  • X is an integer from 9 to 28;
  • each Nu is a nucleobase which taken together forms a targeting sequence; each instance of R L is ---N(R l0 ) 2 R n wherein each R 10 is independently C C 6 aikyi, and R I ! is selected from an electron pair and H; and
  • G is a cell penetrating peptide ("CPP") and linker moiety selected
  • G is of the formula:
  • At least one instance of R ! is -N ⁇ CH 3 ⁇ 2 .
  • each instance of R 1 is -N ⁇ CH 3 ⁇ 2 .
  • an antisense oligomer of the disclosure can be a compound of formula
  • X is an integer from 9 to 18; each Nu is a nuc!eobase which taken together forms a targeting sequence; each instance of R 1 is -N(R "L0 ) 2 R ! l wherein each R 10 is independently C C 6 alkyl, and R 11 is selected from an electron pair and H;
  • R 2 is selected from H, trityl, 4-methoxytrifyi, acyl, benzoyl, and stearoyi ;
  • R 3 is selected from an electron pair, H, and Ci-C 6 alkyl
  • G is a ceil penetrating peptide ("CPP") and linker moiety selected
  • G is of the formula:
  • At least one instance of R 1 is -N ⁇ CS-J 3 ) 2 .
  • each instance of R 1 is -N ⁇ CH 3 ) 2 .
  • an antisense oligomer of the disclosure includes a compound of formula
  • X is an integer from 9 to 28;
  • each Nu is a nucleobase which taken together forms a targeting sequence
  • R 2 is selected from H or acyl
  • G is a cell penetrating peptide ("CPP") and linker moiety selected
  • G is of the formula:
  • the antisense oligomers can be prepared by stepwise solid-phase synthesis, employing methods known in the art and described in the references cited herein.
  • the antisense oligomer is conjugated to a cell-penetrating peptide (CPP).
  • CPP cell-penetrating peptide
  • the CPP is an arginine-rich peptide.
  • arginine-rich carrier peptide is meant that the CPP has at least 2, and preferably 2, 3, 4, 5, 6, 7, or 8 arginine residues, each optionally separated by one or more uncharged, hydrophobic residues, and optionally containing about 6-14 amino acid residues.
  • Figures 1F-1H show exemplary chemical structures of CPP-PMO conjugates used in the Examples, including 5' and 3' P O conjugates.
  • Exemplary CPPs are provided in Table CI (SEQ ID NOS:21-35).
  • X 6-arninohexanoic acid
  • B ⁇ -alanine
  • F is phenylalanine
  • Y is tyrosine
  • G is glycine
  • R is arginine
  • the CPP is linked at its C-terminus to the 3' -end or the 5'-end of the oligomer via a 1, 2, 3, 4, or 5 amino acid linker.
  • the CPP is linked at its C-ferminus to the 3' -end or the 5'-end of the oligomer via a 1, 2, 3, 4, or 5 amino acid linker, in particular embodiments, including antisense oligomer compounds of formula (i)-(Vi), the linkers can include: -C(0)(CH 2 )sN H-CPP (X
  • G is selected from SEQ ID NOS: 23-24 and 28-34.
  • the CPP is selected from SEQ I D NO: 21, 22, 25-27, and 35.
  • the CPP is selected from:
  • the targeting sequence can specifically hybridizes to a bacterial mRNA target sequence that encodes a protein associated with a biochemical pathway and/or cellular process, or a rRNA target sequence.
  • the target sequence comprises a translational start codon of the bacterial mRNA and/or a sequence within about 30 bases upstream or downstream of the translational start codon of the bacteria! mRNA.
  • the protein associated with a biochemical pathway and/or cellular process may be a fatty acid biosynthesis protein.
  • the fatty acid biosynthesis protein can be an acyl carrier protein.
  • the acyl carrier protein may be AcpP.
  • the fatty acid biosynthesis protein may be an acyl carrier protein synthase.
  • the acyl carrier protein synthase may be FabB.
  • the fatty acid biosynthesis protein may be a carboxyltransferase alpha subunit of an acetyl Coenzyme A carboxylase.
  • the carboxyltransferase alpha subunit of an acetyl Coenzyme A carboxylase may be AccA.
  • the target sequence may be SEQ ID NQs:l-3, wherein thymine bases (T) are optionally uracil bases (U).
  • the targeting sequence comprises or consists of at least one of the targeting sequences in Table 1A (e.g., SEQ ID NOS:l-3), comprises or consists of a fragment of at least 10 contiguous nucleotides of a targeting sequence in Table 1A (e.g., SEQ ID NOS:l-3), or comprises or consists of a variant having at least 80% sequence identity to a targeting sequence in Table 1A (e.g., SEQ ID NOS:l ⁇ 3), wherein thymine bases (T) are optionally uracil bases (U).
  • T thymine bases
  • U uracil bases
  • the protein associated with a biochemical pathway and/or cellular process may be a peptidogiycan biosynthesis protein.
  • the peptidoglycan biosynthesis protein can be a UDP-N-acetylglucosamine 1-carboxyvinyltransferase.
  • the UDP-N-acetylglucosamine 1-carboxyvinyltransferase may be MurA.
  • the protein associated with a biochemical pathway and/or cellular process is a ribosomal protein.
  • the ribosomal protein is a 50S ribosomai protein L28.
  • the 50S ribosomal protein L28 is RpmB.
  • the ribosomal protein is a 30S ribosomal protein, in some embodiments, the 30S ribosomal protein is RpsJ.
  • the protein associated with a biochemical pathway and/or cellular process is a ribosomal RNA (rRNA).
  • rRNA ribosomal RNA
  • examples of rRNA include 5S, 16S, and 23S rRNA.
  • the rRNA is a 16S rRNA.
  • the rRNA is a 23S rRNA.
  • the protein associated with a biochemical pathway and/or cellular process is a DNA or chromosomal replication protein.
  • the DNA or chromosomal replication protein is a topoisomerase. In some embodiments, the topoisomerase is GyrA.
  • the DNA or chromosomal replication protein is a helicase. in some embodiments, the helicase is DnaB. In some embodiments, the DNA or chromosomal replication protein is a DNA polymerase, in some embodiments, the DNA polymerase is PoiB.
  • the protein associated with a biochemical pathway and/or cellular process is a lipopolysaccharide biosynthesis protein.
  • the lipopolysaccharide biosynthesis protein is a N-acetyigiucosamine deacetylase.
  • the N- acetylglucosamine deacetylase is LpxC.
  • the protein associated with a biochemical pathway and/or cellular process is a cellular energy homeostasis protein.
  • the cellular energy homeostasis protein is an adenylate kinase, in certain embodiments, the adenylate kinase is Adk.
  • the protein associated with a biochemical pathway and/or cellular process is a protein biosynthesis protein.
  • the protein biosynthesis protein is a translation initiation factor.
  • the translation initiation factor is InfA.
  • the protein associated with a biochemical pathway and/or cellular process is a ceil division protein
  • the cell division protein is a protein that assembles into a ring at the future site of the septum of bacterial ceil division.
  • the protein that assembles into a ring at the future site of the septum of bacterial ceil division is FtsZ.
  • the protein associated with a biochemical pathway and/or cellular process is an RNA synthesis protein.
  • the RNA synthesis protein is a sigma D factor of RNA polymerase.
  • the sigma D factor of RNA polymerase is RpoD.
  • the protein associated with a biochemical pathway and/or cellular process is an aromatic compound biosynthesis protein.
  • the aromatic compound biosynthesis protein is a chorismate synthase (5-enolpyruvylshikimate-3-phosphate phospholyase).
  • the chorismate synthase (5- enolpyruvylshikimate-3-phosphate phospholyase) is AroC.
  • the protein associated with antibiotic resistance is selected from one or more of BiaT, Cml, and AdeA.
  • the protein associated with a biochemical pathway and/or cellular process may be a murein biosynthesis protein, cell division protein, global gene regulatory protein, fatty acid biosynthesis protein, ribosomal protein, ribosomal RNA (rRNA),
  • the targeting sequence comprises or consists of at least one of the targeting sequences set forth in Table IB (e.g., SEQ ID NOS:4-20), comprises or consists of a fragment of at least 10 contiguous nucleotides of a targeting sequence in Table IB (e.g., SEQ ID NOS:4-20), or comprises or consists of a variant having at least 80% sequence identity to a targeting sequence in Table IB (e.g., SEQ ID NOS:4-20), wherein thymine bases (T) are optionally uracil bases (U).
  • Table IB e.g., SEQ ID NOS:4-20
  • the targeting sequence is selected from:
  • X is 9, wherein thymine bases (T) may be uracil bases (U).
  • the targeting sequence is selected from:
  • Exemplary antisense oligomers (AONs) of the disclosure include those described in Tables 2A-B below.
  • Embodiments of the present disclosure include methods of using the antisense oligomers described herein to reduce the expression and activity of one or more bacterial proteins associated with biochemical pathways, cellular processes, and/or antibiotic resistance. Certain embodiments include methods of using the antisense oligomers to reduce replication, proliferation, or growth of a bacteria, for example, to treat a bacterial infection in a subject, either alone or in combination with one or more additional antimicrobial agents. In some instances, the antisense oligomers increase the susceptibility of the bacterium to one or more antimicrobial agents.
  • compositions comprising the antisense oligomers, typically in combination with a pharmaceuticaiiy-acceptable carrier.
  • Certain pharmaceutical compositions can further comprise one or more antimicrobial agents.
  • the methods provided herein can be practiced in vitro or in vivo.
  • certain embodiments include methods of treating a bacterial infection in a subject, comprising administering to a subject in need thereof (e.g., subject having or at risk for having a bacterial infection) an antisense oligomer or pharmaceutical composition described herein. Also included are methods of reducing replication of a bacteria, comprising contacting the bacterium with an antisense oligomer described herein.
  • the bacterium is selected from the genus Klebsiella, Pseudomonas, Acinetobacter, and Escherichia.
  • Klebsiella is a genus of a Gram -negative, nonmotile, encapsulated, lactose-fermenting, facultative anaerobic, rod- shaped bacterium that includes the species Klebsiella pneumoniae, which is responsible for the vast majority of Klebsiella -related pathogenesis.
  • Pseudomonas is a genus of Gram-negative, aerobic rod-shaped bacterium that commonly- found in skin, soil, and water.
  • the genus includes the species Pseudomonas aeruginosa, an opportunistic pathogen that is responsible for the vast majority of Pseudomonas-related infections, it causes urinary tract infections, respiratory system infections, dermatitis, soft tissue infections, bacteremia, bone and joint infections, gastrointestinal infections and a variety of systemic infections, particularly in patients with severe burns and in cancer and AIDS patients who are
  • Pseudomonas aeruginosa infections are a serious problem in patients hospitalized with cancer, cystic fibrosis, and burns.
  • Acinetobacter is a genus of Gram-negative bacteria belonging to the class of
  • Gammaproteobacteria Examples of clinically-relevant Acinetobacter complexes include the
  • Acinetobacter caicoaceticus-baumannii complex (glucose-oxidizing nonhemolytic), Acinetobacter iwoffii (glucose-negative nonhemolytic), and Acinetobacter haemoiyticus (hemolytic).
  • Specific examples include Acinetobacter baumannii.
  • Escherichia is a genus of Gram-negative, non-spore forming, facultatively anaerobic, rod- shaped bacteria from the family Enterobacteriaceae, and includes the species Escherichia coli, which is responsible for the vast majority of Escherichia-reiated pathogenesis.
  • the bacterium is any of the foregoing members of the genera Klebsiella, Pseudomonas, Acinetobacter or Escherichia, In specific embodiments, the bacterium is Klebsiella pneumoniae, Pseudomonas aeruginosa, Acinetobacter baumannii, or Escherichia coii. in some embodiments, the bacterium is selected from one or more of the strains in Table El.
  • the bacterium is a multi-drug resistance (MDR) strain of bacteria.
  • MDR multi-drug resistance
  • Multiple drug resistance (MDR), multi-drug resistance or muitiresistance is a condition enabling disease-causing microorganisms (bacteria, viruses, fungi or parasites) to resist distinct antimicrobials such as antibiotics, antifungal drugs, antiviral medications, antiparasitic drugs, and others.
  • the bacterium is extensively-drug resistant (XDR) or pan-drug resistant (PDR).
  • the bacterium is an extended-spectrum ⁇ -lactamase (ESBLs) producing Gram-negative bacteria, or a muiti-drug-resistant gram negative rod (MDR GNR) MDRGN bacteria
  • ESBLs extended-spectrum ⁇ -lactamase
  • MDR GNR muiti-drug-resistant gram negative rod
  • the bacterium is MDR Klebsiella, for example, MDR Klebsiella pneumoniae, or MDR Pseudomonas, for example, MDR Pseudomonas aeruginosa
  • the bacterium is MDR Escherichia, for example, MDR Escherichia coli, or MDR Acinetobacter, for example, MDR Acinetobacter baumannii.
  • genes associated with biochemical pathways and/or cellular processes include fatty acid biosynthesis genes (and their related proteins) such as acpp, accA, acpS, and/or fab genes, for example, fabB.
  • the bacterium comprises or expresses the acpp gene, which encodes an acyi carrier protein
  • the bacterium comprises or expresses the accA gene, which encodes a carboxyltransferase alpha subunit of an acetyl Coenzyme A carboxylase.
  • the bacterium comprises or expresses th fabB gene, which encodes an carrier protein synthase.
  • the bacterium that comprises or expresses one or more genes associated with fatty acid biosynthesis is a Klebsiella species, for example, Klebsiella pneumoniae.
  • the bacterium that comprises or expresses one or more genes associated with fatty acid biosynthesis is a Pseudomonas species, for example, Pseudomonas aeruginosa.
  • the bacterium that comprises or expresses one or more genes associated with fatty acid biosynthesis is an
  • Acinetobacter species for example, Acinetobacter baumannii.
  • the bacterium that comprises or expresses one or more genes associated with fatt acid biosynthesis is an Escherichia species, for example, Escherichia coii.
  • the subject in need thereof is immunocompromised, in certain embodiments, the subject in need thereof is immunocompromised and has an underlying !ung disease, such as pneumonia, cystic fibrosis (CF), or chronic granulomatous disease (CGD).
  • CF cystic fibrosis
  • CTD chronic granulomatous disease
  • genes associated with biochemical pathways and/or cellular processes include peptidogiycan biosynthesis genes (and their related proteins), in particular embodiments, the bacterium comprises or expresses the murA gene, which encodes a UDP-N-acetylglucosamine 1- carboxyviny!transferase. in some embodiments, the bacterium that comprises or expresses one or more peptidoglycan biosynthesis genes (e.g., murA) is a Klebsiella species, for example, Klebsiella pneumoniae.
  • the bacterium that comprises or expresses one or more peptidoglycan biosynthesis genes is a Pseudomonas species, for example, Pseudomonas aeruginosa.
  • the bacterium that comprises or expresses one or more peptidoglycan biosynthesis genes is an Acinetobacter species, for example,
  • the bacterium that comprises or expresses one or more peptidoglycan biosynthesis genes is an Escherichia species, for example, Escherichia coli.
  • genes associated with biochemical pathways and/or cellular processes include ribosomal protein genes (and their related proteins).
  • the bacterium comprises or expresses the rpmB gene, which encodes a SOS ribosomal protein L28.
  • the bacterium comprises or expresses the rpsJ gene, which encodes a 30S ribosomal protein.
  • the bacterium that comprises or expresses one or more ribosomal protein genes is a Klebsiella species, for example, Klebsiella pneumoniae.
  • the bacterium that comprises or expresses one or more ribosomal protein genes is a Pseudomonas species, for example, Pseudomonas aeruginosa
  • the bacterium that comprises or expresses one or more ribosomal protein genes is an Acinetobacter species, for example, Acinetobacter baumannii.
  • the bacterium that comprises or expresses one or more ribosomal protein genes is an Escherichia species, for example, Escherichia coli.
  • genes associated with biochemical pathways and/or cellular processes include cellular homeostasis genes (and their related proteins).
  • the bacterium comprises or expresses the adk gene, which encodes an adenylate kinase.
  • genes associated with biochemical pathways and/or cellular processes include protein biosynthesis genes (and their related proteins).
  • the bacterium comprises or expresses the infA gene, which encodes a translation initiation factor.
  • genes associated with biochemical pathways and/or cellular processes include cell division genes (and their related proteins), in particular embodiments, the bacterium comprises or expresses the /tsZ gene, which encodes a protein that assembles into a ring at the future site of the septum of bacterial cell division.
  • the bacterium that comprises or expresses one or more genes associated with cell division is a Klebsiella species, for example, Klebsiella pneumoniae.
  • the bacterium that comprises or expresses one or more genes associated with cell division is a Pseudomonas species, for example, Pseudomonas aeruginosa.
  • the bacterium that comprises or expresses one or more genes associated with cell division is an Acinetobacter species, for example, Acinetohacter baumannii.
  • the bacterium that comprises or expresses one or more genes associated with ceil division is an Escherichia species, for example, Escherichia coii.
  • genes associated with DNA or chromosomal replication include topoisomerases and helicases (and their related proteins).
  • the bacterium comprises or expresses the gyrA gene, which encodes a fopoisomerase.
  • the bacterium comprises or expresses the dnaB gene, which encodes a helicase.
  • the bacterium comprises or expresses the polB gene, which encodes a DNA polymerase.
  • the bacterium that comprises or expresses one or more genes associated with DNA or chromosomal replication is a Klebsiella species, for example, Klebsiella pneumoniae
  • the bacterium that comprises or expresses one or more genes associated with DNA or chromosomal replication is a Pseudomonas species, for example, Pseudomonas aeruginosa
  • the bacterium that comprises or expresses one or more genes associated with DNA or chromosomal replication is an Acinetobacter species, for example, Acinetobacter baumannii.
  • the bacterium that comprises or expresses one or more genes associated with DNA or chromosomal replication is an Escherichia species, for example, Escherichia coii.
  • genes associated with lipopoiysaccharide biosynthesis include deacetyiases such as N-acetyigiucosamine deacetylase.
  • the bacterium comprises or expresses the IpxC gene, which encodes an N-acetyigiucosamine deacetylase.
  • the bacterium that comprises or expresses one or more genes associated with lipopoiysaccharide biosynthesis is a Klebsiella species, for example, Klebsiella
  • the bacterium that comprises or expresses one or more genes associated with lipopoiysaccharide biosynthesis is a Pseudomonas species, for example, Pseudomonas aeruginosa.
  • the bacterium that comprises or expresses one or more genes associated with lipopoiysaccharide biosynthesis is an Acinetobacter species, for example, Acinetobacter baumannii.
  • the bacterium that comprises or expresses one or more genes associated with lipopoiysaccharide biosynthesis is an Escherichia species, for example, Escherichia coii.
  • RNA synthesis genes examples include genes associated with biochemical pathways and/or cellular processes.
  • the bacterium comprises or expresses the rpoD gene, which encodes a sigma D factor of RNA polymerase.
  • the bacterium that comprises or expresses one or more RNA synthesis genes is a Klebsiella species, for example, Klebsiella pneumoniae.
  • the bacterium that comprises or expresses one or more one or more RNA synthesis genes is a Pseudomonas species, for example, Pseudomonas aeruginosa.
  • the bacterium that comprises or expresses one or more one or more RNA synthesis genes is an Acinetobacter species, for example, Acinetobacter baumannii.
  • the bacterium that comprises or expresses one or more RNA synthesis genes is an Acinetobacter species, for example, Acinetobacter baumannii.
  • the bacterium that comprises or expresses one or more RNA synthesis genes is an Acinetobacter species, for example, Acinetobacter baumannii.
  • the bacterium that comprises or expresses one or more RNA synthesis genes is an Acinetobacter species, for example, Acinetobacter baumannii.
  • Escherichia species for example, Escherichia coli.
  • the bacterium comprises or expresses the aroC gene, which encodes a chorismate synthase (5- enolpyruvylshikimate-3-phosphate phosphoiyase).
  • the bacteria or bacterium comprises (e.g., encodes) one or more antibiotic resistance genes.
  • antibiotic resistance genes include beta-lactamases, which can enzymatically deactivate certain antimicrobial agents, and genes/proteins which increase the permeability or active efflux (pumping out) of an
  • antibiotic resistance genes include TEM beta-lactamase (biaT), chloramphenicol resistance gene cml and resistance-nodulation-celi division (RN D)-type multidrug efflux pump subunit AdeA (adeA).
  • the bacterium is Klebsiella pneumonia, Pseudomonas aeruginosa, Acinetobacter spp., or Escherichia coli, which comprises or expresses at least one antibiotic resistance gene selected from biaT, cm! and adeA.
  • the antisense oligomer reduces expression of the gene(s) associated with biochemical pathways, cellular processes, and/or antibiotic resistance in the bacteria or bacterium.
  • the antisense oligomer reduces expression by about or at least about 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150, 200, 250, 300, 350, 400, 450, 500, 600, 700, 800, 900, or 1000% or more (including all integers and ranges in between), relative to a control (e.g., absence of the antisense oligomer, scrambled oligomer, prior to contacting with the oligomer), or by about or at least about 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 200, 300, 400, 500, 1000-fold or more (including all integers and
  • the antisense oligomer reduces expression of one or more of AcpP, FabB, AccA, MurA, Rpm B, RpsJ, Adk, InfA, 16S rRNA, 30S rRNA, GyrA, DnaB, Pol B, FtsZ, LpxC, RpoD, AroC, BiaT, Cml and/or AdeA and the bacterium is an Klebsiella, Pseudomonas, Acinetobacter, or Escherichia species which comprises or expresses one or more of AcpP, FabB, AccA, MurA, RpmB, RpsJ, Adk, InfA, 16S rRNA, 30S rRNA, GyrA, DnaB, Po!B, FtsZ, LpxC, RpoD, AroC, BlaT, Cm! and/or AdeA.
  • Gene or protein expression can be measured in vitro (see,
  • the antisense oligomer reduces or inhibits the growth of the bacteria or bacterium.
  • the antisense oligomer reduces growth of the bacteria or bacterium by about or at least about 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, SO, 85, 90, 95, 100, 150, 200, 250, 300, 350, 400, 450, 500, 600, 700, 800, 900, or 1000% or more (including all integers and ranges in between), relative to a control (e.g., absence of the antisense oligomer, scrambled oligomer, prior to contacting with the oligomer), or by about or at least about 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 200, 300, 400, 500, 1000-fold or more (including all integers and ranges in between), relative to a control
  • Bacterial growth can be measured in vitro (see, e.g., the Examples) or in vivo.
  • the antisense oiigomer that reduces growth of the bacterium is targeted against expression a protein associated with a biochemical pathway and/or cellular process selected from one or more of AcpP, FabB, AccA, MurA, RpmB, RpsJ, Adk, InfA, 16S rRNA, 30S rRNA, GyrA, DnaB, PolB, FtsZ, LpxC, RpoD, AroC, BlaT, Cml and/or AdeA and the bacterium is an Klebsiella,
  • the antisense oligomer is employed in combination with one or more antimicrobial agents, for example, to reduce (e.g., synergistically reduce) the growth of the bacteria or bacterium.
  • the methods are practiced in vivo, and comprise administering the antisense oligomer to a subject in need thereof, for example, a subject in need thereof that is infected or at risk for being infected by one or more of the bacteria described herein.
  • the antisense oligomers described herein can thus be administered to subjects to treat (prophyiacticaily or therapeutically) an infection by any of the bacteria described herein.
  • pharmacogenomics e.g., the study of the relationship between an individual's genotype/phenotype and that individual's response to a foreign compound or drug
  • Differences in metabolism of therapeutics can lead to severe toxicity or therapeutic failure by altering the relation between dose and blood concentration of the pharmacologically active drug.
  • a physician or clinician may consider applying knowledge obtained in relevant pharrnacogenomics studies in determining whether to administer a therapeutic agent as well as tailoring the dosage and/or therapeutic regimen of treatment with a therapeutic agent.
  • Effective delivery of the antisense oligomer to the target nucleic acid is one aspect of treatment.
  • Routes of antisense oligomer delivery include, but are not limited to, various systemic routes, including oral and parenteral routes, e.g., intravenous, subcutaneous, intraperitoneal, and intramuscular, as well as inhalation, transdermal , and topical delivery.
  • the appropriate route may be determined by one of skill in the art, as appropriate to the condition of the subject under treatment.
  • Vascular or extravascular circulation, the blood or lymph system, and the cerebrospinal fluid are some non-limiting sites where the antisense oligomers may be introduced.
  • Direct CNS delivery may be employed, for instance, intracerebral, intraventricular, or intrathecal administration may be used as routes of administration.
  • the antisense oligomers can be delivered by transdermal methods (e.g., via incorporation of the antisense oligomers into, e.g., emulsions, with such antisense oligomers optionally packaged into liposomes).
  • transdermal and emulsion/liposome-mediated methods of delivery are described for delivery of antisense oligomers in the art, e.g., in U.S. Pat. No. 6,965,025, the contents of which are incorporated in their entirety by reference herein.
  • the antisense oligomers described herein may also be delivered via an implantable device.
  • Design of such a device is an art-recognized process, with, e.g., synthetic implant design described in, e.g., U.S. Pat. No. 6,969,400, the contents of which are incorporated by reference.
  • Antisense oligomers can be introduced into cells using art-recognized techniques (e.g., transfection, eiectroporation, fusion, liposomes, colloidal polymeric particles and viral and non-viral vectors as well as other means known in the art).
  • the method of delivery selected will depend at least on the oligomer chemistry, the ceils to be treated and the location of the cells and will be apparent to the skilled artisan. For instance, localization can be achieved by liposomes with specific markers on the surface to direct the liposome, direct injection into tissue containing target cells, specific receptor-mediated uptake, or the like.
  • antisense oligomers may be delivered using, e.g., methods involving iiposome-mediated uptake, lipid conjugates, poiyiysine-mediated uptake, nanoparticie-mediated uptake, and receptor-mediated endocytosis, as well as additional non-endocytic modes of delivery, such as microinjection, permeabllization (e.g., streptolysin-0 permeabllization, anionic peptide permeabiiization), eiectroporation, and various non-invasive non-endocytic methods of delivery that are known in the art (see, e, g., Dokka and Rojanasakui, Advanced Drug Delivery Reviews 44:35-49, incorporated by reference in its entirety).
  • the antisense oligomers may be administered in any convenient vehicle or carrier which is physiologically and/or pharmaceutically acceptable.
  • a composition may include any of a variety of standard pharmaceutically acceptable carriers employed by those of ordinary skill in the art. Examples include, but are not limited to, saline, phosphate buffered saline (PBS), water, aqueous ethanol, emulsions, such as oil/water emulsions or triglyceride emulsions, tablets and capsules.
  • PBS phosphate buffered saline
  • emulsions such as oil/water emulsions or triglyceride emulsions, tablets and capsules.
  • suitable physiologically acceptable carrier will vary dependent upon the chosen mode of administration.
  • “Pharmaceutically acceptable carrier” is intended to include any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents, and the like, compatible with pharmaceutical administration.
  • the use of such media and agents for pharmaceutically active substances is well known in the art. Except insofar as any conventional media or agent is incompatible with the active compound, use thereof in the compositions is contemplated. Supplementary active compounds can also be incorporated into the compositions
  • the compounds (e.g., antisense oligomers, antimicrobial agents) described herein may generally be utilized as the free acid or free base.
  • the compounds described herein may be used in the form of acid or base addition salts.
  • Acid addition salts of the free amino compounds described herein may be prepared by methods well known in the art, and may be formed from organic and inorganic acids.
  • Suitable organic acids include maleic, fumaric, benzoic, ascorbic, succinic, methanesulfonic, acetic, trifluoroacetic, oxalic, propionic, tartaric, salicylic, citric, gluconic, lactic, mandelic, cinnamic, aspartic, stearic, palmitic, giycolic, glutamic, and
  • Suitable inorganic acids include hydrochloric, hydrobromic, sulfuric, phosphoric, and nitric acids.
  • Base addition salts included those salts that form with the carboxyiate anion and include salts formed with organic and inorganic cations such as those chosen from the alkali and alkaline earth metals (for example, lithium, sodium, potassium, magnesium, barium and calcium), as well as the ammonium ion and substituted derivatives thereof (for example, dibenzylammonium,
  • prodrugs are also included within the context of this disclosure.
  • Prodrugs are any covIERly bonded carriers that release a compound in vivo when such prodrug is administered to a patient.
  • Prodrugs are generally prepared by modifying functional groups in a way such that the modification is cleaved, either by routine manipulation or in vivo, yielding the parent compound.
  • Prodrugs include, for example, compounds of this disclosure wherein hydroxy, amine or suifhydryl groups are bonded to any group that, when administered to a patient, cleaves to form the hydroxy, amine or suifhydryl groups.
  • prodrugs include (but are not limited to) acetate, formate and benzoate derivatives of alcohol and amine functional groups of the antisense oligomers described herein.
  • esters may be employed, such as methyl esters, ethyl esters, and the like.
  • liposomes may be employed to facilitate uptake of the antisense oligomer into cells (see, e.g., Williams, S.A., Leukemia 10(12):198Q-1989, 1996; Lappaiainen et al., Antiviral Res. 23:119, 1994; Uhimann et al., antisense oligomers: a new therapeutic principle, Chemical Reviews, Volume 90, Mo. 4, 25 pages 544-584, 1990; Gregoriadis, G., Chapter 14,
  • Hydrogels may also be used as vehicles for antisense oligomer administration, for example, as described in WO 93/01286.
  • the oligomers may be administered in microspheres or microparticles. (See, e.g., Wu, G.Y. and Wu, C.H., J. Biol. Chem. 262:4429-4432, 30 1987).
  • the use of gas- filled microbubbles complexed with the antisense oligomers can enhance delivery to target tissues, as described in US Patent Mo. 6,245,747.
  • Sustained release compositions may also be used. These may include semipermeable polymeric matrices in the form of shaped articles such as films or microcapsules.
  • the antisense oligomer is administered to a mammalian subject, e.g., human or domestic animal, exhibiting the symptoms of a bacterial infection (e.g., antibiotic resistance or D bacterial infection), in a suitable pharmaceutical carrier.
  • a mammalian subject e.g., human or domestic animal
  • the subject is a human subject, e.g., a patient diagnosed as having a bacterial infection.
  • the antisense oligomer is contained in a pharmaceutically acceptable carrier, and is delivered orally.
  • the antisense oligomer is contained in a pharmaceutically acceptable carrier, and is delivered intravenously (i.v.j.
  • the antisense oligomer is administered in an amount and manner effective to result in a peak blood concentration of at least 200-400 nM antisense oligomer.
  • one or more doses of antisense oligomer are administered, generally at regular intervals, for a period of about one to two weeks.
  • Certain doses for oral administration are from about 1-1000 mg oligomer per 70 kg. In some cases, doses of greater than 1000 mg oligomer/patient may be necessary. For i.v. administration, some doses are from about 0.5 mg to 1000 mg oligomer per 70 kg.
  • the antisense oligomer may be administered at regular intervals for a short time period, e.g., daily for two weeks or less. However, in some cases the antisense oligomer is administered intermittently over a longer period of time.
  • Administration may be followed by, or concurrent with, administration of an antimicrobial (e.g., antibiotic) or other therapeutic treatment, as described herein.
  • the treatment regimen may be adjusted (dose, frequency, route, etc.) as indicated, based on the results of immunoassays, other biochemical tests and physiological examination of the subject under treatment.
  • An effective in vivo treatment regimen using the antisense oligomers described herein may vary according to the duration, dose, frequency and route of administration, as well as the condition of the subject under treatment (i.e., prophylactic administration versus administration in response to localized or systemic infection). Accordingly, such in vivo therapy will often include monitoring by tests appropriate to the particular type of disorder or bacterial infection under treatment, and corresponding adjustments in the dose or treatment regimen, in order to achieve an optimal therapeutic outcome.
  • Treatment may be monitored, e.g., by general indicators of disease known in the art.
  • the efficacy of an in vivo administered antisense oligomer described herein may be determined from biological samples (tissue, blood, urine etc.) taken from a subject prior to, during and subsequent to administration of the antisense oligomer.
  • Assays of such samples include (1) monitoring the presence or absence of heteroduplex formation with target and non -target sequences, using procedures known to those skilled in the art, e.g., an electrophoretic gel mobility assay; (2) monitoring the amount of a mutant m NA in relation to a reference normal m RMA or protein as determined by standard techniques such as RT-PCR, Northern blotting, ELISA or Western blotting.
  • Certain embodiments include combination therapies, for example, the administration of antisense oligomers in combination with antimicrobial agents such as antibiotics.
  • Combination therapies can be employed, for example, to increase the sensitivit or susceptibilit of a given bacteria to one or more antimicrobial agents, and thereb improve the therapeutic outcome (e.g., resolution of the infection).
  • certain combination therapies can be employed, for example, to reduce or reverse the resistance of a given bacteria to one or more antimicrobial agents.
  • the antisense oligomer reduces the minimum inhibitory concentration (M IC) of an antibiotic against a given bacterium.
  • M IC minimum inhibitory concentration
  • the antisense oligomer and the antimicrobial agent display synergy in reducing bacterial growth and/or increasing bacterial cell- killing.
  • pharmaceutical compositions as described herein, which comprise an antisense oligomer and an antimicrobial agent such as antibiotic.
  • the antisense oligomer and the antimicrobial agent are administered separately, in certain embodiments, the antisense oligomer and the antimicrobial agent are administered sequentially. In some embodiments, the antisense oligomer and the antimicrobial agent are administered concurrently, for example, as part of the same or different pharmaceutical composition.
  • antimicrobial agents e.g., antibiotics
  • beta-!actam antibiotics such as carbapenems, penicillin and penicillin derivatives (or penams), ampicil!in, chloramphenicol, cephalosporins (e.g., Cefacetrile (cephacetriie), Cefadroxil (cefadroxyi; Duricef), Cephalexin (cefaiexin; Keflex), Cefaloglycin
  • cephaiogiycin Cefalonium (cephalonium), Cefaioridine (cephaloradine), Cefaiotin (cephalothin; Keflin), Cefapirin (cephapirin; Cefadryi), Cefatrizine, Cefazaflur, Cefazedone, Cefazolin (cephazolin; Ancef, Kefzol), Cefradine (cephradine; Velosef), Cefroxadine, Ceftezole, Cefaclor (Cedar, Distaclor, Keflor, Ranicior), Cefonicid ( onocid), Cefprozii (cefproxil; Cefzil), Cefuroxime (Zefu, Zinnat, Zinacef, Ceftin, Biofuroksym, Xorimax), Cefuzonam, Cefmetazole, Cefotetan, Cefoxitin, loracarbef (Lora
  • Cefteram Ceftibuten (Cedax), Ceftiofur, Ceftiolene, Ceftizoxime (Cefizox), Ceftriaxone (Rocephin), Cefoperazone (Cefobid), Ceftazidime ( eezat, Fortum, Fortaz), iatamoxef (moxalactam), Cefclidine, cefepime (Maxipime), cefluprenam, cefoselis, Cefozopran, Cefpirome (Cefrom), Cefquinome, flomoxef, Ceftobiproie, Ceftaroline, Cefaloram, Cefaparole, Cefcanel, Cefedroior, Cefempidone, Cefetrizoie, Cef
  • quinoiones such as cinoxacin, nalidixic acid, oxolinic acid (Uroxin), piromidic acid (Panacid), pipemidic acid (Dolcol) rosoxacsn (Eradacil), ciprofloxacin (Alcipro,Ciprobay, Cipro, Ciproxin, ultracipro), enoxacin (Enroxil, Penetrex), fleroxacsn ( egaione, Roquinol), lomefloxacin (Maxaquin), nadifloxacin (Acuatim, Nadoxin, Nadixa), norfloxacin (Lexinor, Noroxin, Quinabic, .!anacin), ofloxacin (Flox
  • any one or more of the foregoing antibiotics can be combined with any of the antisense oligomers described herein, for the treatment of any of the bacterium or bacteria described herein.
  • the antimicrobial agent is selected from one or more of
  • the bacterium comprises or expresses a gene selected from one or more of acpP and fabB, and the antisense oligomer is targeted against expression of the fatty acid biosynthesis gene. In some of these and related embodiments, the bacterium comprises or expresses a gene selected from one or more of murA, and the antisense oligomer is targeted against expression of the peptidoglycan biosynthesis gene.
  • the bacterium comprises or expresses a gene selected from one or more of rpmB and rpsJ, and the antisense oligomer is targeted against expression of the ribosomai protein gene. In some of these and related embodiments, the bacterium comprises or expresses a gene selected from one or more of ftsZ, and the antisense oligomer is targeted against expression of the cell division gene. In some of these and related embodiments, the bacterium comprises or expresses a gene selected from one or more of gyrA, dnaB, and po!B, and the antisense oligomer is targeted against expression of the DNA or chromosomal replication gene.
  • the bacterium comprises or expresses a gene selected from one or more of IpxC, and the antisense oligomer is targeted against expression of the lipopoiysaccharide biosynthesis gene.
  • the bacterium comprises or expresses a ribosomai RNA selected from one or more of 55 rRNA, 16S rRNA, and 23s rRNA, and the antisense oligomer is targeted against the rRNA.
  • the bacterium is Klebsiella pneumoniae, Pseudomonas aeruginosa, Acinetobacter spp., or Escherichia coii, including DR strains thereof.
  • the antimicrobial agent is a beta-!actam antibiotic, as described herein.
  • the antimicrobial agent is a carbapenem.
  • carbapenems include meropenem, imipenem, ertapenem, doripenem, panipenem, biapenem, razupenem, tebipenem, lenapenem, tomopenern, and ampicillin.
  • the antimicrobial agent is meropenem.
  • the antimicrobiai agent is a cephalosporin (cephem), penicillin or penicillin derivative (penam).
  • the antisense oligomer reduces the M IC of a carbapenem such as meropenem against a bacteria, for example, a strain or M DR strain of Klebsiella pneumoniae, Pseudomonos aeruginosa, Acinetobacter baumannii, or £ coli.
  • the combination of the antisense oligomer and the carbapenem such as meropenem reduces (e.g., synergistically reduces) bacterial cell growth or increase (e.g., synergistically increases) bacterial cell-killing, for example, of a strain or M DR strain of Klebsiella pneumoniae, Pseudomonos aeruginosa, Acinetobacter baumannii, or f . coli.
  • the antimicrobial agent is an aminoglycoside, as described herein.
  • aminoglycosides include tobramycin, gentamicin, kanamycin a, amikacin, dibekacin, sisomicin, netilmicin, neomycin B, neomycin C, neomycin E (paromomycin), and streptomycin.
  • the antimicrobiai agent is tobramycin.
  • the antisense oligomer reduces the M IC of an aminoglycoside such as tobramycin against a bacteria, for example, a strain or M DR strain of Klebsiella pneumoniae, Pseudomonos aeruginosa, Acinetobacter baumannii, or E. coli.
  • the combination of the antisense oligomer and the aminoglycoside such as tobramycin reduces (e.g., synergistically reduces) bacterial cell growth or increases (e.g., synergistically increases) bacterial cell-killing, for example, of a strain or M DR strain of Klebsiella pneumoniae, Pseudomonos aeruginosa, Acinetobacter baumannii, or E. coli.
  • the antimicrobiai agent is a polymyxin such as colistin (polymyxin E), po!ysporin, neosporin, or polymyxin B. in specific embodiments, the antimicrobial agent is colistin.
  • the antisense oligomer reduces the M IC of a polymyxin such as coiistin against a bacteria, for example, a strain or DR strain of Klebsiella pneumoniae,
  • the combination of the antisense oligomer and the polymyxin such as coiistin reduces (e.g.,
  • the antimicrobial agent includes one or more of ceftazidime, doxycyc!ine, piperacillin, meropenem, chloramphenicol, and/or co-trimoxazoie
  • the antisense oligomer increases the susceptibility or sensitivity of a given bacterium to the antimicrobial agent, relative to the antimicrobiai agent alone.
  • the antisense oligomer increases the susceptibility or sensitivity of the bacteria or bacterium to the antimicrobial agent by increasing the bactericidal (cell-killing) and/or bacteriostatic (growth-slowing) activity of the antimicrobial agent against the bacteria or bacterium being targeted, relative to the antimicrobial agent alone.
  • the anfisense oligomer increases the susceptibility or sensitivity by about or at least about 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150, 200, 250, 300, 350, 400, 450, 500, 600, 700, 800, 900, or 1000% or more (including all integers and ranges in between), relative to the antimicrobial agent alone, or by about or at least about 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 200, 300, 400, 500, 1000-fold or more (including all integers and ranges in between), relative to the antimicrobial agent alone, in some embodiments, the antisense oligomer synergistically increases the susceptibility or sensitivity of a given bacterium to the antimicrobial agent, relative to the antimicrobial agent alone.
  • the bacterium is Kleb
  • the antisense oligomer reduces the minimum inhibitory
  • MIC concentration of an antimicrobial agent against the bacteria or bacterium being targeted, relative to the antimicrobial agent alone.
  • minimum inhibitory concentration or “MIC” refers to the lowest concentration of an antimicrobial agent that will inhibit the visible growth of a microorganism after overnight (in vitro) incubation.
  • Minimum inhibitory concentrations are important in diagnostic laboratories to confirm resistance of microorganisms to an antimicrobial agent and also to monitor the activity of new antimicrobial agents.
  • the IC is generally regarded as the most basic laboratory measurement of the activity of an antimicrobial agent against a bacterial organism.
  • the oligomer reduces the minimum inhibitory
  • concentration (MIC) of an antimicrobial agent against the bacteria or bacterium by at least about 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150, 200, 250, 300, 350, 400, 450, 500, 600, 700, 800, 900, or 1000% or more (including all integers and ranges in between), relative to the antimicrobial agent alone.
  • the oligomer reduces the minimum inhibitory concentration (MIC) of an antimicrobial agent against the bacteria or bacterium by about or at least about 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 200, 300, 400, 500, 1000-fold or more (including all integers and ranges in between), relative to the antimicrobial agent alone.
  • the antisense oligomer synergistically reduces the M IC of an antimicrobial agent against the bacteria or bacterium being targeted, relative to the antimicrobial agent alone.
  • the bacterium is Klebsiella pneumoniae, Pseudomonas aeruginosa, Acinetobacter baurnannii, or E. coli, or an MDR strain thereof. V!. Treatment Mariitormg Methods
  • CBC complete blood count
  • nucleic acid detection methods such as nucleic acid detection methods
  • immunodiagnostic tests such as immunodiagnostic tests, or bacterial culture.
  • identification and monitoring of bacterial infection involves one or more of (1) nucleic acid detection methods, (2) serological detection methods, i.e., conventional immunoassay, (3) culture methods, and (4) biochemical methods. Such methods may be qualitative or quantitative.
  • Nucleic acid probes may be designed based on publicly available bacterial nucleic acid sequences, and used to detect target genes or metabolites (i.e., toxins) indicative of bacterial infection, which may be specific to a particular bacterial type, e.g., a particular species or strain, or common to more than one species or type of bacteria (i.e., Gram positive or Gram negative bacteria).
  • Nucleic amplification tests e.g., PGR
  • PGR nucleic amplification tests
  • Serological identification may be accomplished using a bacterial sample or culture isolated from a biological specimen, e.g., stool, urine, cerebrospinal fluid, blood, etc.
  • immunoassay for the detection of bacteria is generally carried out by methods routinely employed by those of skill in the art, e.g., ELISA or Western blot.
  • monoclonal antibodies specific to particular bacterial strains or species are often commercially available.
  • Culture methods may be used to isolate and identify particular types of bacteria, by employing techniques including, but not limited to, aerobic versus anaerobic culture, growth and morphology under various culture conditions.
  • Exemplary biochemical tests include Gram stain (Gram, 1884; Gram positive bacteria stain dark blue, and Gram negative stain red), enzymatic analyses, and phage typing.
  • the status of the bacterial infection is also monitored using diagnostic techniques typically used by those of skill in the art to monitor the particular type of bacterial infection under treatment.
  • the PMO or PPMO treatment regimen may be adjusted (dose, frequency, route, etc), as indicated, based on the results of immunoassays, other biochemical tests and physiological examination of the subject under treatment.
  • the method provides an improvement in therapy against bacterial infection, for example, multi-drug resistant (M DR) bacteria, using various PPMOs to achieve enhanced cell uptake and anti-bacterial action.
  • M DR multi-drug resistant
  • One exemplary aspect is that compounds effective against virtually any pathogenic bacterial can be readily designed and tested, e.g., for rapid response against new drug-resistant strains.
  • PPMOs Peptide-Conjugated Phosphorodiamidate Morpholino Oligomers.
  • PPMOs were synthesized and purified at Sarepta Therapeutics Inc. (Cambridge, MA, USA) as previously described (Tiliey et al., Antimicrob Agents Chemother 50:2789-2796, 2006). Lyophilized PPMOs were dissolved in uitrapure water and sterile-filtered. PPMO peptides were attached to either the 5' or 3' end of the oligomer sequence as indicated.
  • Bacteria, Bacterial strains were obtained through the clinical microbiology lab at UT Southwestern unless otherwise noted.
  • Minimal Inhibitory Concentration Assays Minimal inhibitory concentration (M IC) assays were performed in Mueller Hinton 11 medium using the microdilution method as described by the Clinical and Laboratory Standards Institute (CLSI). Optical density (OD) of cultures was read in a micropiate spectrophotometer at 595-600 nm. After 18-20 hours of aerobic growth (200 -250 rpm) at 37°C, 100 ⁇ cultures with an OD of ⁇ 0.06 were scored as no growth.
  • M IC Minimum inhibitory concentration
  • PPMOs Activity of PPMOs Targeted Against Expression of Essential Genes of K. pneumoniae PPMOs were designed, synthesized, and tested against the expression of essential genes representing a variety of biochemical pathways and cellular processes in Klebsiella pneumoniae. These included: murein biosynthesis, cell division, global gene regulatory mechanisms, fatty acid biosynthesis, ribosomai proteins, DMA replication, transcription, translation initiation,
  • each PPMO was tested by measuring the minima! inhibitory concentration (M IC) according to the method described above (CLSI microdilution assay).
  • M IC inhibitory concentration
  • the M IC of each PPMO was tested using a pane! of 38 strains of K. pneumoniae, shown in TabSe El below, including eight that express the KPC carbapenemase, five that express the N DM-1 carbapenemase, two that express the OXA-48 carbapenemase, and others that are multidrug resistant (M DR).
  • PPMOs targeted against ribosomal RIMA were designed by positioning them at highly conserved regions of the 5S, 16S and 23S rRNA. Each sequence was then aligned and compared with the equivalent rRNAs in Homo sapiens, and any PP O sequence with a complementary match of 10 or more bases was eliminated.
  • MIC minimal inhibitory concentration
  • the results of MIC testing show that at least three of the PPMOs (PPMO#15, PPMO#17, and PPMO#18 targeted to 23S-858, 16S-11Q1, and 165-1101, respectively) inhibited growth of at least two of the three targeted pathogens.
  • the inhibitory concentration of 75% of the strains tested (IC75) was 8 ⁇ or less for PPMO#15 in K. pneumoniae and P. aeruginosa, and for PPMO#18 in P. aeruginosa and Acinetobacter baumannii.

Abstract

Provided are antisense oligomers targeted against bacterial mRNAs and other macromolecules associated with a biochemical pathway and/or cellular process, and related compositions and methods of using the oligomers and compositions to treat an infected mammalian subject, for example, as primary antimicrobials or as adjunctive therapies with classic antimicrobials.

Description

ANTISENSE ANTIBACTERIAL COMPOUNDS AND METHODS
C OSS-REFE EiMCE TO RELATED APPLICATIO S
This application claims the benefit of priority to U.S. Provisional Application No. 62/387, 178, filed December 23, 2015, which is herein incorporated by reference in its entirety.
STATEMENT REGARDING THE SEQUENCE LISTIMG
The Sequence Listing associated with this application is provided in text format in lieu of a paper copy, and is hereby incorporated by reference into the specification. The name of the text file containing the Sequence Listing is SATH-008_01VVO_SeqList_ST25.txt. The text file is about 14KB, was created on December 19, 2016, and is being submitted electronically via EFS-Web.
BACKGROUND
Technical Field
The present disclosure includes antisense oligomers targeted against bacterial m RNAs and other macromolecules involved in a biochemical pathway and/or cellular process, and related compositions and methods of using the oligomers and compositions to treat an infected mammalian subject, for example, as primary antimicrobials or as adjunctive therapies with classic antimicrobials.
Description of the Related Art
Currently, there are several types of antibiotic compounds in use against bacterial pathogens and these compounds act through a variety of anti-bacterial mechanisms. For example, beta-lactam antibiotics, such as penicillin and cephalosporin, act to inhibit the final step in peptidoglycan synthesis. Glycopeptide antibiotics, including vancomycin and teichopianin, inhibit both
transgiycosyiation and transpeptidation of muramyl-pentapeptide, again interfering with peptidoglycan synthesis. Other well-known antibiotics include the quinolones, which inhibit bacterial DNA replication, inhibitors of bacterial RNA polymerase, such as rifampin, and inhibitors of enzymes in the pathway for production of tetrahydrofolate, including the sulfonamides.
Some classes of antibiotics act at the level of protein synthesis. Notable among these are the aminoglycosides, such as kanamycin and gentamicin. This class of compounds targets the bacterial 30S ribosome subunit, preventing the association with the 50S subunit to form functional ribosomes. Tetracyclines, another important class of antibiotics, also target the 30S ribosome subunit, acting by preventing alignment of aminoacylated tRNAs with the corresponding mRNA codon. acroiides and lincosamides, another class of antibiotics, inhibit bacterial synthesis by binding to the 50S ribosome subunit, and inhibiting peptide elongation or preventing ribosome translocation.
Despite impressive successes in controlling or eliminating bacterial infections by antibiotics, the widespread use of antibiotics both in human medicine and as a feed supplement in poultry and livestock production has led to drug resistance in many pathogenic bacteria. Antibiotic resistance mechanisms can take a variety of forms. One of the major mechanisms of resistance to beta lactams, particularly in Gram-negative bacteria, is the enzyme befa-lactamase, which renders the antibiotic inactive by cleaving the lactam ring. Likewise, resistance to aminoglycosides often involves an enzyme capable of inactivating the antibiotic, in this case by adding a phosphoryi, adenyl, or acetyl group. Active efflux of antibiotics is another way that many bacteria develop resistance. Genes encoding efflux proteins, such as the tetA, tetG, tetL, and tetK genes for tetracycline efflux, have been identified. A bacterial target may develop resistance by altering the target of the drug. For example, the so-called penicillin binding proteins (PBPs) in many beta-lactam resistant bacteria are altered to inhibit the critical antibiotic binding to the target protein. Resistance to tetracycline may involve, in addition to enhanced efflux, the appearance of cytoplasmic proteins capable of competing with ribosomes for binding to the antibiotic. For those antibiotics that act by inhibiting a bacterial enzyme, such as for sulfonamides, point mutations in the target enzyme may confer resistance.
Klebsiella pneumoniae is found in the normal flora of the mouth, skin and intestines.
However, it can cause severe lung problems if aspirated, and is a significant cause of hospital- acquired infections. Klebsiella can also cause infections in the urinary tract, lower biliary tract, and surgical wound sites, among other sides. The range of clinical diseases includes pneumonia, thrombophlebitis, urinary tract infection, cholecystitis, diarrhea, upper respiratory tract infection, wound infection, osteomyelitis, meningitis, and bacteremia, and septicemia. Klebsiella species are often resistant to multiple antibiotics. In fact, the spread of carbapenem-resistant
Enterobacteriaceae (CRE) (including K. pneumoniae) has happened worldwide, including in the U.S. where carbapenemase-producing CRE has now been reported in most states.
Pseudomonas aeruginosa is a common Gram-negative bacterium that is found in soil, water, skin flora, and most man-made environments throughout the world. But it can cause serious disease in humans. For example, if Pseudomonas infections occur in critical body organs, such as the lungs, the urinary tract, and kidneys, the results can be fatal. It is also the major pathogen associated with lung infections in cystic fibrosis. CF patients typically become infected with strains of Pseudomonas aeruginosa from the environment, after which they evolve in the CF lung. Eighty percent of CF patients are infected with Pseudomonas aeruginosa by adulthood and chronic lung infections with this pathogen are the primary cause of morbidity and mortality. In the CF patient, complete eradication of Pseudornonas aeruginosa is rarely achieved. Pseudornonas aeruginosa is naturally resistant to many antibiotics and is becoming increasingly resistant to previously effective antibiotics. Multi-drug resistant isolates of Pseudornonas aeruginosa are now common in both CF and non-CF patients, leaving virtually no therapeutic options.
Acinetobacter baumannii is a ubiquitous organism that has emerged over the years to be a significant cause of hospital-acquired infections. This change in epidemiology is especially concerning given that A baumannii has become one of the most antibiotic-resistant Gram-negative pathogens that the medical community faces world-wide. The rapid increase in multi-drug resistance in A baumannii has left few therapeutic choices for the treating physician. Drugs such as coiistin are now frequently used, although colistin-resistant strains have appeared. Acinetobacter baumannii can cause a variety of clinical infections, with pneumonia being one of the most frequent.
Escherichia coii normally inhabits the large intestine of humans as a commensal organism. However, it can also cause a variety of clinical infections, and is a leading cause of bacteremia. There has been an alarming increase in the number of antibiotic-resistant strains of E. coii isolated from patients with nosocomial and community-acquired bacteremia. It is not uncommon for strains to be resistant to multiple antibiotics.
The appearance of antibiotic resistance in many pathogenic bacteria, including cases involving multi-drug resistance (MDR), raises the fear of a post-antibiotic era in which many bacterial pathogens were simply untreatable by medical intervention. Thus, there is a need for antimicrobial agents that (i) are not subject to the principal types of antibiotic resistance currently hampering antibiotic treatment of bacterial infection, (ii) can be developed rapidly and with some reasonable degree of predictability as to target-bacteria specificity, (iii) are effective at low doses, and (iv) show few side effects.
BRIEF SUMMARY
Embodiments of the present disclosure relate, in part, to the discovery that the antisense targeting of bacterial genes associated with biochemical pathways, cellular processes, and/or antibiotic resistance can increase the antibiotic susceptibility of otherwise antibiotic-resistant pathogenic bacteria, and reduce the ability of certain pathogenic bacteria to grow. For example, the antisense targeting of genes associated with murein biosynthesis, ceil division, global gene regulatory mechanisms, fatty acid biosynthesis, ribosomal proteins, ribosoma! RIMA (rRNA), DNA replication, transcription, translation initiation, lipopolysaccharide biosynthesis, nucleic acid biosynthesis, intermediary metabolism, RIMA biosynthesis, protein biosynthesis, peptidogiycan biosynthesis, cellular energy homeostasis, aromatic compound biosynthesis, and antibiotic resistance have been shown to be bactericidal at clinically-relevant concentrations. The antisense oligomers described herein could thus find utility in the treatment of such bacteria, for instance, in combination with antibiotics or as standalone therapies.
Embodiments of the present disclosure therefore include a substantially uncharged antisense morpholino oligomer, composed of morphoiino subunits and phosphorus-containing intersubunit linkages joining a morphoiino nitrogen of one subunit to a 5'-exocyclic carbon of an adjacent subunit, and having (a) about 10-40 nucleotide bases, and (b) a targeting sequence of sufficient length and complementarity to specifically hybridize to a bacterial mRNA target sequence that encodes a protein associated with a biochemical pathway and/or cellular process, or a ribosomal RNA target sequence, as described herein. In some instances, the oligomer is conjugated to a cell-penetrating peptide (CPP).
In certain embodiments, the targeting sequence is selected from Tables 1A-B. In some embodiments, the oligomer is about 10-15 or about 11-12 nucleotide bases in length and has a targeting sequence selected from Tables 1A-B.
In certain embodiments, an antisense oligomer of the disclosure is of formula (I):
Figure imgf000006_0001
or a pharmaceutically acceptable salt thereof,
where each Nu is a nucleobase which taken together forms a targeting sequence;
X is an integer from 9 to 38; T is selected from OH and a moiety of the formula:
Figure imgf000007_0001
where each R4 is independentiy Ci-C6 alkyl, and RE' is selected from an electron pair and H, and R6 is selected from OH, -N{R7)CH2C a moiety of the formula:
Figure imgf000007_0002
where:
R'' is selected from H and C C6 alkyl, and
Rs is selected from G, -C(0)-R9OH, acyi, trityi, and 4-methoxytrityl, where:
R9 is of the formula -(0-alkyl)y- wherein y is an integer from 3 to 10 and each of
the y alky! groups is independently selected from C2-C6 alkyl;
each instance of R! is -N(R10)2R wherein each R'° is independently C Cs alkyl, and selected from an electron pair and H;
R" is selected from H, G, acyi, trityi, 4-methoxytrityl, benzoyl, stearoyl, and a moiety of the formula:
Figure imgf000007_0003
where L is selected from -C(0)(CH2)6C(0)- and -C(0)(CH2)2S2(CH2)2C{0)-, and each R12 is of the formula ---(CH2)2OC{0)N{R14)2 wherein each R14 is of the formula -{CH2)6M HC(=iMH)iMH2; and
R3 is selected from an electron pair, H, and C C6 alkyl,
wherein G is a ceil penetrating peptide ("CPP") and linker moiety selected from
-C(0)(CH2)5NH-CPP, -C(0)(CH2)2M H-CPP, -C(0)(CH2)2N HC(0)(CH2)5NH-CPP, and -C(0)CH2NH-CPP, or G is of the formula:
O oc
Figure imgf000008_0001
, wherein the CPP is attached to the linker moiety by an amide bond at the CPP carboxy terminus, with the proviso that only one instance of G is present,
wherein the targeting sequence specifically hybridizes to a bacterial mRNA target sequence that encodes a protein associated with a biochemical pathway and/or cellular process, or a ribosomai RNA target sequence, or a protein associated with antibiotic resistance, as described herein.
In some embodiments, the target sequence comprises a translational start codon of the bacterial mRIMA and/or a sequence within about 30 bases upstream or downstream of the translational start codon of the bacterial rn RNA.
In some embodiments, the protein associated with a biochemical pathway and/or cellular process is a fatty acid biosynthesis protein. In certain embodiments, the fatty acid biosynthesis protein is an acyl carrier protein, in certain embodiments, the acyi carrier protein is encoded by acpp, In some embodiments, the fatty acid biosynthesis protein is an acyl carrier protein synthase. In some embodiments, the acyl carrier protein synthase is encoded b fobB. in certain embodiments, the targeting sequence is set forth in SEQ ID NOS:l-3, comprises a fragment of at least 10 contiguous nucleotides of SEQ ID i\!OS: 1-3, or comprises a variant having at least 80% sequence identity to SEQ ID NOS: 1-3, where thymine bases (T) are optionally uracil bases (U).
In some embodiments, the protein associated with a biochemical pathway and/or cellular process is a peptidoglycan biosynthesis protein. In certain embodiments, the peptidoglycan
biosynthesis protein is a U DP-N-acetylglucosamine 1-carboxyvinyltransferase. In particular embodiments, the UDP-N-acetylglucosamine 1-carboxyvinyltransferase is encoded by murA.
In certain embodiments, the protein associated with a biochemical pathway and/or cellular process is a ribosomai protein. In some embodiments, the ribosomai protein is a 50S ribosomai protein L28. In certain embodiments, the 50S ribosomai protein L28 is encoded by rpmB, In some embodiments, the ribosomai protein is a 30S ribosomai protein. In some embodiments, the 30S ribosomai protein is encoded by rpsJ,
In some embodiments, the protein associated with a biochemical pathway and/or cellular process is a ribosomai RNA (rRNA). in particular embodiments, rRNA is selected from a 16S rRNA and a 23S rRNA. In certain embodiments, the protein associated with a biochemical pathway and/or cellular process is a ceil division protein, in particular embodiments, the cell division protein is a protein that assembles into a ring at the future site of the septum of bacterial ceil division. In some
embodiments, the protein that assembles into a ring at the future site of the septum of bacterial ceil division is encoded byftsZ.
In certain embodiments, the protein associated with a biochemical pathway and/or cellular process is a DNA or chromosomal replication protein. In some embodiments, DIMA or chromosomal replication protein is a topoisomerase. in specific embodiments, the topoisomerase is encoded by gyrA. in some embodiments, DNA or chromosomal replication protein is a helicase. In some embodiments, the helicase is encoded by dnaB. In some embodiments, DNA or chromosomal replication protein is a DNA polymerase. In some embodiments, the DMA polymerase is encoded by poiB.
In specific embodiments, the targeting sequence is set forth in SEQ ID NQS:4-2Q, comprises a fragment of at least 10 contiguous nucleotides of SEQ ID NOS: 4-20, or comprises a variant having at least 80% sequence identity to SEQ ID NOS: 4-20, where thymine bases (T) are optionally uracil bases (U).
Also included are pharmaceutical compositions, comprising a pharmaceutically acceptable carrier and an antisense oligomer described herein. Some pharmaceutical compositions further comprising an antimicrobial agent as described herein. Illustrative examples of antimicrobial agents include tobramycin, meropenem, and colistin, and combinations thereof.
Some embodiments include methods of reducing expression and activity of a protein associated with a biochemical pathway and/or cellular process in a bacterium, comprising contacting the bacterium with an antisense oligomer and/or a pharmaceutical composition described herein.
In certain embodiments, the bacterium is in a subject, and the method comprises administering the antisense oligomer to the subject. In some embodiments, the bacterium is selected from the genera Klebsiella, Pseudomonas, Acm' etobocter, and Escherichia. In particular embodiments, the bacterium is an antibiotic-resistant strain of Klebsiella, Pseudomonas,
Aclnetobacter, or Escherichia, in some embodiments, the bacterium is a multi-drug resistant (MDR) strain of Klebsiella, Pseudomonas, Aclnetobacter, or Escherichia, in specific embodiments, the bacterium is Klebsiella pneumonia, Pseudomonas aeruginosa, Aclnetobacter baumannii, or
Escherichia cols.
Some methods comprise administering the oligomer separately or concurrently with an antimicrobial agent, optionally where administration of the oligomer increases susceptibility of the bacterium to the antimicrobial agent. In certain embodiments, the antimicrobial agent is selected from one or more of a β-lactam antibiotic, an aminoglycoside antibiotic, and a polymyxin.
In some embodiments, the β-lactam antibiotic is selected from at least one of carbapenems, penicillin derivatives (penams), cephalosporins (cephems), and monobactams.
In particular embodiments, the carbapenem is selected from one or more of meropenem, imipenem, ertapenem, doripenem, panipenem, biapenem, razupenem, tebipenem, lenapenem, and tomopenem. In specific embodiments, the carbapenem is meropenem.
In certain embodiments, the aminoglycoside antibiotic is selected from one or more of tobramycin, gentamicin, kanamycin a, amikacin, dibekacin, sisomicin, netilmicin, neomycin B, neomycin C, neomycin E (paromomycin), and streptomycin, in specific embodiments, the aminoglycoside antibiotic is tobramycin.
In certain embodiments, the polymyxin is selected from one or more of colistin (polymyxin E), polysporin, neosporin, or polymyxin B. In specific embodiments, the polymyxin is colistin.
In some embodiments, the β-lactam antibiotic is selected from at least one of meropenem, imipenem, ertapenem, doripenem, panipenem, biapenem, razupenem, tebipenem, lenapenem, tomopenem, cephalosporins (cephems), penicillin, penicillin derivatives (penams) and ampicillin.
In certain embodiments, the aminoglycoside antibiotic is selected from at least one of tobramycin, gentamicin, kanamycin a, amikacin, dibekacin, sisomicin, netilmicin, neomycin B, neomycin C, neomycin E (paromomycin), and streptomycin.
In some embodiments, the tetracycline antibiotic is selected from at least one of tetracycline, chlortetracycline, oxytetracyciine, demeciocycline, lymecycline, meclocyciine, methacycline, minocycline, roiitetracyciine, and doxycyiine.
In particular embodiments, the β-lactam antibiotic is selected from at least one of carbapenems, penicillin derivatives (penams), cephalosporins (cephems), and monobactams.
In some embodiments, the oligomer reduces the minimum inhibitory concentration (M IC) of the antimicrobial agent against the bacterium by at least about 10% relative to the antimicrobial agent alone.
In some embodiments, the oligomer increases the susceptibility of the bacterium to the antimicrobial agent by at least about 10% relative to the antimicrobial agent alone.
In certain embodiments, the combination of oligomer and the antimicrobial agent synergisticaliy increases the susceptibility of the bacterium to the antibiotic relative to the oligomer and/or the microbial agent alone.
In certain embodiments, the antimicrobial agent and the antisense oligomer are administered separately, in various embodiments, the antimicrobial agent and the antisense oligomer are administered sequentially. In some embodiments, the antimicrobial agent and the antisense oligomer are administered concurrently.
BRIEF DESCRIPTION OF THE FIGURES
Figure 1A shows an exemplary morphoiino oligomer structure with a phosphorodiamidate linkage. Figures 1B-E show the repeating subunit segment of exemplary morphoiino oligomers, designated B through E. Figures 1F-H show exemplary peptide PMO conjugates structures used in the exemplary PPMOs.
Figure 2 shows a minimal inhibitory concentration ( iC) heatmap of PPMOs targeted against essential genes from Klebsiella pneumoniae.
Figure 3 shows a MIC heatmap of PPMOs targeted against ribosomal NA from Klebsiella pneumoniae, Pseudomonas aeruginosa, and Acinetobacter baumannii.
DETAILED DESCRIPTION
f, Definitions
Unless defined otherwise, ail technical and scientific terms used herein have the same meaning as commonly understood by those of ordinary skill in the art. Although any methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present disclosure, preferred methods and materials are described. For the purposes of the present disclosure, the following terms are defined below.
The articles "a" and "an" are used herein to refer to one or to more than one (i.e., to at least one) of the grammatical object of the article. By way of example, "an element" means one element or more than one element.
By "about" is meant a quantity, level, value, number, frequency, percentage, dimension, size, amount, weight, or length that varies by as much as 30, 25, 20, 15, 10, 9, 8, 7, 6, 5, 4, 3, 2 or 1% to a reference quantity, level, value, number, frequency, percentage, dimension, size, amount, weight, or length.
By "coding sequence" is meant any nucleic acid sequence that contributes to the code for the polypeptide product of a gene. By contrast, the term "non-coding sequence" refers to any nucleic acid sequence that does not directly contribute to the code for the polypeptide product of a gene.
Throughout this specification, unless the context requires otherwise, the words "comprise," "comprises," and "comprising" will be understood to imply the inclusion of a stated step or element or group of steps or elements but not the exclusion of any other step or element or group of steps or elements.
By "consisting of" is meant including, and limited to, whatever follows the phrase "consisting of:" Thus, the phrase "consisting of" indicates that the listed elements are required or mandatory, and that no other elements may be present. By "consisting essentially of" is meant including any elements listed after the phrase, and limited to other elements that do not interfere with or contribute to the activity or action specified in the disclosure for the listed elements. Thus, the phrase "consisting essentially of" indicates that the listed elements are required or mandatory, but that other elements are optional and may or may not be present depending upon whether or not they materially affect the activity or action of the listed elements.
As used herein, the terms "contacting a cell", "introducing" or "delivering" include delivery of the oligomers described herein into a cell by methods routine in the art, e.g., transfection (e.g., liposome, calcium-phosphate, polyethyleneimine), electroporation (e.g., nucleofection),
microinjection), transformation, and administration.
The terms "cell penetrating peptide" (CPP) or "a peptide moiety which enhances cellular uptake" are used interchangeably and refer to cationic cell penetrating peptides, also called
"transport peptides", "carrier peptides", or "peptide transduction domains". In some aspects, the peptides have the capability of inducing ceil penetration within about or at least about 30%, 40%, 50%, 60%, 70%, 80%, 90%, or 100% of ceils of a given population and/or allow macromolecuiar translocation to or within multiple tissues in vivo upon systemic administration. Particular examples of CPPs include "arginine-rich peptides." CPPs are well-known in the art and are disclosed, for example, in U.S. Application No. 2010/0016215 and International Patent Application Publication Nos. WO 2004/097017, WO 2009/005793, and WO 2012/150960, ail of which are incorporated by reference in their entirety.
"An electron pair" refers to a valence pair of electrons that are not bonded or shared with other atoms.
"Homology" refers to the percentage number of amino acids that are identical or constitute conservative substitutions. Homology may be determined using sequence comparison programs such as GAP (Deveraux et a!., 1984, Nucleic Acids Research 12, 387-395) or BLAST, in this way sequences of a similar or substantially different length to those cited herein could be compared by insertion of gaps into the alignment, such gaps being determined, for example, by the comparison algorithm used by GAP.
By "isolated" is meant material that is substantially or essentially free from components that normally accompany it in its native state. For example, an "isolated polynucleotide" or "isolated oligomer," as used herein, may refer to a polynucleotide that has been purified or removed from the sequences that flank if in a naturally-occurring state, e.g., a DIMA fragment that is removed from the sequences that are adjacent to the fragment in the genome. The term "isolating" as it relates to cells refers to the purification of cells (e.g., fibroblasts, lymphoblasts) from a source subject (e.g., a subject with a polynucleotide repeat disease). In the context of mRNA or protein, "isolating" refers to the recovery of mRNA or protein from a source, e.g., cells.
The term "modulate" includes to "increase" or "decrease" one or more quantifiable parameters, optionally by a defined and/or statistically significant amount. By "increase" or
"increasing," "enhance" or "enhancing," or "stimulate" or "stimulating," refers generally to the ability of one or antisense compounds or compositions to produce or cause a greater physiological response (i.e., downstream effects) in a cell or a subject relative to the response caused by either no antisense compound or a control compound. Relevant physiological or cellular responses (in vivo or in vitro) will be apparent to persons skilled in the art. An "increased" or "enhanced" amount is typically a "statistically significant" amount, and may include an increase that is 1.1, 1.2, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 30, 40, 50 or more times (e.g., 500, 1000 times) (including all integers and ranges between and above 1), e.g., 1.5, 1.6, 1.7. 1.8) the amount produced by no antisense compound (the absence of an agent) or a control compound. The term "reduce" or "inhibit" may relate generally to the ability of one or more antisense compounds or compositions to "decrease" a relevant physiological or cellular response, such as a symptom of a disease or condition described herein, as measured according to routine techniques in the diagnostic art. Relevant physiological or cellular responses (in vivo or in vitro) will be apparent to persons skilled in the art, and may include reductions in bacterial cell growth, reductions in the minimum inhibitory concentration (MIC) of an antimicrobial agent, and others. A "decrease" in a response may be "statistically significant" as compared to the response produced by no antisense compound or a control composition, and may include a 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% decrease, including ail integers and ranges in between.
As used herein, an "antisense oligomer," "oligomer," or "oligomer" refers to a linear sequence of nucleotides, or nucleotide analogs, which allows the nucleobase to hybridize to a target sequence in an RNA by Watson-Crick base pairing, to form an oiigomer:RNA heteroduplex within the target sequence. The terms "antisense oligomer," "antisense oligomer," "oligomer," and
"compound" may be used interchangeably to refer to an oligomer. The cyclic subunits may be based on ribose or another pentose sugar or, in certain embodiments, a morpholino group (see description of morpholino oligomers below). The term "oligomer," "oligomer," or "antisense oligomer" also encompasses an oligomer having one or more additional moieties conjugated to the oligomer, e.g., at its 3'- or 5'-end, such as a polyethylene glycol moiety or other hydrophilic polymer, e.g., one having 10-100 monomeric subunits, which may be useful in enhancing solubility, or a moiety such as a lipid or peptide moiety that is effective to enhance the uptake of the compound into target bacterial cells and/or enhance the activity of the compound within the cell, e.g., enhance its binding to a target polynucleotide.
A "nuclease-resistant" oligomers refers to one whose backbone is substantially resistant to nuclease cleavage, in non-hybridized or hybridized form; by common extracellular and intracellular nucleases in the body or in a bacterial cell (for example, by exonucleases such as 3'-exonucleases, endonucieases, RNase H); that is, the oligomer shows little or no nuclease cleavage under normal nuclease conditions to which the oligomer is exposed. A "nuclease-resistant heteroduplex" refers to a heteroduplex formed by the binding of an antisense oligomer to its complementary target, such that the heteroduplex is substantially resistant to in vivo degradation by intracellular and extracellular nucleases, which are capable of cutting double-stranded RNA/RNA or RNA/DNA complexes. A "heteroduplex" refers to a duplex between an antisense oligomer and the
complementary portion of a target RNA.
As used herein, "nucleobase" (Nu), "base pairing moiety" or "base" are used
interchangeably to refer to a purine or pyrimidine base found in native DMA or RNA (uracil, thymine, adenine, cytosine, and guanine), as well as analogs of the naturally occurring purines and pyrimidines, that confer improved properties, such as binding affinity to the oligomer. Exemplary analogs include hypoxanthine (the base component of the nucleoside inosine); 2, 6-diaminopurine; 5-methyl cytosine; C5-propynyl-modifed pyrimidines; 9-(aminoethoxy)phenoxazine (G-ciamp) and the like.
A nucleobase covalently linked to a ribose, sugar analog or morpholino comprises a nucleoside. "Nucleotides" are composed of a nucleoside together with one phosphate group. The phosphate groups covalently link adjacent nucleotides to one another to form an oligomer.
An oligomer "specifically hybridizes" to a target sequence if the oligomer hybridizes to the target under physiological conditions, with a Tm substantially greater than 40°C or 45°C, preferably at least 50°C, and typically 60°C-80°C or higher. Such hybridization preferably corresponds to stringent hybridization conditions. At a given ionic strength and pH, the Tm is the temperature at which 50% of a target sequence hybridizes to a complementary polynucleotide. Such hybridization may occur with "near" or "substantial" complementarity of the antisense oligomer to the target sequence, as well as with exact complementarity. As used herein, "sufficient length" includes an antisense oligomer that is complementary to at least about 8, more typically about 8-10, 8-11, 8-12, 8-13, 8-14, 8-15, 8-16, 8-17, 8-18, 8-19, 8-20, 8-30, 8-40, or 10-11, 10-12, 10-13, 10-14, 10-15, 10-16, 10-17, 10-18, 10-19, 10-20, 10-30, 10-40 (including all integers and ranges in between) contiguous or non-contiguous nucleobases in a region of a bacterial mRNA target sequence or a bacterial rR!MA target sequence. An antisense oligomer of sufficient length has at least a minimal number of nucleotides to be capable of specifically hybridizing to a region of the bacterial mRNA or rRNA target. Preferably an oligomer of sufficient length is from 8 to 30 nucleotides in length, for example, about 10-20 nucleotides in length.
The terms "sequence identity" or, for example, comprising a "sequence 50% identical to," as used herein, refer to the extent that sequences are identical on a nucleotide-by-nucleotide basis or an amino acid-by-amino acid basis over a window of comparison. Thus, a "percentage of sequence identity" may be calculated by comparing two optimally aligned sequences over the window of comparison, determining the number of positions at which the identical nucleic acid base (e.g., A, T, C, G, I) or the identical amino acid residue (e.g., Ala, Pro, Ser, Thr, Gly, Val, Leu, lie, Phe, Tyr, Trp, Lys, Arg, His, Asp, Glu, Asn, Gin, Cys and Met) occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison (i.e., the window size), and multiplying the result by 100 to yield the percentage of sequence identity. Optimal alignment of sequences for aligning a comparison window may be conducted by computerized implementations of algorithms (GAP, BESTFIT, FAST A, and TFASTA in the Wisconsin Genetics Software Package Release 7.0, Genetics Computer Group, 575 Science Drive Madison, Wis., USA) or by inspection and the best alignment (i.e., resulting in the highest percentage homology over the comparison window) generated by any of the various methods selected.
Reference also may be made to the BLAST family of programs as for example disclosed by Aitschui et al., Nucl. Acids Res. 25:3389, 1997.
A "subject" or a "subject in need thereof" includes a mammalian subject such as a human subject.
The terms "TEG," "EG3," or "triethylene glycol tail" refer to triethylene glycol moieties conjugated to the oligomer, e.g., at its 3'- or 5' -end. For example, in some embodiments, "TEG" includes, for example, wherein T of the compound of formula (I), (Π), or (III) is of the formula:
Figure imgf000016_0001
The term "pip-PDA" refers to a 5' terminal piperazine-phosphorodiamidate moiety that connects a G group, where the G group comprises a cel!-penetrating peptide (CPP) and linker moiety further discussed below, to the 5'end of the oligomer by way of an amide bond between the G group linker and the piperazinyl nitrogen. For example, in some embodiments, "pip-PDA" includes wherein T of the compound of formula (1) or (II) is of the formula:
Figure imgf000016_0002
The term "target sequence" refers to a portion of the target RNA, for example, a bacterial mR!MA or rRNA, against which the antisense oligomer is directed, that is, the sequence to which the oligomer will hybridize by Watson-Crick base pairing of a complementary sequence, in certain embodiments, the target sequence may be a contiguous region of the translation initiation region of a bacterial mRIMA or a ribosomal RNA.
The term "targeting sequence" or "antisense targeting sequence" refers to the sequence in an oligomer that is complementary or substantially complementary to the target sequence in the RNA, e.g., the bacterial mRNA, the bacterial rRNA. The entire sequence, or only a portion, of the antisense compound may be complementary to the target sequence. For example, in an oligomer of about 10-30 bases, about 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, or 29 of the bases may be targeting sequences that are complementary to the target region. Typically, the targeting sequence is formed of contiguous bases, but may alternatively be formed of non-contiguous sequences that when placed together, e.g., from opposite ends of the oligomer, constitute sequence that spans the target sequence. A "targeting sequence" may have "near or "substantia!" complementarity to the target sequence and still function for the purpose of the present disclosure, that is, still be
"complementary." Preferably, the oligomer analog compounds employed in the present disclosure have at most one mismatch with the target sequence out of 10 nucleotides, and preferably at most one mismatch out of 20. Alternatively, the antisense oligomers employed have at least 90% sequence homology, and preferably at least 95% sequence homology, with the exemplary targeting sequences as designated herein.
As used herein, the term "quantifying", "quantification" or other related words refer to determining the quantity, mass, or concentration in a unit volume, of a nucleic acid, polynucleotide, oligomer, peptide, polypeptide, or protein.
As used herein, "treatment" of a subject (e.g. a mammal, such as a human) or a cell is any type of intervention used in an attempt to alter the natural course of the individual or cell.
Treatment includes, but is not limited to, administration of a pharmaceutical composition, and may¬ be performed either prophyiactically or subsequent to the initiation of a pathologic event or contact with an etioiogic agent. Also included are "prophylactic" treatments, which can be directed to reducing the rate of progression of the disease or condition being treated, delaying the onset of that disease or condition, or reducing the severity of its onset. "Treatment" or "prophylaxis" does not necessarily indicate complete eradication, cure, or prevention of the disease or condition, or associated symptoms thereof. if. Bacterial Targeting Sequences
Certain embodiments relate to antisense oligomers, and related compositions and methods, which are of sufficient length and complementarity to specifically hybridize to a bacterial rnRNA target sequence that encodes a gene in a biochemical pathway and/or cellular process, or a ribosomai RNA target sequence. General examples include: murein biosynthesis, cell division, global gene regulatory mechanisms, fatty acid biosynthesis, ribosomai proteins, ribosomai RNA (rRNA), DNA/chromosomal replication, transcription, translation initiation, lipopolysaccharide biosynthesis, nucleic acid biosynthesis, intermediary metabolism, RNA biosynthesis, protein biosynthesis, peptidoglycan biosynthesis, cellular energy homeostasis, aromatic compound biosynthesis, and antibiotic resistance. Particular examples of genes in biochemical pathways and cellular processes include: rpsJ and rpmB (ribosomai proteins); IpxC, waaC, waaG, waaA, waaF, IpxA, and ipxB
(lipopolysaccharide biosynthesis); iriurA (formerly known as murZ), mraY, murC, murB, murE, rnurF, and murG (peptidoglycan biosynthesis); fahG, acpP, accA, fabB, accB, and fabZ (fatty acid biosynthesis); adk (cellular energy homeostasis); infA (transcription antitermination and/or protein synthesis); /tsZ (cell division); rpoD (R!MA synthesis); aroC (aromatic compound biosynthesis); gyrA, dnaB, pol B (chromosomal and DMA replication). Examples of antibiotic resistance genes include hiaJ, cml, and adeA. In some embodiments, the rRNA target sequence or mRNA target sequence that encodes the gene is from Kiebsielio, e.g., Klebsiella pneumoniae. In some embodiments, the rRNA target sequence or the mRNA target sequence that encodes the gene is from Pseudomonas, e.g., Pseudomonas aeruginosa. In some embodiments, the rRNA target sequence or the m RNA target sequence that encodes the gene is from Acinetobacter, e.g., Acinetobacter baumannii. In some embodiments, the rRIMA target sequence or the m RNA target sequence that encodes the gene is from Escherichia, e.g., E. coii.
In some embodiments, the bacterial target is a gene or protein that is associated with biosynthesis of fatty acids. General examples of proteins associated with fatty acid biosynthesis include: acyl carrier protein (ACP), such as AcpP, that plays an essential role in stabilizing and shuttling the intermediate fatty acid chain to each of the enzymes in the fatty acid synthase complex; acyl carrier protein synthase (AcpS), an enzyme that transfers the 4'-phosphopantetheine prosthetic group to apo-ACP to form the functional holo-ACP; acetyl-CoA carboxylase, an enzyme composed of four proteins that catalyzes the conversion of acetyl-CoA to malonyl-CoA in the first committed step of fatty acid biosynthesis: AccA (carboxyltransferase alpha subunit catalyzing the transfer of the carboxyl group from biotin to acetyl-CoA to form malonyl-CoA), AccB (biotin carboxyl carrier protein, BCCP, carrying the biotin prosthetic group covalentiy attached to a lysine residue proximal to the carboxyl terminus), AccC (biotin carboxylase catalyzing the carboxylation of protein bound biotin with bicarbonate), AccD (carboxyltransferase beta subunit catalyzing the transfer of the carboxyl group from biotin to acetyl-CoA to form maionyi-CoA); fatty acid biosynthesis (Fab) enzymes, such as Fab A, FabB, Fabl, FabF, FabD, FabH, FabG and FabZ, that each catalyze either elongation or tailoring steps on the growing fatty acid chain. Particular examples of genes associated with fatty acid biosynthesis include acpP, the carboxyltransferase alpha subunit accA, and the acyl carrier protein synthase fabB.
Specific embodiment therefore relate to antisense oligomers, and related compositions and methods, which are of sufficient length and complementarity to specifically hybridize to an mRNA target sequence of a bacterial acpP gene, which encodes an acyl carrier protein (ACP). in some embodiments, the acpP gene is from Klebsiella, e.g., Klebsiella pneumoniae. In some embodiments, the acpP gene is from Pseudomonas, e.g., Pseudomonas aeruginosa. In some embodiments, the acpP gene is from Acinetobacter, e.g., Acinetobacter baumannii. In some embodiments, the acpP gene is from Escherichia, e.g., E. coii. Certain embodiment relate to antisense oligomers, and related compositions and methods, which are of sufficient length and complementarity to specifically hybridize to an mRNA target sequence of a bacterial fabB gene. In some embodiments, the fabB gene is from Klebsiella, e.g., Klebsiella pneumoniae. In some embodiments, the fabB gene is from Pseudomonas, e.g.,
Pseudomonas aeruginosa. In some embodiments, the fabB gene is from Acinetobacter, e.g., Acinetobacter baumannii. In some embodiments, the fabB gene is from Escherichia, e.g., E. coli.
The bacterial cell wall peptidoglycan is an essential cellular component involved in the maintenance of shape and protection from osmotic shock lysis. Typically, peptidoglycan is assembled from a basic building block composed of N-acetyigiucosamine (Glc!NiAc) and N-acetyimuramic acid with an attached pentapeptide. In some embodiments, the bacterial target is a gene or protein that is associated with peptidoglycan biosynthesis. A particular example of a gene associated with peptidoglycan biosynthesis include murA (formerly known as murZ}, which encodes a UDP-N- acetylglucosamine 1-carboxyvinyltransferase, which catalyzes the first committed step of peptidoglycan biosynthesis. The enzyme catalyzes the transfer of enoipyruvate from
phosphoenolpyruvate to the 3-OH of UDP-N-acetylglucosamine. In some embodiments, the murA gene is from Klebsiella, e.g., Klebsiella pneumoniae. In some embodiments, the murA gene is from Pseudomonas, e.g., Pseudomonas aeruginosa, in some embodiments, the murA gene is from Acinetobacter, e.g., Acinetobacter baumanii. In some embodiments, the murA gene is from
Escherichia, e.g., E. coli.
The ribosome is crucial for translation of mRNA molecules into proteins. In some embodiments, the bacterial target is a gene or protein that is associated with ribosomal proteins. A particular example of a gene associated with ribosomal proteins is rp B, a 50S ribosomal protein L28 essential for ribosome assembly and translation. Another example of a gene associated with ribosomal proteins is rpsJ, a 30S ribosomal protein. In some embodiments, the rpmB or rpsJ gene is from Klebsiella, e.g., Klebsiella pneumoniae. In some embodiments, the rpmB or rpsJ gene is from Pseudomonas, e.g., Pseudomonas aeruginosa. In some embodiments, the rpmB or rpsJ gene is from Acinetobacter, e.g., Acinetobacter baumanii. In some embodiments, the rpmB or rpsJ gene is from Escherichia, e.g., f. coli.
In some embodiments, the bacterial target is a ribosomal RNA (rRNA). Examples of rRIMA include 5S, 16S, and 23S rRNA. In some embodiments, the rRNA (e.g., 55, 16S, 23S) is from Klebsiella, e.g., Klebsiella pneumoniae, in some embodiments, the rRNA (e.g., 5S, 16S, 23S) is from
Pseudomonas, e.g., Pseudomonas aeruginosa, in some embodiments, the rRNA (e.g., 5S, 16S, 23S) is from Acinetobacter, e.g., Acinetobacter baumanii. In some embodiments, the rRNA (e.g., 5S, 16S, 23S) is from Escherichia, e.g., E. coli. In some embodiments, the bacterial target is a gene or protein that is associated with cellular energy homeostasis. A particular example of a gene associated with cellular energy homeostasis includes an adenylate kinase (adk) gene, which encodes a phosphotransferase enzyme that catalyzes the inferconversion of adenine nucleotides.
In some embodiments, the bacterial target is a gene or protein that is associated with transcription antitermination and/or protein biosynthesis. A particular example of a gene associated with transcription antitermination and/or protein biosynthesis includes translation initiation factor IF1. IF1, encoded by infA, is a protein containing an Sl-iike domain that may play a role in binding and melting nucleic acid secondary structure and transcription antitermination. Other functions may also include increasing the rate of 70S ribosome dissociation and subunit association and
involvement in the fidelity of translation initiation through stimulation of other translation initiation factor activities, such as IF2 and IF3.
In some embodiments, the bacterial target is a gene or protein that is associated with cell division. A particular example of a gene associated with cell division includes a /tsZ gene, which encodes a protein that assembles into a ring at the future site of the septum of bacterial ceil division. This is a prokaryotic homoiogue to the eukaryotic protein tubulin. In some embodiments, the ftsZ gene is from Klebsiella, e.g., Klebsiella pneumoniae. In some embodiments, the/fsZ gene is from Pseudomonas, e.g., Pseudomonas aeruginosa. In some embodiments, the /tsZ gene is from
Acinetobacter, e.g., Acinetobacter baumanii. In some embodiments, the /tsZ gene is from
Escherichia, e.g., f. coil.
In some embodiments, the bacterial target is a gene or protein that is associated with DMA or chromosomal replication. One example of a gene associated with DNA or chromosomal replication is gyrA, which encodes a topoisomerase. Another example of a gene associated with DNA or chromosomal replication is dnaB, which encodes a helicase. Another example of a gene associated with DNA or chromosomal replication is polB, which encodes a DNA polymerase, in some embodiments, the gyrA or dnaB or polB gene is from Klebsiella, e.g., Klebsiella pneumoniae. In some embodiments, the gyrA or dnaB or polB gene is from Pseudomonas, e.g., Pseudomonas aeruginosa. in some embodiments, the gyrA or dnaB or polB gene is from Acinetobacter, e.g., Acinetobacter baumanii. in some embodiments, the gyrA or dnaB or polB gene is from Escherichia, e.g., E. coii.
In some embodiments, the bacterial target is a gene or protein that is associated with lipopolysaccharide biosynthesis. One example of a gene associated with lipopolysaccharide biosynthesis is IpxC, which encodes an N-acety!g!ucosamine deacetylase. In some embodiments, the IpxC, gene is from Klebsiella, e.g., Klebsiella pneumoniae. In some embodiments, the IpxC gene is from Pseudomonas, e.g., Pseudomonas aeruginosa. In some embodiments, the IpxC gene is from Acinetobacter, e.g., Acinetobacter baumanii. In some embodiments, the IpxC gene is from
Escherichia, e.g., f. coii.
In some embodiments, the bacterial target is a gene or protein that is associated with RNA synthesis. A particular example of a gene associated with RNA synthesis includes an rpoD gene, which encodes a sigma D (sigma 70) factor of RNA polymerase that allows binding of the polymerase to gene promoters and is important for transcribing most genes in growing cells. Genes recognized by this sigma factor have promoter consensus sequences centered at 10 and 35 nucleotides before the start of transcription. In some embodiments, the rpoD gene is from Klebsiella, e.g., Klebsiella pneumoniae. In some embodiments, the rpoD gene is from Pseudomonas, e.g., Pseudomonas aeruginosa, in some embodiments, the rpoD gene is from Acinetobacter, e.g., Acinetobacter baumanii. In some embodiments, the rpoD gene is from Escherichia, e.g., E. coli.
The biosynthesis of aromatic compounds is important for the growth and survival of bacterial cells. The shikimate pathway is a biosynthetic route in microorganisms that lead to the synthesis of chorismic acid, a central precursor for other aromatic compounds, in some
embodiments, the bacterial target is a gene or protein that is associated with aromatic compound biosynthesis. A particular example of a gene associated with aromatic compound biosynthesis includes an aroC gene, which encodes chorismate synthase (5-enolpyruvylshikimate-3-phosphate phosphoiyase), the final enzyme in the shikimate pathway that catalyzes the conversion of 5- enolpyruvylshikimate-3-phosphate to chorismic acid.
In some embodiments, the gene or protein is associated with resistance of the bacteria to at least one antimicrobial agent, i.e., an antibiotic resistance gene. General examples of antibiotic resistance genes include beta-lactamases, which can enzymatically deactivate certain antimicrobial agents, and proteins that increase the permeability or active efflux (pumping-out) of an
antimicrobial agent. Particular examples of antibiotic resistance genes include TE beta-lactamase (blaT), chloramphenicol resistance gene {cm!}, and resistance-nodulation-ceii division (RN D)-type multidrug efflux pump subunit AdeA (adeA).
In certain embodiments, the target sequence contains all or a portion (e.g., 1 or 2 nucleotides) of a transiationai start codon of the bacterial m RNA. In some embodiments, the target sequence contains a sequence that is about or within about 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, 26, 27, 28, 29, 30 bases upstream or downstream of a transiationai start codon of the bacterial m RNA target sequence, including common and alternative start codons (e.g., AUG, GUG, U UG, AUU, CUG). For example, in particular embodiments, the 5'-end of the target sequence is the adenine, uracil, or guanine nucleotide (respectively) in an AUG start codon of the bacterial mRNA. In some embodiments, the 5'-end of the target sequence is the guanine, uracil, or guanine nucleotide (respectively) in a GUG start codon of the bacterial mRNA. In some embodiments, the 5' -end of the target sequence is the uracil, uracil, or guanine nucleotide (respectively) in a UUG start codon of the bacterial mRNA. in some embodiments, the 5'-end or 3- end of the target sequence begins at residue 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, 26, 27, 28, 29, or 30 downstream of the last (third) nucleotide of a translational start codon of the bacterial mRNA. In some embodiments, the 5' -end or 3-end of the target sequence begins at residue 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, 26, 27, 28, 29, or 30 upstream of the first nucleotide of a translational start codon of the bacterial mRNA.
Thus, in certain embodiments, antisense targeting sequences are designed to hybridize to a region of one or more of the target genes described herein. Selected antisense targeting sequences can be made shorter, e.g., about 8, 9, 10, 11, 12. 13, 14. or 15 bases, or longer, e.g., about 20, 30, or 40 bases, and include a small number of mismatches, as long as the sequence is sufficiently complementary to reduce transcription or translation upon hybridization to the target sequence, and optionally forms with the RNA a heteroduplex having a Tm of 45°C or greater.
In certain embodiments, the degree of complementarity between the target sequence and antisense targeting sequence is sufficient to form a stable duplex. The region of complementarity of the antisense oligomers with the target RNA sequence may be as short as 8-9 bases, 8-10 bases, 8- 11 bases, 8-12 bases, 10-11 bases, 10-12 bases, but can be 12-15 bases or more, e.g., 10-40 bases, 12-30 bases, 12-25 bases, 15-25 bases, 12-20 bases, or 15-20 bases, including ail integers in between these ranges. An antisense oligomer of about 10-15 bases is generally long enough to have a unique complementary sequence, in certain embodiments, a minimum length of complementary bases may be required to achieve the requisite binding Tm, as discussed herein.
In certain embodiments, oligomers as long as 40 bases may be suitable, where at least a minimum number of bases, e.g., 10-12 bases, are complementary to the target sequence. In general, however, facilitated or active uptake in cells is optimized at oligomer lengths of less than about 30 or less than about 20 bases. Included are antisense oligomers that consist of about 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, or 40 bases, in which at least about 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, or 40 contiguous or non-contiguous bases are complementary to a target gene described herein.
In certain embodiments, antisense oligomers may be 100% complementary to the target sequence, or may include mismatches, e.g., to accommodate variants, as long as a heteroduplex formed between the oligomer and target sequence is sufficiently stable to withstand the action of cellular nucleases and other modes of degradation which may occur in vivo, and reduce expression of the targeted mRNA. Hence, certain oligomers 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 oligomer and the target sequence. Oligomer 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 oligomer, 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. Although such an antisense oligomer is not necessarily 100% complementary to the target sequence, it is effective to stably and specifically bind to the target sequence, for example, such that translation of the target RNA is reduced.
The stability of the duplex formed between an oligomer and a target sequence is a function of the binding Tm and the susceptibility of the duplex to cellular enzymatic cleavage. The Tm of an oligomer with respect to complementary-sequence RNA may be measured by conventional methods, such as those described by Names et al., Nucleic Acid Hybridization, IRL Press, 1985, ρρ. 107-108 or as described in iyada C. G. and Wallace R. B., 1987, Oligomer Hybridization Techniques, Methods Enzymol. Vol. 154 pp. 94-107. In certain embodiments, antisense oligomers may have a binding Tm, with respect to a complementary-sequence RNA, of greater than body temperature and preferably greater than about 45°C or 50°C. Trn's in the range 60-80°C. or greater are also included. According to well-known principles, the Tm of an oligomer, with respect to a complementary-based RNA hybrid, can be increased by increasing the ratio of C:G paired bases in the duplex, and/or by increasing the length (in base pairs) of the heterodupiex. At the same time, for purposes of optimizing cellular uptake, it may be advantageous to limit the size of the oligomer.
Tables 1A-B below show exemplary targeting sequences (in a 5'-to-3' orientation) of the antisense oligomers described herein.
Figure imgf000024_0001
Certain antisense oligomers thus comprise, consist, or consist essentially of a targeting sequence in Tables 1A-B (e.g., SEQ ID MOS: 1-20) or a variant or contiguous or non-contiguous portion(s) thereof. For instance, certain antisense oligomers comprise about or at least about 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, or 27 contiguous or non-contiguous nucleotides of any of the targeting sequences in Tables 1A-B (e.g., SEQ ID NOS:1-20). For noncontiguous portions, intervening nucleotides can be deleted or substituted with a different nucleotide, or intervening nucleotides can be added. Additional examples of variants include oligomers having about or at least about 70% sequence identity or homology, 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 identity or homology, over the entire length of any of the targeting sequences in Tables 1A-B (e.g., SEQ ID NQS: 1-20).
The activity of antisense oligomers and variants thereof can be assayed according to routine techniques in the art (see, e.g., the Examples). ίίί, Antisense Oligomer Compounds
The antisense oligomers typically comprises a base sequence of sufficient length and complementarity to specifically hybridize to a bacterial rnRNA target sequence that encodes a protein associated with a biochemical pathway and/or cellular process and thereby reduce expression (e.g., translation) of the protein, or a ribosoma! RNA target sequence and thereby inhibit its interaction with other macromolecules. This requirement is optionally met when the oligomer compound has the ability to be actively taken up by bacterial ceils, and once taken up, form a stable duplex (or heterodupiex) with the target mRNA or target rRNA, optionally with a Tm greater than about 40°C or 45°C.
A. Arstisersse Oligomer Chemical Features In certain embodiments, the backbone of the antisense oligomer is substantially uncharged, and is optionally recognized as a substrate for active or facilitated transport across a ceil wall and/or cell membrane. The ability of the oligomer to form a stable duplex with the target RiMA may also relate to other features of the backbone, including the length and degree of complementarity of the antisense oligomer with respect to the target, the ratio of G:C to A:T base matches, and the positions of any mismatched bases. The ability of the antisense oligomer to resist cellular nucleases may promote survival and ultimate delivery of the agent to the ceil. Exemplary antisense oligomer targeting sequences are listed in Tables 1A-B (supra).
In certain embodiments, the antisense oligomer is a morpholino-based oligomer, for example, a phosphorodiamidate morpholino oligomer (PMO). Morpholino-based oligomers refer to an oligomer comprising morpholino subunits supporting a nucieobase and, instead of a ribose, contains a morpholine ring. Exemplary internucleoside linkages include, for example,
phosphoramidate or phosphorodiamidate internucleoside linkages joining the morpholine ring nitrogen of one morpholino subunit to the 4' exocyclic carbon of an adjacent morpholino subunit. Each morpholino subunit comprises a purine or pyrimidine nucieobase effective to bind, by base - specific hydrogen bonding, to a base in an oligomer.
IVlorphoiino-based oligomers (including antisense oligomers) are detailed, for example, in U.S. Patent Mos. 5,698,685; 5,217,866; 5, 142,047; 5,034,506; 5, 166,315; 5, 185,444; 5,521,063; 5, 506,337 and pending US Patent Application Mos. 12/271,036; 12/271,040; and PCT Publication No. WO/2009/064471 and WO/2012/043730 and Summerton et al. 1997, Antisense and Nucleic Acid Drug Development, 7, 187-195, which are hereby incorporated by reference in their entirety.
Within the oligomer structure, the phosphate groups are commonl referred to as forming the "internucleoside linkages" of the oligomer. The naturally occurring internucleoside linkage of R1MA and DNA is a 3' to 5' phosphodiester linkage. A "phosphoramidate" group comprises phosphorus having three attached oxygen atoms and one attached nitrogen atom, while a
"phosphorodiamidate" group comprises phosphorus having two attached oxygen atoms and two attached nitrogen atoms. In the uncharged or the cationic internucleoside linkages of the morpholino-based oligomers described herein, one nitrogen is always pendant to the linkage chain. The second nitrogen, in a phosphorodiamidate linkage, is typically the ring nitrogen in a morpholine ring structure.
In particular embodiments, the morpholino subunits are joined by phosphorous-containing intersubunit linkages in accordance with the structure: w
Figure imgf000026_0001
or sulfur, preferably oxygen; Pj is a purine or pyrimidine base-pairing moiety effective to bind, by base-specific hydrogen bonding, to a base in a polynucleotide, and X is -NRR' where R and R' are the same or different and are either H or alkyl. In particular embodiments, X is -NRR', where R and R' are the same or different and are either H or methyl.
Also included are antisense oligomer that comprise a sequence of nucleotides of the formula in Figures 1A-1E. in Figure 1A, B is a purine or pyrimidine base-pairing moiety effective to bind, by base-specific hydrogen bonding, to a base in a polynucleotide. Yi or Y2 may be oxygen, sulfur, nitrogen, or carbon, preferably oxygen. The X moiety pendant from the phosphorus may be fluorine, an alkyl or substituted alkyl, an alkoxy or substituted aikoxy, a thioalkoxy or substituted thioalkoxy, or unsubstituted, monosubstituted, or disubstituted nitrogen, including cyclic structures, such as morphoiines or piperidines. Alkyl, aikoxy and thioalkoxy include 1-6 carbon atoms. The Z moieties may be sulfur or oxygen, and are preferably oxygen.
Accordingly, various embodiments of the disclosure include a substantially uncharged antisense morpholino oligomer, composed of morpholino subunits and phosphorus-containing intersubunit linkages joining a morpholino nitrogen of one subunit to a 5'-exocyclic carbon of an adjacent subunit, and having (a) about 10-40 nucleotide bases, and (b) a targeting sequence of sufficient length and complementarity to specifically hybridize to a bacterial mRNA target sequence that encodes a protein associated with a biochemical pathway and/or cellular process, or a ribosomal RiMA target sequence, as described herein. In some instances, the oligomer is conjugated to a cell-penetrating peptide (CPP).
In various aspects, an antisense oligomer of the disclosure includes a compound of formula
(I):
Figure imgf000027_0001
or a pharmaceutically acceptable salt thereof,
where each i\!u is a nucleobase which taken together forms a targeting sequence;
X is an integer from 9 to 38;
T is selected from OH and a moiet of the formula:
Figure imgf000027_0002
where each R4 is independently Ci-C6 alkyl, and R5 is selected from an electron pair and H, and R6 is selected from OH, -N(R')CH2C a moiety of the formula:
Figure imgf000027_0003
where:
R' is selected from H and C Cs alkyl, and
R8 is selected from G, -C{Q)-R9OH, acyl, trityl, and 4-methoxytrityl, where:
R9 is of the formula -(0-alkyl)y- wherein y is an integer from 3 to 10 and each of the y alky! groups is independently selected from C2-C6 alkyi; each instance of R! is -N(R10)2R wherein each Rll} is independently C Cs alky!, and
Rn is
selected from an electron pair and H;
R2 is selected from H, G, acy!, trityl, 4-methoxytrityl, benzoyl, stearoyl, and a moiety of the formula:
Figure imgf000028_0001
where L is selected from -C(0)(CH2)6C(0)- and -C(0)(CH2)2S2(CH2)2C(0)- and each R12 is of the formula -fCH2)2OC{0)N{R14)2 wherein each R14 is of the formula -(CH2)6N HC(=NH)NH2; and
R3 is selected from an electron pair, H, and CrC6 alkyi,
wherein G is a cell penetrating peptide ("CPP") and linker moiety selected from
-C(0)(CH2)5NH -CPP, -C(0)(CH2)2N H-CPP, -C(0)(CH2)2N HC(0)(CH2)5NH-CPP,
and -C(0)CH2NH-CPP, or G is of the formula:
Figure imgf000028_0002
, wherein the CPP is attached to the linker moiety by an amide bond at the CPP carboxy terminus, with the proviso that only one instance of G is present,
wherein the targeting sequence specifically hybridizes to a bacterial rnRMA target sequence that encodes a protein associated with a biochemical pathway and/or cellular process, or a rRNA target sequence.
In some embodiments, X is from 9 to 18. In certain embodiments, X is 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29 or 30.
In certain embodiments, T is selected from :
Figure imgf000029_0001
In some embodiments, R is selected from H, G, acyl, trityi, 4-methoxytrityi, benzoyl, and stearoyl.
In various embodiments, T is selected from :
Figure imgf000029_0002
In some embodiments, T is of the formula:
0=P N(CH3)2
0N " is of the formula:
Figure imgf000029_0003
and R2 is G,
In certain embodiments, T is of the formula:
Figure imgf000029_0004
and R2 is G, In certain embodiments, T is of the formula:
Figure imgf000030_0001
In some embodiments, R2 is G or T is of the formula:
Figure imgf000030_0002
In some embodiments, R" is selected from H, acyl, trityi, 4-methoxytrityi, benzoyl, and stearoyl.
In various embodiments, R2 is selected from H or G, and R3 is selected from an electron pair or H, in a particular embodiment, R2 is G. In some embodiments, R2 is H or acyl. In some embodiments, each R L is -IM(CH3)2. in some embodiments, at least one instance of R1 is -N(CH3)2. In certain embodiments, each instance of is -N(CH3)2.
In various embodiments of the disclosure, an antisense oligomer of the disclosure includes a compound of formula (II):
Figure imgf000031_0001
or a pharmaceutically acceptable salt thereof,
where each Nu is a nucleobase which taken together forms a targeting sequence; X is an integer from 9 to 28;
T is selected from:
Figure imgf000031_0002
Rz is selected from H, G, acyl, trityi, 4-methoxytrityi, benzoyl, and stearoyi; and R3 is selected from an electron pair, H, and C:l-C6 aikyi,
wherein G is a cell penetrating peptide ("CPP") and linker moiety selected from -C(0)(CH2)5NH-CPP, -C(0)(CH2)2NH-CPP, -C(0){CH2)2MHC(0)(CH2)5NH-CPP,
and -C(0)CH2NH-CPP, or G is of the formula:
Figure imgf000032_0001
, wherein the CPP is attached to the linker moiety by an amide bond at the CPP carboxy terminus, with the proviso that only one instance of G is present. In some embodiments, T is TEG as defined above, R'" is G, and R3 is an electron pair or H. in certain embodiments, R" is selected from H, acyl, trityi, 4-methoxytrityi, benzoyl, and stearoyl and T is of the formula:
Figure imgf000032_0002
In some embodiments, R2 is G or T is of the formula:
Figure imgf000032_0003
In various aspects, an antlsense oligomer of the disclosure includes a compound of formul
Figure imgf000033_0001
or a pharmaceutically acceptable salt thereof,
where each Nu is a nucleobase which taken together forms a targeting sequence; X is an integer from 9 to 28;
T is selected from :
Figure imgf000033_0002
each instance of R1 is -N(Ri0)2Ra wherein each R10 is independently C C6 a!kyi, and R l is selected from an electron pair and H;
R2 is selected from an electron pair, H, and C C6 alkyi; and G is a cell penetrating peptide ("CPP") and linker moiety selected
from -C(0){CH2)5NH-CPP, -C(0)(CH2)2NH-CPP, -C(0)(CH2)2i\iHC{0)(CH2)5NH-CPPJ
and -C(0)CH2NH-CPP, or G is of the formula:
Figure imgf000034_0001
, wherein the CPP is attached to the linker moiety by an amide bond at the CPP carboxy terminus. In some embodiments, at least one instance of R! is -M(CH3}2. In certain embodiments, each instance of R1 is -M(CH3}2.
In various aspects, an ant isense oligomer of the disclosure includes a compound of formula
(IV):
Figure imgf000034_0002
or a pharmaceutically acceptable salt thereof, wherein:
X is an integer from 9 to 28;
each Nu is a nucleobase which taken together forms a targeting sequence; each instance of R L is ---N(Rl0)2Rn wherein each R10 is independently C C6 aikyi, and RI ! is selected from an electron pair and H; and
G is a cell penetrating peptide ("CPP") and linker moiety selected
from -C{0){CH2)5NH-CPP, -C(0}{CH2}2NH-CPP, -C(0){CH2)2MHC{0)(CH2)EiNH-CPPJ
and -C(0)CH2NH-CPP, or G is of the formula:
Figure imgf000035_0001
, wherein the CPP is attached to the linker moiety by an amide bond at the CPP carboxy terminus. In some embodiments, at least one instance of R! is -N{CH3}2. In certain embodiments, each instance of R1 is -N{CH3}2.
In various aspects, an antisense oligomer of the disclosure can be a compound of formula
(V):
Figure imgf000035_0002
wherein:
X is an integer from 9 to 18; each Nu is a nuc!eobase which taken together forms a targeting sequence; each instance of R1 is -N(R"L0)2R! l wherein each R10 is independently C C6 alkyl, and R11 is selected from an electron pair and H;
R2 is selected from H, trityl, 4-methoxytrifyi, acyl, benzoyl, and stearoyi ; and
R3 is selected from an electron pair, H, and Ci-C6 alkyl,
wherein G is a ceil penetrating peptide ("CPP") and linker moiety selected
from -C(0)(CH2)5NH-CPP, -C(0)(CH2)2N H-CPP, -C(0)(CH2}2MHC{0){CH2)5N H-CPP,
and -C(0)CH2NH-CPP, or G is of the formula:
Figure imgf000036_0001
, wherein the CPP is attached to the linker moiety by an amide bond at the CPP carboxy terminus, in some embodiments, at least one instance of R1 is -N{CS-J3)2. In certain embodiments, each instance of R1 is -N{CH3)2.
In various aspects, an antisense oligomer of the disclosure includes a compound of formula
(VI):
Figure imgf000036_0002
or a pharmaceutically acceptable salt thereof, wherein:
X is an integer from 9 to 28;
each Nu is a nucleobase which taken together forms a targeting sequence;
R2 is selected from H or acyl; and
G is a cell penetrating peptide ("CPP") and linker moiety selected
from -C(0)(CH2)5NH-CPP, -C(0)(CH2)2N H-CPP, -C(OHCH2)2iNSHC{0){CH2)5N H-CPP,
and -C(0)CH2NH-CPP, or G is of the formula:
Figure imgf000037_0001
, wherein the CPP is attached to the linker moiety by an amide bond at the CPP carboxy terminus.
The antisense oligomers can be prepared by stepwise solid-phase synthesis, employing methods known in the art and described in the references cited herein.
B. Cell-Penetrating Peptides
In certain embodiments, the antisense oligomer is conjugated to a cell-penetrating peptide (CPP). in some embodiments, the CPP is an arginine-rich peptide. By "arginine-rich carrier peptide" is meant that the CPP has at least 2, and preferably 2, 3, 4, 5, 6, 7, or 8 arginine residues, each optionally separated by one or more uncharged, hydrophobic residues, and optionally containing about 6-14 amino acid residues. Figures 1F-1H show exemplary chemical structures of CPP-PMO conjugates used in the Examples, including 5' and 3' P O conjugates.
Exemplary CPPs are provided in Table CI (SEQ ID NOS:21-35).
Figure imgf000037_0002
(R)6 RRRRRR 35
X is 6-arninohexanoic acid; B is β-alanine; F is phenylalanine; Y is tyrosine; G is glycine; R is arginine
In some embodiments, the CPP is linked at its C-terminus to the 3' -end or the 5'-end of the oligomer via a 1, 2, 3, 4, or 5 amino acid linker.
CPPs, their synthesis, and methods of conjugating a CPP to an oligomer are detailed, for example, in International Patent Application Publication Nos. WO 2004/097017, WO 2009/005793, and WO 2012/150960, which are all incorporated by reference in their entirety.
In some embodiments, the CPP is linked at its C-ferminus to the 3' -end or the 5'-end of the oligomer via a 1, 2, 3, 4, or 5 amino acid linker, in particular embodiments, including antisense oligomer compounds of formula (i)-(Vi), the linkers can include: -C(0)(CH2)sN H-CPP (X
linker), -C(0)(CH2)2N H-CPP (B linker), -C(0)(CH2)2NHC(0)(CH2)5NH-CPP (XB peptide
linker),and -C(0)CH2N H-CPP (G linker), or formula:
Figure imgf000038_0001
, wherein the CPP is attached to the linker moiety by an amide bond at the CPP carboxy terminus, in some embodiments of the disclosure, including antisense oligomer compounds of formula (i)-(VI), G is selected from SEQ ID NOS: 23-24 and 28-34. In various embodiments, including antisense oligomer compounds of formula (i)-(VI), the CPP is selected from SEQ I D NO: 21, 22, 25-27, and 35.
In some embodiments, including antisense oligomer compounds of formula (i)-(VI), the CPP is selected from:
Figure imgf000038_0002
Figure imgf000039_0001

Figure imgf000040_0001

Figure imgf000041_0001
Figure imgf000042_0001
Figure imgf000042_0002
Figure imgf000042_0003
40
Figure imgf000043_0001
41
Figure imgf000044_0001
42
Figure imgf000045_0001
Figure imgf000045_0002
(VII N) wherein X is an integer from 9 to 38, Ra is selected from H, acetyl, benzoyl, and stearoyi, Rb is selected from H, acetyl, benzoyl, stearoyi, trityl, and 4-methoxytrifyi, and each Nu is a purine or pyrimidine base-pairing moiety which taken together form a targeting sequence described above.
C. Aratisense Oligomer Targeting Sequences
In various embodiments of the antisense oligomers of the disclosure, including the antisense oligomer compounds of formulas (i)-(VII), the targeting sequence can specifically hybridizes to a bacterial mRNA target sequence that encodes a protein associated with a biochemical pathway and/or cellular process, or a rRNA target sequence. In some embodiments, the target sequence comprises a translational start codon of the bacterial mRNA and/or a sequence within about 30 bases upstream or downstream of the translational start codon of the bacteria! mRNA.
In various embodiments, the protein associated with a biochemical pathway and/or cellular process may be a fatty acid biosynthesis protein. In some embodiments, the fatty acid biosynthesis protein can be an acyl carrier protein. In certain embodiments, the acyl carrier protein may be AcpP. in some embodiments, the fatty acid biosynthesis protein may be an acyl carrier protein synthase. In certain embodiments, the acyl carrier protein synthase may be FabB. in some embodiments, the fatty acid biosynthesis protein may be a carboxyltransferase alpha subunit of an acetyl Coenzyme A carboxylase. In certain embodiments, the carboxyltransferase alpha subunit of an acetyl Coenzyme A carboxylase may be AccA. In some embodiments, the target sequence may be SEQ ID NQs:l-3, wherein thymine bases (T) are optionally uracil bases (U). In certain embodiments, the targeting sequence comprises or consists of at least one of the targeting sequences in Table 1A (e.g., SEQ ID NOS:l-3), comprises or consists of a fragment of at least 10 contiguous nucleotides of a targeting sequence in Table 1A (e.g., SEQ ID NOS:l-3), or comprises or consists of a variant having at least 80% sequence identity to a targeting sequence in Table 1A (e.g., SEQ ID NOS:l~3), wherein thymine bases (T) are optionally uracil bases (U).
In some embodiments, the protein associated with a biochemical pathway and/or cellular process may be a peptidogiycan biosynthesis protein. In certain embodiments, the peptidoglycan biosynthesis protein can be a UDP-N-acetylglucosamine 1-carboxyvinyltransferase. In some embodiments, the UDP-N-acetylglucosamine 1-carboxyvinyltransferase may be MurA.
In some embodiments, the protein associated with a biochemical pathway and/or cellular process is a ribosomal protein. In certain embodiments, the ribosomal protein is a 50S ribosomai protein L28. In some embodiments, the 50S ribosomal protein L28 is RpmB. In certain embodiments, the ribosomal protein is a 30S ribosomal protein, in some embodiments, the 30S ribosomal protein is RpsJ.
In some embodiments, the protein associated with a biochemical pathway and/or cellular process is a ribosomal RNA (rRNA). Examples of rRNA include 5S, 16S, and 23S rRNA. In some embodiments, the rRNA is a 16S rRNA. in certain embodiments, the rRNA is a 23S rRNA.
In some embodiments, the protein associated with a biochemical pathway and/or cellular process is a DNA or chromosomal replication protein. In certain embodiments, the DNA or chromosomal replication protein is a topoisomerase. In some embodiments, the topoisomerase is GyrA. In certain embodiments, the DNA or chromosomal replication protein is a helicase. in some embodiments, the helicase is DnaB. In some embodiments, the DNA or chromosomal replication protein is a DNA polymerase, in some embodiments, the DNA polymerase is PoiB.
In certain embodiments, the protein associated with a biochemical pathway and/or cellular process is a lipopolysaccharide biosynthesis protein. In some embodiments, the lipopolysaccharide biosynthesis protein is a N-acetyigiucosamine deacetylase. in some embodiments, the N- acetylglucosamine deacetylase is LpxC.
In various embodiments, the protein associated with a biochemical pathway and/or cellular process is a cellular energy homeostasis protein. In some embodiments, the cellular energy homeostasis protein is an adenylate kinase, in certain embodiments, the adenylate kinase is Adk.
In some embodiments, the protein associated with a biochemical pathway and/or cellular process is a protein biosynthesis protein. In certain embodiments, the protein biosynthesis protein is a translation initiation factor. In various embodiments, the translation initiation factor is InfA.
In some embodiments, the protein associated with a biochemical pathway and/or cellular process is a ceil division protein, in certain embodiments, the cell division protein is a protein that assembles into a ring at the future site of the septum of bacterial ceil division. For example, in some embodiments, the protein that assembles into a ring at the future site of the septum of bacterial ceil division is FtsZ.
In certain embodiments, the protein associated with a biochemical pathway and/or cellular process is an RNA synthesis protein. In some embodiments, the RNA synthesis protein is a sigma D factor of RNA polymerase. For example, in certain embodiments, the sigma D factor of RNA polymerase is RpoD.
In some embodiments, the protein associated with a biochemical pathway and/or cellular process is an aromatic compound biosynthesis protein. In certain embodiments, the aromatic compound biosynthesis protein is a chorismate synthase (5-enolpyruvylshikimate-3-phosphate phospholyase). For example, in some embodiments, the chorismate synthase (5- enolpyruvylshikimate-3-phosphate phospholyase) is AroC.
In some embodiments, the protein associated with antibiotic resistance is selected from one or more of BiaT, Cml, and AdeA.
In some embodiments where the protein associated with a biochemical pathway and/or cellular process may be a murein biosynthesis protein, cell division protein, global gene regulatory protein, fatty acid biosynthesis protein, ribosomal protein, ribosomal RNA (rRNA),
DNA/chromosomal replication protein, transcription protein, translation initiation protein, lipopolysaccharide biosynthesis protein, nucleic acid biosynthesis protein, intermediary metabolism protein, RNA biosynthesis protein, protein biosynthesis protein, peptidoglycan biosynthesis protein, cellular energy homeostasis protein, aromatic compound biosynthesis protein, and antibiotic resistance protein, or other protein described herein, the targeting sequence comprises or consists of at least one of the targeting sequences set forth in Table IB (e.g., SEQ ID NOS:4-20), comprises or consists of a fragment of at least 10 contiguous nucleotides of a targeting sequence in Table IB (e.g., SEQ ID NOS:4-20), or comprises or consists of a variant having at least 80% sequence identity to a targeting sequence in Table IB (e.g., SEQ ID NOS:4-20), wherein thymine bases (T) are optionally uracil bases (U).
In certain embodiments, including the antisense oligomer compounds of formulas (l)-(VII), the targeting sequence is selected from:
a) SEQ ID NO: 1 (CTC ATA CCT TG);
b) SEQ ID NO: 2 (TGC TCA TAG TC);
c) SEQ ID NO: 3 (CGT TTC ATT AA);
wherein X is 9, wherein thymine bases (T) may be uracil bases (U).
In some embodiments, including the antisense oligomer compounds of formulas (l)-(VII), the targeting sequence is selected from:
a) SEQ D NO: 4 (TTT ATC CAT TG);
b) SEQ D NO: 5 (GCA TTT GAC CT);
c) SEQ D NO: 6 (GTC TAT TCT CC);
d) SEQ D NO: 7 (GAC ATG TCT AT);
e) SEQ D NO: 8 (TGG TTC TGC AT);
f) SEQ D NO: 9 (AGT TTC TCT CC);
g) SEQ D NO: 10 (GTT CAA ACA TA);
h) SEQ D NO: 11 (CGC TCA TCT AA);
i) SEQ D NO: 12 (TTC CTG CCA TA);
j) SEQ D NO: 13 (TTT GAT CAT CG);
k) SEQ D NO: 14 (AGT GCT CTA CC);
I) SEQ D NO: 15 (GCC TGT TAT CC);
m) SEQ D NO: 16 (CCA TGC AGC AC);
n) SEQ D NO: 17 (TTG CGC TCG TT);
) SEQ D NO: 18 (GGC TGC TGG CA);
P) SEQ D NO: 19 (TCA TCT TTG CT);
q) SEQ D NO: 20 (AGT AAC TCC AC);
wherein X is 9, and wherein thymine bases (T) may be uracil bases (U). D. Exemplary Antisense Oligomers
Exemplary antisense oligomers (AONs) of the disclosure include those described in Tables 2A-B below.
Figure imgf000049_0001
IV. Methods of Use and Formulations
Embodiments of the present disclosure include methods of using the antisense oligomers described herein to reduce the expression and activity of one or more bacterial proteins associated with biochemical pathways, cellular processes, and/or antibiotic resistance. Certain embodiments include methods of using the antisense oligomers to reduce replication, proliferation, or growth of a bacteria, for example, to treat a bacterial infection in a subject, either alone or in combination with one or more additional antimicrobial agents. In some instances, the antisense oligomers increase the susceptibility of the bacterium to one or more antimicrobial agents.
Also included are pharmaceutical compositions comprising the antisense oligomers, typically in combination with a pharmaceuticaiiy-acceptable carrier. Certain pharmaceutical compositions can further comprise one or more antimicrobial agents. The methods provided herein can be practiced in vitro or in vivo.
For example, certain embodiments include methods of treating a bacterial infection in a subject, comprising administering to a subject in need thereof (e.g., subject having or at risk for having a bacterial infection) an antisense oligomer or pharmaceutical composition described herein. Also included are methods of reducing replication of a bacteria, comprising contacting the bacterium with an antisense oligomer described herein.
In some embodiments, the bacterium is selected from the genus Klebsiella, Pseudomonas, Acinetobacter, and Escherichia.
Klebsiella is a genus of a Gram -negative, nonmotile, encapsulated, lactose-fermenting, facultative anaerobic, rod- shaped bacterium that includes the species Klebsiella pneumoniae, which is responsible for the vast majority of Klebsiella -related pathogenesis.
Pseudomonas is a genus of Gram-negative, aerobic rod-shaped bacterium that commonly- found in skin, soil, and water. The genus includes the species Pseudomonas aeruginosa, an opportunistic pathogen that is responsible for the vast majority of Pseudomonas-related infections, it causes urinary tract infections, respiratory system infections, dermatitis, soft tissue infections, bacteremia, bone and joint infections, gastrointestinal infections and a variety of systemic infections, particularly in patients with severe burns and in cancer and AIDS patients who are
imrnunosuppressed. Pseudomonas aeruginosa infections are a serious problem in patients hospitalized with cancer, cystic fibrosis, and burns.
Acinetobacter is a genus of Gram-negative bacteria belonging to the class of
Gammaproteobacteria. Examples of clinically-relevant Acinetobacter complexes include the
Acinetobacter caicoaceticus-baumannii complex (glucose-oxidizing nonhemolytic), Acinetobacter iwoffii (glucose-negative nonhemolytic), and Acinetobacter haemoiyticus (hemolytic). Specific examples include Acinetobacter baumannii.
Escherichia is a genus of Gram-negative, non-spore forming, facultatively anaerobic, rod- shaped bacteria from the family Enterobacteriaceae, and includes the species Escherichia coli, which is responsible for the vast majority of Escherichia-reiated pathogenesis.
Thus, in some embodiments, the bacterium is any of the foregoing members of the genera Klebsiella, Pseudomonas, Acinetobacter or Escherichia, In specific embodiments, the bacterium is Klebsiella pneumoniae, Pseudomonas aeruginosa, Acinetobacter baumannii, or Escherichia coii. in some embodiments, the bacterium is selected from one or more of the strains in Table El.
In certain embodiments, the bacterium is a multi-drug resistance (MDR) strain of bacteria. Multiple drug resistance (MDR), multi-drug resistance or muitiresistance is a condition enabling disease-causing microorganisms (bacteria, viruses, fungi or parasites) to resist distinct antimicrobials such as antibiotics, antifungal drugs, antiviral medications, antiparasitic drugs, and others. In particular embodiments, the bacterium is extensively-drug resistant (XDR) or pan-drug resistant (PDR). In some embodiments, the bacterium is an extended-spectrum β-lactamase (ESBLs) producing Gram-negative bacteria, or a muiti-drug-resistant gram negative rod (MDR GNR) MDRGN bacteria, in specific embodiments, the bacterium is MDR Klebsiella, for example, MDR Klebsiella pneumoniae, or MDR Pseudomonas, for example, MDR Pseudomonas aeruginosa, in some embodiments, the bacterium is MDR Escherichia, for example, MDR Escherichia coli, or MDR Acinetobacter, for example, MDR Acinetobacter baumannii.
Examples of genes associated with biochemical pathways and/or cellular processes include fatty acid biosynthesis genes (and their related proteins) such as acpp, accA, acpS, and/or fab genes, for example, fabB. in particular embodiments, the bacterium comprises or expresses the acpp gene, which encodes an acyi carrier protein, in particular embodiments, the bacterium comprises or expresses the accA gene, which encodes a carboxyltransferase alpha subunit of an acetyl Coenzyme A carboxylase. In some embodiments, the bacterium comprises or expresses th fabB gene, which encodes an carrier protein synthase.
In some embodiments, the bacterium that comprises or expresses one or more genes associated with fatty acid biosynthesis (e.g., acpP. fabB) is a Klebsiella species, for example, Klebsiella pneumoniae. In some embodiments, the bacterium that comprises or expresses one or more genes associated with fatty acid biosynthesis (e.g., acpP, fabB) is a Pseudomonas species, for example, Pseudomonas aeruginosa. In some embodiments, the bacterium that comprises or expresses one or more genes associated with fatty acid biosynthesis (e.g., acpP, fabB) is an
Acinetobacter species, for example, Acinetobacter baumannii. In specific embodiments, the bacterium that comprises or expresses one or more genes associated with fatt acid biosynthesis (e.g., acpP, fabB) is an Escherichia species, for example, Escherichia coii. In some of these and related embodiments, the subject in need thereof is immunocompromised, in certain embodiments, the subject in need thereof is immunocompromised and has an underlying !ung disease, such as pneumonia, cystic fibrosis (CF), or chronic granulomatous disease (CGD).
Examples of genes associated with biochemical pathways and/or cellular processes include peptidogiycan biosynthesis genes (and their related proteins), in particular embodiments, the bacterium comprises or expresses the murA gene, which encodes a UDP-N-acetylglucosamine 1- carboxyviny!transferase. in some embodiments, the bacterium that comprises or expresses one or more peptidoglycan biosynthesis genes (e.g., murA) is a Klebsiella species, for example, Klebsiella pneumoniae. In some embodiments, the bacterium that comprises or expresses one or more peptidoglycan biosynthesis genes (e.g., murA) is a Pseudomonas species, for example, Pseudomonas aeruginosa. In some embodiments, the bacterium that comprises or expresses one or more peptidoglycan biosynthesis genes (e.g., murA) is an Acinetobacter species, for example,
Acinetobacter baumannii. In specific embodiments, the bacterium that comprises or expresses one or more peptidoglycan biosynthesis genes (e.g., murA) is an Escherichia species, for example, Escherichia coli.
Examples of genes associated with biochemical pathways and/or cellular processes include ribosomal protein genes (and their related proteins). In particular embodiments, the bacterium comprises or expresses the rpmB gene, which encodes a SOS ribosomal protein L28. In particular embodiments, the bacterium comprises or expresses the rpsJ gene, which encodes a 30S ribosomal protein. In some embodiments, the bacterium that comprises or expresses one or more ribosomal protein genes (e.g., rpmB, rpsJ) is a Klebsiella species, for example, Klebsiella pneumoniae. In some embodiments, the bacterium that comprises or expresses one or more ribosomal protein genes (e.g., rpmB, rpsJ) is a Pseudomonas species, for example, Pseudomonas aeruginosa, in some embodiments, the bacterium that comprises or expresses one or more ribosomal protein genes (e.g., rpmB, rpsJ) is an Acinetobacter species, for example, Acinetobacter baumannii. In specific embodiments, the bacterium that comprises or expresses one or more ribosomal protein genes (e.g., rpmB, rpsJ) is an Escherichia species, for example, Escherichia coli.
Examples of genes associated with biochemical pathways and/or cellular processes include cellular homeostasis genes (and their related proteins). In particular embodiments, the bacterium comprises or expresses the adk gene, which encodes an adenylate kinase. Examples of genes associated with biochemical pathways and/or cellular processes include protein biosynthesis genes (and their related proteins). In particular embodiments, the bacterium comprises or expresses the infA gene, which encodes a translation initiation factor.
Examples of genes associated with biochemical pathways and/or cellular processes include cell division genes (and their related proteins), in particular embodiments, the bacterium comprises or expresses the /tsZ gene, which encodes a protein that assembles into a ring at the future site of the septum of bacterial cell division. In specific embodiments, the bacterium that comprises or expresses one or more genes associated with cell division (e.g., ftsZ) is a Klebsiella species, for example, Klebsiella pneumoniae. In some embodiments, the bacterium that comprises or expresses one or more genes associated with cell division (e.g., ftsZ) is a Pseudomonas species, for example, Pseudomonas aeruginosa. In some embodiments, the bacterium that comprises or expresses one or more genes associated with cell division (e.g., ftsZ) is an Acinetobacter species, for example, Acinetohacter baumannii. In specific embodiments, the bacterium that comprises or expresses one or more genes associated with ceil division (e.g., j¾Z) is an Escherichia species, for example, Escherichia coii.
Examples of genes associated with DNA or chromosomal replication include topoisomerases and helicases (and their related proteins). In particular embodiments, the bacterium comprises or expresses the gyrA gene, which encodes a fopoisomerase. In some embodiments, the bacterium comprises or expresses the dnaB gene, which encodes a helicase. in some embodiments, the bacterium comprises or expresses the polB gene, which encodes a DNA polymerase. In specific embodiments, the bacterium that comprises or expresses one or more genes associated with DNA or chromosomal replication (e.g., gyrA, dnaB, polB) is a Klebsiella species, for example, Klebsiella pneumoniae, In some embodiments, the bacterium that comprises or expresses one or more genes associated with DNA or chromosomal replication (e.g., gyrA, dnaB, polB) is a Pseudomonas species, for example, Pseudomonas aeruginosa, in some embodiments, the bacterium that comprises or expresses one or more genes associated with DNA or chromosomal replication (e.g., gyrA, dnaB, polB) is an Acinetobacter species, for example, Acinetobacter baumannii. In specific embodiments, the bacterium that comprises or expresses one or more genes associated with DNA or chromosomal replication (e.g., gyrA, dnaB, polB) is an Escherichia species, for example, Escherichia coii.
Examples of genes associated with lipopoiysaccharide biosynthesis include deacetyiases such as N-acetyigiucosamine deacetylase. In particular embodiments, the bacterium comprises or expresses the IpxC gene, which encodes an N-acetyigiucosamine deacetylase. In specific
embodiments, the bacterium that comprises or expresses one or more genes associated with lipopoiysaccharide biosynthesis (e.g., IpxC) is a Klebsiella species, for example, Klebsiella
pneumoniae. In some embodiments, the bacterium that comprises or expresses one or more genes associated with lipopoiysaccharide biosynthesis (e.g., IpxC] is a Pseudomonas species, for example, Pseudomonas aeruginosa. In some embodiments, the bacterium that comprises or expresses one or more genes associated with lipopoiysaccharide biosynthesis (e.g., IpxC) is an Acinetobacter species, for example, Acinetobacter baumannii. In specific embodiments, the bacterium that comprises or expresses one or more genes associated with lipopoiysaccharide biosynthesis (e.g., IpxC) is an Escherichia species, for example, Escherichia coii.
Examples of genes associated with biochemical pathways and/or cellular processes include RNA synthesis genes (and their related proteins). In particular embodiments, the bacterium comprises or expresses the rpoD gene, which encodes a sigma D factor of RNA polymerase. In specific embodiments, the bacterium that comprises or expresses one or more RNA synthesis genes (e.g., rpoD) is a Klebsiella species, for example, Klebsiella pneumoniae. In some embodiments, the bacterium that comprises or expresses one or more one or more RNA synthesis genes (e.g., rpoD) is a Pseudomonas species, for example, Pseudomonas aeruginosa. In some embodiments, the bacterium that comprises or expresses one or more one or more RNA synthesis genes (e.g., rpoD) is an Acinetobacter species, for example, Acinetobacter baumannii. In specific embodiments, the bacterium that comprises or expresses one or more RNA synthesis genes (e.g., rpoD) is an
Escherichia species, for example, Escherichia coli.
Examples of genes associated with biochemical pathways and/or cellular processes include aromatic compound biosynthesis genes (and their related proteins). In particular embodiments, the bacterium comprises or expresses the aroC gene, which encodes a chorismate synthase (5- enolpyruvylshikimate-3-phosphate phosphoiyase).
In some embodiments, the bacteria or bacterium comprises (e.g., encodes) one or more antibiotic resistance genes. General examples of antibiotic resistance genes (and their related proteins) include beta-lactamases, which can enzymatically deactivate certain antimicrobial agents, and genes/proteins which increase the permeability or active efflux (pumping out) of an
antimicrobial agent. Particular examples of antibiotic resistance genes include TEM beta-lactamase (biaT), chloramphenicol resistance gene cml and resistance-nodulation-celi division (RN D)-type multidrug efflux pump subunit AdeA (adeA). in specific embodiments, the bacterium is Klebsiella pneumonia, Pseudomonas aeruginosa, Acinetobacter spp., or Escherichia coli, which comprises or expresses at least one antibiotic resistance gene selected from biaT, cm! and adeA.
In some embodiments, the antisense oligomer reduces expression of the gene(s) associated with biochemical pathways, cellular processes, and/or antibiotic resistance in the bacteria or bacterium. For instance, in some embodiments, the antisense oligomer reduces expression by about or at least about 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150, 200, 250, 300, 350, 400, 450, 500, 600, 700, 800, 900, or 1000% or more (including all integers and ranges in between), relative to a control (e.g., absence of the antisense oligomer, scrambled oligomer, prior to contacting with the oligomer), or by about or at least about 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 200, 300, 400, 500, 1000-fold or more (including all integers and ranges in between), relative to a control. In some embodiments, the antisense oligomer reduces expression of one or more of AcpP, FabB, AccA, MurA, Rpm B, RpsJ, Adk, InfA, 16S rRNA, 30S rRNA, GyrA, DnaB, Pol B, FtsZ, LpxC, RpoD, AroC, BiaT, Cml and/or AdeA and the bacterium is an Klebsiella, Pseudomonas, Acinetobacter, or Escherichia species which comprises or expresses one or more of AcpP, FabB, AccA, MurA, RpmB, RpsJ, Adk, InfA, 16S rRNA, 30S rRNA, GyrA, DnaB, Po!B, FtsZ, LpxC, RpoD, AroC, BlaT, Cm! and/or AdeA. Gene or protein expression can be measured in vitro (see, e.g., the Examples) or in vivo.
In some embodiments, the antisense oligomer reduces or inhibits the growth of the bacteria or bacterium. For instance, in some embodiments, the antisense oligomer reduces growth of the bacteria or bacterium by about or at least about 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, SO, 85, 90, 95, 100, 150, 200, 250, 300, 350, 400, 450, 500, 600, 700, 800, 900, or 1000% or more (including all integers and ranges in between), relative to a control (e.g., absence of the antisense oligomer, scrambled oligomer, prior to contacting with the oligomer), or by about or at least about 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 200, 300, 400, 500, 1000-fold or more (including all integers and ranges in between), relative to a control. Bacterial growth can be measured in vitro (see, e.g., the Examples) or in vivo. In particular embodiments, the antisense oiigomer that reduces growth of the bacterium is targeted against expression a protein associated with a biochemical pathway and/or cellular process selected from one or more of AcpP, FabB, AccA, MurA, RpmB, RpsJ, Adk, InfA, 16S rRNA, 30S rRNA, GyrA, DnaB, PolB, FtsZ, LpxC, RpoD, AroC, BlaT, Cml and/or AdeA and the bacterium is an Klebsiella,
Pseudomonas, Acinetobacter, or Escherichia species which comprises or expresses one or more of AcpP, FabB, AccA, MurA, RpmB, RpsJ, Adk, InfA, 16S rRNA, 30S rRNA, GyrA, DnaB, PolB, FtsZ, LpxC, RpoD, AroC, BlaT, Cml and/or AdeA. In some embodiments, as described herein, the antisense oligomer is employed in combination with one or more antimicrobial agents, for example, to reduce (e.g., synergistically reduce) the growth of the bacteria or bacterium.
In some embodiments, the methods are practiced in vivo, and comprise administering the antisense oligomer to a subject in need thereof, for example, a subject in need thereof that is infected or at risk for being infected by one or more of the bacteria described herein. The antisense oligomers described herein can thus be administered to subjects to treat (prophyiacticaily or therapeutically) an infection by any of the bacteria described herein. In conjunction with such treatment, pharmacogenomics (e.g., the study of the relationship between an individual's genotype/phenotype and that individual's response to a foreign compound or drug) may be considered. Differences in metabolism of therapeutics can lead to severe toxicity or therapeutic failure by altering the relation between dose and blood concentration of the pharmacologically active drug.
Thus, a physician or clinician may consider applying knowledge obtained in relevant pharrnacogenomics studies in determining whether to administer a therapeutic agent as well as tailoring the dosage and/or therapeutic regimen of treatment with a therapeutic agent. Effective delivery of the antisense oligomer to the target nucleic acid is one aspect of treatment. Routes of antisense oligomer delivery include, but are not limited to, various systemic routes, including oral and parenteral routes, e.g., intravenous, subcutaneous, intraperitoneal, and intramuscular, as well as inhalation, transdermal , and topical delivery. The appropriate route may be determined by one of skill in the art, as appropriate to the condition of the subject under treatment. Vascular or extravascular circulation, the blood or lymph system, and the cerebrospinal fluid are some non-limiting sites where the antisense oligomers may be introduced. Direct CNS delivery may be employed, for instance, intracerebral, intraventricular, or intrathecal administration may be used as routes of administration.
In certain embodiments, the antisense oligomers can be delivered by transdermal methods (e.g., via incorporation of the antisense oligomers into, e.g., emulsions, with such antisense oligomers optionally packaged into liposomes). Such transdermal and emulsion/liposome-mediated methods of delivery are described for delivery of antisense oligomers in the art, e.g., in U.S. Pat. No. 6,965,025, the contents of which are incorporated in their entirety by reference herein.
The antisense oligomers described herein may also be delivered via an implantable device. Design of such a device is an art-recognized process, with, e.g., synthetic implant design described in, e.g., U.S. Pat. No. 6,969,400, the contents of which are incorporated by reference.
Antisense oligomers can be introduced into cells using art-recognized techniques (e.g., transfection, eiectroporation, fusion, liposomes, colloidal polymeric particles and viral and non-viral vectors as well as other means known in the art). The method of delivery selected will depend at least on the oligomer chemistry, the ceils to be treated and the location of the cells and will be apparent to the skilled artisan. For instance, localization can be achieved by liposomes with specific markers on the surface to direct the liposome, direct injection into tissue containing target cells, specific receptor-mediated uptake, or the like.
As known in the art, antisense oligomers may be delivered using, e.g., methods involving iiposome-mediated uptake, lipid conjugates, poiyiysine-mediated uptake, nanoparticie-mediated uptake, and receptor-mediated endocytosis, as well as additional non-endocytic modes of delivery, such as microinjection, permeabllization (e.g., streptolysin-0 permeabllization, anionic peptide permeabiiization), eiectroporation, and various non-invasive non-endocytic methods of delivery that are known in the art (see, e, g., Dokka and Rojanasakui, Advanced Drug Delivery Reviews 44:35-49, incorporated by reference in its entirety).
The antisense oligomers may be administered in any convenient vehicle or carrier which is physiologically and/or pharmaceutically acceptable. Such a composition may include any of a variety of standard pharmaceutically acceptable carriers employed by those of ordinary skill in the art. Examples include, but are not limited to, saline, phosphate buffered saline (PBS), water, aqueous ethanol, emulsions, such as oil/water emulsions or triglyceride emulsions, tablets and capsules. The choice of suitable physiologically acceptable carrier will vary dependent upon the chosen mode of administration. "Pharmaceutically acceptable carrier" is intended to include any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents, and the like, compatible with pharmaceutical administration. The use of such media and agents for pharmaceutically active substances is well known in the art. Except insofar as any conventional media or agent is incompatible with the active compound, use thereof in the compositions is contemplated. Supplementary active compounds can also be incorporated into the compositions
The compounds (e.g., antisense oligomers, antimicrobial agents) described herein may generally be utilized as the free acid or free base. Alternatively, the compounds described herein may be used in the form of acid or base addition salts. Acid addition salts of the free amino compounds described herein may be prepared by methods well known in the art, and may be formed from organic and inorganic acids. Suitable organic acids include maleic, fumaric, benzoic, ascorbic, succinic, methanesulfonic, acetic, trifluoroacetic, oxalic, propionic, tartaric, salicylic, citric, gluconic, lactic, mandelic, cinnamic, aspartic, stearic, palmitic, giycolic, glutamic, and
benzenesulfonic acids.
Suitable inorganic acids include hydrochloric, hydrobromic, sulfuric, phosphoric, and nitric acids. Base addition salts included those salts that form with the carboxyiate anion and include salts formed with organic and inorganic cations such as those chosen from the alkali and alkaline earth metals (for example, lithium, sodium, potassium, magnesium, barium and calcium), as well as the ammonium ion and substituted derivatives thereof (for example, dibenzylammonium,
benzyiammonium, 2-hydroxyethyiammonium, and the like). Thus, the term "pharmaceutically acceptable salt" is intended to encompass any and ail acceptable salt forms.
In addition, prodrugs are also included within the context of this disclosure. Prodrugs are any covaiently bonded carriers that release a compound in vivo when such prodrug is administered to a patient. Prodrugs are generally prepared by modifying functional groups in a way such that the modification is cleaved, either by routine manipulation or in vivo, yielding the parent compound. Prodrugs include, for example, compounds of this disclosure wherein hydroxy, amine or suifhydryl groups are bonded to any group that, when administered to a patient, cleaves to form the hydroxy, amine or suifhydryl groups. Thus, representative examples of prodrugs include (but are not limited to) acetate, formate and benzoate derivatives of alcohol and amine functional groups of the antisense oligomers described herein. Further, in the case of a carboxy!ic acid (-COOH), esters may be employed, such as methyl esters, ethyl esters, and the like.
In some instances, liposomes may be employed to facilitate uptake of the antisense oligomer into cells (see, e.g., Williams, S.A., Leukemia 10(12):198Q-1989, 1996; Lappaiainen et al., Antiviral Res. 23:119, 1994; Uhimann et al., antisense oligomers: a new therapeutic principle, Chemical Reviews, Volume 90, Mo. 4, 25 pages 544-584, 1990; Gregoriadis, G., Chapter 14,
Liposomes, Drug Carriers in Biology and Medicine, pp. 287-341, Academic Press, 1979). Hydrogels may also be used as vehicles for antisense oligomer administration, for example, as described in WO 93/01286. Alternatively, the oligomers may be administered in microspheres or microparticles. (See, e.g., Wu, G.Y. and Wu, C.H., J. Biol. Chem. 262:4429-4432, 30 1987). Alternatively, the use of gas- filled microbubbles complexed with the antisense oligomers can enhance delivery to target tissues, as described in US Patent Mo. 6,245,747. Sustained release compositions may also be used. These may include semipermeable polymeric matrices in the form of shaped articles such as films or microcapsules.
In certain embodiments, the antisense oligomer is administered to a mammalian subject, e.g., human or domestic animal, exhibiting the symptoms of a bacterial infection (e.g., antibiotic resistance or D bacterial infection), in a suitable pharmaceutical carrier. In some aspects, the subject is a human subject, e.g., a patient diagnosed as having a bacterial infection. In particular embodiments, the antisense oligomer is contained in a pharmaceutically acceptable carrier, and is delivered orally. In some embodiments, the antisense oligomer is contained in a pharmaceutically acceptable carrier, and is delivered intravenously (i.v.j.
In some embodiments, the antisense oligomer is administered in an amount and manner effective to result in a peak blood concentration of at least 200-400 nM antisense oligomer.
Typically, one or more doses of antisense oligomer are administered, generally at regular intervals, for a period of about one to two weeks. Certain doses for oral administration are from about 1-1000 mg oligomer per 70 kg. In some cases, doses of greater than 1000 mg oligomer/patient may be necessary. For i.v. administration, some doses are from about 0.5 mg to 1000 mg oligomer per 70 kg. The antisense oligomer may be administered at regular intervals for a short time period, e.g., daily for two weeks or less. However, in some cases the antisense oligomer is administered intermittently over a longer period of time. Administration may be followed by, or concurrent with, administration of an antimicrobial (e.g., antibiotic) or other therapeutic treatment, as described herein. The treatment regimen may be adjusted (dose, frequency, route, etc.) as indicated, based on the results of immunoassays, other biochemical tests and physiological examination of the subject under treatment. An effective in vivo treatment regimen using the antisense oligomers described herein may vary according to the duration, dose, frequency and route of administration, as well as the condition of the subject under treatment (i.e., prophylactic administration versus administration in response to localized or systemic infection). Accordingly, such in vivo therapy will often include monitoring by tests appropriate to the particular type of disorder or bacterial infection under treatment, and corresponding adjustments in the dose or treatment regimen, in order to achieve an optimal therapeutic outcome.
Treatment may be monitored, e.g., by general indicators of disease known in the art. The efficacy of an in vivo administered antisense oligomer described herein may be determined from biological samples (tissue, blood, urine etc.) taken from a subject prior to, during and subsequent to administration of the antisense oligomer. Assays of such samples include (1) monitoring the presence or absence of heteroduplex formation with target and non -target sequences, using procedures known to those skilled in the art, e.g., an electrophoretic gel mobility assay; (2) monitoring the amount of a mutant m NA in relation to a reference normal m RMA or protein as determined by standard techniques such as RT-PCR, Northern blotting, ELISA or Western blotting.
V. Combination Therapies
Certain embodiments include combination therapies, for example, the administration of antisense oligomers in combination with antimicrobial agents such as antibiotics. Combination therapies can be employed, for example, to increase the sensitivit or susceptibilit of a given bacteria to one or more antimicrobial agents, and thereb improve the therapeutic outcome (e.g., resolution of the infection). Likewise, certain combination therapies can be employed, for example, to reduce or reverse the resistance of a given bacteria to one or more antimicrobial agents. In particular embodiments, the antisense oligomer reduces the minimum inhibitory concentration (M IC) of an antibiotic against a given bacterium. In certain embodiments, the antisense oligomer and the antimicrobial agent display synergy in reducing bacterial growth and/or increasing bacterial cell- killing. Also included are pharmaceutical compositions, as described herein, which comprise an antisense oligomer and an antimicrobial agent such as antibiotic.
In some embodiments, the antisense oligomer and the antimicrobial agent are administered separately, in certain embodiments, the antisense oligomer and the antimicrobial agent are administered sequentially. In some embodiments, the antisense oligomer and the antimicrobial agent are administered concurrently, for example, as part of the same or different pharmaceutical composition. Examples of antimicrobial agents (e.g., antibiotics) that can be administered in combination with an antisense oligomer include beta-!actam antibiotics such as carbapenems, penicillin and penicillin derivatives (or penams), ampicil!in, chloramphenicol, cephalosporins (e.g., Cefacetrile (cephacetriie), Cefadroxil (cefadroxyi; Duricef), Cephalexin (cefaiexin; Keflex), Cefaloglycin
(cephaiogiycin), Cefalonium (cephalonium), Cefaioridine (cephaloradine), Cefaiotin (cephalothin; Keflin), Cefapirin (cephapirin; Cefadryi), Cefatrizine, Cefazaflur, Cefazedone, Cefazolin (cephazolin; Ancef, Kefzol), Cefradine (cephradine; Velosef), Cefroxadine, Ceftezole, Cefaclor (Cedar, Distaclor, Keflor, Ranicior), Cefonicid ( onocid), Cefprozii (cefproxil; Cefzil), Cefuroxime (Zefu, Zinnat, Zinacef, Ceftin, Biofuroksym, Xorimax), Cefuzonam, Cefmetazole, Cefotetan, Cefoxitin, loracarbef (Lorabid); Cephamycins: cefbuperazone, cefmetazole (Zefazone), cefminox, cefotetan (Cefotan), cefoxitin (Mefoxin), Cefotiam (Pansporin), Cefcapene, Cefdaloxime, Cefdinir (Sefdin, Zinir, Omnicef, Kefnir), Cefditoren, Cefetamet, Cefixirne (Fixx, Zifi, Suprax), Cefmenoxime, Cefodizime, Cefotaxime
(Ciaforan), Cefovecin (Convenia), Cefpimizole, Cefpodoxime (Vantin, PECEF). Cefteram, Ceftibuten (Cedax), Ceftiofur, Ceftiolene, Ceftizoxime (Cefizox), Ceftriaxone (Rocephin), Cefoperazone (Cefobid), Ceftazidime ( eezat, Fortum, Fortaz), iatamoxef (moxalactam), Cefclidine, cefepime (Maxipime), cefluprenam, cefoselis, Cefozopran, Cefpirome (Cefrom), Cefquinome, flomoxef, Ceftobiproie, Ceftaroline, Cefaloram, Cefaparole, Cefcanel, Cefedroior, Cefempidone, Cefetrizoie, Cefivitrii, Cefmatiien, Cefmepidium, Cefoxazoie, Cefrotii, Cefsumide, Ceftioxide, Cefuracetime), and monobactams (e.g., aztreonam, tigemonam, nocardin A, tabtoxin); aminoglycosides such as tobramycin, gentamicin, kanamycin a, amikacin, dibekacin, sisomicin, netilmicin, neomycin B, neomycin C, neomycin E (paromomycin), and streptomycin; tetracyclines such as tetracycline, chlortetracycline, oxytetracycline, demeclocycline, lymecycline, meclocyciine, methacycline, minocycline, rolitetracycline, and doxycyline; sulfonamides such as sulfacetamide, sulfadiazine, sulfadimidine, sulfafurazole, suifisomidine, sulfadoxine, sulfamethoxazole, suifamoxole,
sulfadimethoxsne, sulfamethoxypyrsdazine, suifametoxydiazine, sulfadoxine, and suifametopyrazine; quinoiones such as cinoxacin, nalidixic acid, oxolinic acid (Uroxin), piromidic acid (Panacid), pipemidic acid (Dolcol) rosoxacsn (Eradacil), ciprofloxacin (Alcipro,Ciprobay, Cipro, Ciproxin, ultracipro), enoxacin (Enroxil, Penetrex), fleroxacsn ( egaione, Roquinol), lomefloxacin (Maxaquin), nadifloxacin (Acuatim, Nadoxin, Nadixa), norfloxacin (Lexinor, Noroxin, Quinabic, .!anacin), ofloxacin (Floxin, Oxaldin, Tarivid), pefloxacin (Peflacine), rufloxacin (Uroflox), balofloxacin (Baloxin), grepafloxacin (Raxar), levofloxacin (Cravit, Levaquin, Tavanic), pazufloxacin (Pasii, Pazucross), sparfioxacin (Zagam), temafioxacin (O niflox), tosufioxacin (Ozex, Tosacin), ciinafioxacin, gatifloxacin (Zigat, Tequin) (Zymar -opth.), gemifioxacin (Factive), moxifloxacin (Acflox Woodward, Aveiox,Vigamox, sitafioxacin (Gracevit), trovafloxacin (Trovan), prulifloxacin (Quisnon); oxazolidinones such as eperezolid, linezo!id, posizoiid, radezolid, ranbezoiid, sutezolid, and tedizoiid; polymyxins such as poiysporin, neosporin, polymyxin B, polymyxin E (coiistin); rifamycins such as rifampicin or rifampin, rifabutin, rifapentine, and rifaximin; iipiarmycins such as fidaxomicin;
macrolides such as azithromycin, clarithromycin, dirithromycin, erythromycin, roxithromycin, teiithromycin, carbomycin A, josamycin, kitasamycin, midecamycin/midecamycin acetate, oleandomycin, solithromycin, spiramycin, and troleandomycin; iincosamides such as iincomycin, clindamycin, and piriimycin; cyclic lipopeptides such as dapfomycin; glycopeptides such as vancomycin and teichoplanin; glycylcyciines such as tigecyciine. Thus, any one or more of the foregoing antibiotics can be combined with any of the antisense oligomers described herein, for the treatment of any of the bacterium or bacteria described herein.
In some embodiments, the antimicrobial agent is selected from one or more of
aminoglycoside antibiotics, tetracycline antibiotics, and β-lactam antibiotics, as described herein. In some of these and related embodiments, the bacterium comprises or expresses a gene selected from one or more of acpP and fabB, and the antisense oligomer is targeted against expression of the fatty acid biosynthesis gene. In some of these and related embodiments, the bacterium comprises or expresses a gene selected from one or more of murA, and the antisense oligomer is targeted against expression of the peptidoglycan biosynthesis gene. In some of these and related embodiments, the bacterium comprises or expresses a gene selected from one or more of rpmB and rpsJ, and the antisense oligomer is targeted against expression of the ribosomai protein gene. In some of these and related embodiments, the bacterium comprises or expresses a gene selected from one or more of ftsZ, and the antisense oligomer is targeted against expression of the cell division gene. In some of these and related embodiments, the bacterium comprises or expresses a gene selected from one or more of gyrA, dnaB, and po!B, and the antisense oligomer is targeted against expression of the DNA or chromosomal replication gene. In some of these and related embodiments, the bacterium comprises or expresses a gene selected from one or more of IpxC, and the antisense oligomer is targeted against expression of the lipopoiysaccharide biosynthesis gene. In some of these and related embodiments, the bacterium comprises or expresses a ribosomai RNA selected from one or more of 55 rRNA, 16S rRNA, and 23s rRNA, and the antisense oligomer is targeted against the rRNA. In specific embodiments, the bacterium is Klebsiella pneumoniae, Pseudomonas aeruginosa, Acinetobacter spp., or Escherichia coii, including DR strains thereof.
In some embodiments, the antimicrobial agent is a beta-!actam antibiotic, as described herein. In particular embodiments, the antimicrobial agent is a carbapenem. Examples of carbapenems include meropenem, imipenem, ertapenem, doripenem, panipenem, biapenem, razupenem, tebipenem, lenapenem, tomopenern, and ampicillin. In specific embodiments, the antimicrobial agent is meropenem. In particular embodiments, the antimicrobiai agent is a cephalosporin (cephem), penicillin or penicillin derivative (penam). In particular embodiments, the antisense oligomer reduces the M IC of a carbapenem such as meropenem against a bacteria, for example, a strain or M DR strain of Klebsiella pneumoniae, Pseudomonos aeruginosa, Acinetobacter baumannii, or £ coli. In some embodiments, the combination of the antisense oligomer and the carbapenem such as meropenem reduces (e.g., synergistically reduces) bacterial cell growth or increase (e.g., synergistically increases) bacterial cell-killing, for example, of a strain or M DR strain of Klebsiella pneumoniae, Pseudomonos aeruginosa, Acinetobacter baumannii, or f . coli.
In some embodiments, the antimicrobial agent is an aminoglycoside, as described herein. Examples of aminoglycosides include tobramycin, gentamicin, kanamycin a, amikacin, dibekacin, sisomicin, netilmicin, neomycin B, neomycin C, neomycin E (paromomycin), and streptomycin. In specific embodiments, the antimicrobiai agent is tobramycin. In particular embodiments, the antisense oligomer reduces the M IC of an aminoglycoside such as tobramycin against a bacteria, for example, a strain or M DR strain of Klebsiella pneumoniae, Pseudomonos aeruginosa, Acinetobacter baumannii, or E. coli. In some embodiments, the combination of the antisense oligomer and the aminoglycoside such as tobramycin reduces (e.g., synergistically reduces) bacterial cell growth or increases (e.g., synergistically increases) bacterial cell-killing, for example, of a strain or M DR strain of Klebsiella pneumoniae, Pseudomonos aeruginosa, Acinetobacter baumannii, or E. coli.
In certain embodiments, the antimicrobiai agent is a polymyxin such as colistin (polymyxin E), po!ysporin, neosporin, or polymyxin B. in specific embodiments, the antimicrobial agent is colistin. In particular embodiments, the antisense oligomer reduces the M IC of a polymyxin such as coiistin against a bacteria, for example, a strain or DR strain of Klebsiella pneumoniae,
Pseudomonos aeruginosa, Acinetobacter baumannii, or E. coli. In some embodiments, the combination of the antisense oligomer and the polymyxin such as coiistin reduces (e.g.,
synergistically reduces) bacterial cell growth or increases (e.g., synergistically increases) bacterial cell-killing, for example, of a strain or M DR strain of Klebsiella pneumoniae, Pseudomonos aeruginosa, Acinetobacter baumannii, or E. coli.
In certain embodiments, the antimicrobial agent includes one or more of ceftazidime, doxycyc!ine, piperacillin, meropenem, chloramphenicol, and/or co-trimoxazoie
(trimethoprim/sulfamethoxazole).
In some embodiments, the antisense oligomer increases the susceptibility or sensitivity of a given bacterium to the antimicrobial agent, relative to the antimicrobiai agent alone. For example, in certain embodiments, the antisense oligomer increases the susceptibility or sensitivity of the bacteria or bacterium to the antimicrobial agent by increasing the bactericidal (cell-killing) and/or bacteriostatic (growth-slowing) activity of the antimicrobial agent against the bacteria or bacterium being targeted, relative to the antimicrobial agent alone. In particular embodiments, the anfisense oligomer increases the susceptibility or sensitivity by about or at least about 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150, 200, 250, 300, 350, 400, 450, 500, 600, 700, 800, 900, or 1000% or more (including all integers and ranges in between), relative to the antimicrobial agent alone, or by about or at least about 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 200, 300, 400, 500, 1000-fold or more (including all integers and ranges in between), relative to the antimicrobial agent alone, in some embodiments, the antisense oligomer synergistically increases the susceptibility or sensitivity of a given bacterium to the antimicrobial agent, relative to the antimicrobial agent alone. In some embodiments, the bacterium is Klebsiella pneumoniae, Pseudomonas aeruginosa, Acinetobacter baurnannii, or E, coli, or an MDR strain thereof.
In some embodiments, the antisense oligomer reduces the minimum inhibitory
concentration (MIC) of an antimicrobial agent against the bacteria or bacterium being targeted, relative to the antimicrobial agent alone. The "minimum inhibitory concentration" or "MIC" refers to the lowest concentration of an antimicrobial agent that will inhibit the visible growth of a microorganism after overnight (in vitro) incubation. Minimum inhibitory concentrations are important in diagnostic laboratories to confirm resistance of microorganisms to an antimicrobial agent and also to monitor the activity of new antimicrobial agents. The IC is generally regarded as the most basic laboratory measurement of the activity of an antimicrobial agent against a bacterial organism. Thus, in certain embodiments, the oligomer reduces the minimum inhibitory
concentration (MIC) of an antimicrobial agent against the bacteria or bacterium by at least about 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150, 200, 250, 300, 350, 400, 450, 500, 600, 700, 800, 900, or 1000% or more (including all integers and ranges in between), relative to the antimicrobial agent alone. In certain embodiments, the oligomer reduces the minimum inhibitory concentration (MIC) of an antimicrobial agent against the bacteria or bacterium by about or at least about 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 200, 300, 400, 500, 1000-fold or more (including all integers and ranges in between), relative to the antimicrobial agent alone. In some embodiments, the antisense oligomer synergistically reduces the M IC of an antimicrobial agent against the bacteria or bacterium being targeted, relative to the antimicrobial agent alone. In some embodiments, the bacterium is Klebsiella pneumoniae, Pseudomonas aeruginosa, Acinetobacter baurnannii, or E. coli, or an MDR strain thereof. V!. Treatment Mariitormg Methods
The efficacy of a given therapeutic regimen involving the methods described herein may be monitored, for example, by general indicators of bacterial infection, such as complete blood count (CBC), nucleic acid detection methods, immunodiagnostic tests, or bacterial culture.
In some aspects, identification and monitoring of bacterial infection involves one or more of (1) nucleic acid detection methods, (2) serological detection methods, i.e., conventional immunoassay, (3) culture methods, and (4) biochemical methods. Such methods may be qualitative or quantitative.
Nucleic acid probes may be designed based on publicly available bacterial nucleic acid sequences, and used to detect target genes or metabolites (i.e., toxins) indicative of bacterial infection, which may be specific to a particular bacterial type, e.g., a particular species or strain, or common to more than one species or type of bacteria (i.e., Gram positive or Gram negative bacteria). Nucleic amplification tests (e.g., PGR) may also be used in such detection methods.
Serological identification may be accomplished using a bacterial sample or culture isolated from a biological specimen, e.g., stool, urine, cerebrospinal fluid, blood, etc. immunoassay for the detection of bacteria is generally carried out by methods routinely employed by those of skill in the art, e.g., ELISA or Western blot. In addition, monoclonal antibodies specific to particular bacterial strains or species are often commercially available.
Culture methods may be used to isolate and identify particular types of bacteria, by employing techniques including, but not limited to, aerobic versus anaerobic culture, growth and morphology under various culture conditions. Exemplary biochemical tests include Gram stain (Gram, 1884; Gram positive bacteria stain dark blue, and Gram negative stain red), enzymatic analyses, and phage typing.
It will be understood that the exact nature of such diagnostic, and quantitative tests as well as other physiological factors indicative of bacterial infection will vary dependent upon the bacterial target, the condition being treated and whether the treatment is prophylactic or therapeutic.
In cases where the subject has been diagnosed as having a particular type of bacterial infection, the status of the bacterial infection is also monitored using diagnostic techniques typically used by those of skill in the art to monitor the particular type of bacterial infection under treatment.
The PMO or PPMO treatment regimen may be adjusted (dose, frequency, route, etc), as indicated, based on the results of immunoassays, other biochemical tests and physiological examination of the subject under treatment.
From the foregoing, it will be appreciated how various objects and features of the present disclosure are met. The method provides an improvement in therapy against bacterial infection, for example, multi-drug resistant (M DR) bacteria, using various PPMOs to achieve enhanced cell uptake and anti-bacterial action. As a result, drug therapy is more effective and less expensive, both in terms of cost and amount of compound required.
One exemplary aspect is that compounds effective against virtually any pathogenic bacterial can be readily designed and tested, e.g., for rapid response against new drug-resistant strains.
The following examples are intended to illustrate but not to limit the disclosure. Each of the patent and non-patent references referred to herein is incorporated by reference in its entirety.
EXAMPLES
Materials and Methods
Peptide-Conjugated Phosphorodiamidate Morpholino Oligomers. PPMOs were synthesized and purified at Sarepta Therapeutics Inc. (Cambridge, MA, USA) as previously described (Tiliey et al., Antimicrob Agents Chemother 50:2789-2796, 2006). Lyophilized PPMOs were dissolved in uitrapure water and sterile-filtered. PPMO peptides were attached to either the 5' or 3' end of the oligomer sequence as indicated.
Bacteria, Bacterial strains were obtained through the clinical microbiology lab at UT Southwestern unless otherwise noted.
Minimal Inhibitory Concentration Assays. Minimal inhibitory concentration (M IC) assays were performed in Mueller Hinton 11 medium using the microdilution method as described by the Clinical and Laboratory Standards Institute (CLSI). Optical density (OD) of cultures was read in a micropiate spectrophotometer at 595-600 nm. After 18-20 hours of aerobic growth (200 -250 rpm) at 37°C, 100 μΙ cultures with an OD of < 0.06 were scored as no growth.
Graphical Software. Standard deviation and graphical analysis was performed on GraphPad Prism®6 software (Graph Pad Software, Inc., San Diego, CA, USA).
Example 1
Activity of PPMOs Targeted Against Expression of Essential Genes of K. pneumoniae PPMOs were designed, synthesized, and tested against the expression of essential genes representing a variety of biochemical pathways and cellular processes in Klebsiella pneumoniae. These included: murein biosynthesis, cell division, global gene regulatory mechanisms, fatty acid biosynthesis, ribosomai proteins, DMA replication, transcription, translation initiation,
lipopolysaccharide biosynthesis, nucleic acid biosynthesis, and intermediary metabolism. Each PPMO was tested by measuring the minima! inhibitory concentration (M IC) according to the method described above (CLSI microdilution assay). The M IC of each PPMO was tested using a pane! of 38 strains of K. pneumoniae, shown in TabSe El below, including eight that express the KPC carbapenemase, five that express the N DM-1 carbapenemase, two that express the OXA-48 carbapenemase, and others that are multidrug resistant (M DR).
Figure imgf000066_0001
The results are shown in Figure 2. At least four of the PPMOs inhibited growth of at least 75% of the strain pane! (IC75) at a concentration of 8 μΜ or less. These data show, inter alia, that PPMOs targeted against biochemical pathways and cellular processes of numerous strains of K. pneumoniae, including MDR strains and those that express antibiotic-resistance genes, are bactericidal at ciinicaily-relevant concentrations (e.g., !C75 of 8μΜ or less).
Example 2
Activity of PPMOs Targeted Against Ribosomal NA
PPMOs targeted against ribosomal RIMA (rRNA) were designed by positioning them at highly conserved regions of the 5S, 16S and 23S rRNA. Each sequence was then aligned and compared with the equivalent rRNAs in Homo sapiens, and any PP O sequence with a complementary match of 10 or more bases was eliminated.
Each PPIVIO was then tested by measuring the minimal inhibitory concentration (MIC) according to the method described above (CLSi microdilution assay).
As shown in Figure 3, the results of MIC testing show that at least three of the PPMOs (PPMO#15, PPMO#17, and PPMO#18 targeted to 23S-858, 16S-11Q1, and 165-1101, respectively) inhibited growth of at least two of the three targeted pathogens. The inhibitory concentration of 75% of the strains tested (IC75) was 8 μΜ or less for PPMO#15 in K. pneumoniae and P. aeruginosa, and for PPMO#18 in P. aeruginosa and Acinetobacter baumannii.
These data show, inter alia, that PPMOs targeted against bacterial rRNA of a variety of strains of K. pneumoniae, P. aeruginosa, and A. baumannii are bactericidal at clinically-relevant concentrations (e.g., IC75 of 8μΜ or less).

Claims

1. An antisense morpholino oligomer, composed of morpholino subunlts and phosphorus-containing intersubunit linkages joining a morpholino nitrogen of one subunit to a 5'- exocyc!ic carbon of an adjacent subunit, and having (a) about 10-40 nucleotide bases, and (b) a targeting sequence of sufficient length and complementarity to specifically hybridize to a bacterial mRMA target sequence that encodes a protein associated with a biochemical pathway and/or cellular process, or a ribosomal RIMA (rRNA) target sequence, where the oligomer is conjugated to a cell-penetrating peptide (CPP).
2. The antisense mor holino oligomer of formula (I):
Figure imgf000068_0001
or a pharmaceutically acceptable salt thereof,
where each Nu is a nucleobase which taken together forms a targeting sequence;
X is an integer from 9 to 38;
T is selected from OH and a moiety of the formula:
Figure imgf000068_0002
where each R4 is independently C Cs alkyi, and R5 is selected from an electron pair and H, and R6 is selected from OH, --N(R7)CH2C a moiety of the formula:
Figure imgf000069_0001
where:
R7 is selected from H and Cr C6 alkyi, and
Rs is selected from G, -CfQ)"R9OH, acyi, trityl, and 4-rnethoxytrityl, where:
R9 is of the formula -(0-alkyl)y- where y is an integer from 3 to 10 and each of
the y alky! groups is independently selected from C2-C6 alkyi;
each instance of R1 is -N( 10)2R where each R10 is independently C C6 alkyi, and R11 is
selected from an electron pair and H;
R2 is selected from H, G, acyi, trityl, 4-methoxytrityl, benzoyl, stearoyi, and a moiety of the formula:
Figure imgf000069_0002
where L is selected from -C(0)(CH2)6C(0)- and -C(0)(CH2)2S2(CH2)2C(0)- and each R12 is of the formula -(CH2)2OC(0)N(R14)2 where each R1'1 is of the formula -(CH2)6NHC(=N H)N H2; and
R;! is selected from an electron pair, H, and C C6 alkyi,
where G is a cell penetrating peptide ("CPP") and linker moiety selected from
-C(0)(CH2)5NH-CPP, -C(0)(CH2)2N H-CPP, -C(0)(CH2)2N HC(0)(CH2)5NH-CPP,
and -C(0)CH2NH-CPP, or G is of the formula:
Figure imgf000070_0001
, where the CPP is attached to the linker moiety by an amide bond at the CPP carboxy terminus, with the proviso that only one instance of G is present,
where the targeting sequence specifically hybridizes to a bacterial nRNA target sequence that encodes a protein associated with a biochemical pathway and/or cellular process, or a ribosomal RNA (rRNA) target sequence.
3. The antisense morpholino oligomer of claim 1 or 2, where the target sequence comprises a trans!ational start codon of the bacterial mRNA and/or a sequence within about 30 bases upstream or downstream of the translational start codon of the bacterial mRNA.
4. The antisense morpholino oligomer of any one of claims 1-3, where the protein associated with a biochemical pathway and/or cellular process is a fatty acid biosynthesis protein.
5. The antisense morpholino oligomer of claim 4, where the fatty acid biosynthesis protein is an acyl carrier protein encoded by acpp,
6. The antisense morpholino oligomer of claim 4, where the fatty acid biosynthesis protein is an acyl carrier protein synthase encoded h fahB,
7. The antisense morpholino oligomer of any of claims 1-6, where the targeting sequence is set forth in SEQ ID NQS:l-3, comprises a fragment of at least 10 contiguous nucleotides of SEQ ID NOS: 1-3, or comprises a variant having at least 80% sequence identity to SEQ ID NOS: 1-3, where thymine bases (T) are optionally uracil bases (U).
8. The antisense morpholino oligomer of any one of claims 1-3, where the protein associated with a biochemical pathway and/or cellular process is a UDP-N-acetylglucosamine 1- carboxyvinyltransferase peptidoglycan biosynthesis protein encoded by murA.
9. The antisense morpholino oligomer of any one of claims 1-3, where the protein associated with a biochemical pathway and/or cellular process is a ribosomal protein.
10. The antisense morphoiino oligomer of claim 9, where the ribosomal protein is a 50S ribosomal protein L28 encoded by rpmB.
11. The antisense morphoiino oligomer of claim 9, where the ribosomal protein is a 30S ribosomal protein encoded by rpsJ.
12. The antisense morphoiino oligomer any one of claims 1-3, where the targeting sequence specifically hybridizes to a rRNA target sequence.
13. The antisense morphoiino oligomer of claim 12, where the rRNA is selected from a 16S rRNA and a 23S rRNA.
14. The antisense morphoiino oligomer of any one of claims 1-3, where the protein associated with a biochemical pathway and/or cellular process is a cell division protein that assembles into a ring at the future site of the septum of bacterial ceil division encoded by ftsZ.
15. The antisense morphoiino oligomer of any one of claims 1-3, where the protein associated with a biochemical pathway and/or cellular process is a DNA or chromosomal replication protein encoded by gyrA, dnaB, or poiB.
16. The antisense morphoiino oligomer of any one of claims 1-3, where the protein associated with a biochemical pathway and/or cellular process is a lipopolysaccharide biosynthesis protein encoded by ipxC.
17. The antisense morphoiino oligomer of any one of claims 1-3 or 8-16, where the targeting sequence is set forth in SEQ ID NOS: 4-20, comprises a fragment of at least 10 contiguous nucleotides of SEQ ID NOS: 4-20, or comprises a variant having at least SQ% sequence identity to SEQ, ID NOS: 4-20, where thymine bases (T) are optionally uracil bases (U).
18. The antisense morphoiino oligomer of claim 2, where T is selected from:
Figure imgf000072_0001
19. The antisense morpholino oligomer of claim 2 or 18. where is selected from H, G, acyl, trityl, 4-methoxytrityl, benzoyl, and stearoyl.
20. The antisense morpholino oligomer of any one of claims 2, 18, or 19, where T is selected from:
Figure imgf000072_0002
R2 is G.
The antisense morpholino oligomer of claim 2, where T is of the formul
Figure imgf000072_0003
R6 is of the formula
Figure imgf000072_0004
and R2 is G.
22. The antisense morpholino oligomer of any one of the preceding claims 2 or 18-21, where T is of the formula:
Figure imgf000073_0001
and R'" is G.
23. The antisense morphoiino oligomer of claim 2, where T is of the formula:
Figure imgf000073_0002
24. The antisense morphoiino oligomer of claim 2.3, where R'~ is selected from H, acyl, trity!, 4-methoxytrityl, benzoyl, and stearoyl.
25. The antisense morpholino oligomer of any one of claims 2 or 18-24, where at least one instance of R1 is --N(CH3)2.
26. The antisense morpholino oligomer of claim 25, where each R1 is --N{CH3)2.
27. The antisense morpholino oligomer of any one of the preceding claims, where the CPP is selected from:
Figure imgf000074_0001
72
28. The antisense morphoiino oligomer of any one of claims 2 or 18-26, where G is selected
Figure imgf000075_0001
Figure imgf000076_0001
where R3 is selected from H, acetyl, benzoyl, and stearoy!
29. The antisense morpholino oligomer of any one of the preceding claims, where the antisense oligomer is of the formula (VII) selected from:
Figure imgf000077_0001
Figure imgf000077_0002
Figure imgf000077_0003
Figure imgf000077_0004
75
Figure imgf000078_0001
Figure imgf000078_0002
Figure imgf000078_0003
76
Figure imgf000079_0001
Figure imgf000079_0002
77
Figure imgf000080_0001
Figure imgf000080_0002
or a pharmaceutically acceptable salt of any of the foregoing,
where Ra is selected from H, acetyl, benzoyl, and stearoyi, Rb is selected from H, acetyl, benzoyl, stearoyi, trityl, and 4-methoxytrityl, and X and Nu are as defined in claim 1.
30. The anfisense morpholino oligomer of claim 29, where Rd is acetyl and Rb is H.
31. The antisense morpholino oligomer of any one of claims 2-3 or 18-30, where the targeting sequence is selected from:
a) SEQID NO: 1 (CTC ATACCTTG);
b) SEQID NO: 2 (TGCTCATACTC);
c) SEQID NO: 3 (CGTTTC ATT A);
where X is 9, and where thymine bases (T) may be uracil bases (U).
32. The antisense morpholino oligomer of any one of claims 2-3 or 18-30, where the targeting sequence is selected from:
a) SEQ ID NO: 4 (TTT ATC CAT TG);
b) SEQ ID NO: 5 (GCATTTGAC CT);
c) SEQ ID NO: 6 (GTC TAT TCT CC);
d) SEQ ID NO: 7 (GAC ATG TCT AT);
e) SEQ ID NO: 8 (TGG TTC TGC AT);
f) SEQ ID NO: 9 (AGT TTC TCT CC);
g) SEQ ID NO: 10 (GTT CAA ACA TA);
h) SEQ ID NO: 11 (CGC TCA TCT AA);
i) SEQ ID NO: 12 (TTC CTG CCA TA);
j) SEQ ID NO: 13 (TTT GAT CAT CG);
k) SEQ ID NO: 14 (AGT GCT CTA CC);
1) SEQ ID NO: 15 (GCC TGT TAT CC);
m) SEQ ID NO: 16 (CCA TGC AGC AC);
n) SEQ ID NO: 17 (TTG CGC TCG TT);
o) SEQ ID NO: 18 (GGC TGC TGG CA);
P) SEQ ID NO: 19 (TCA TCT TTG CT);
q) SEQ ID NO: 20 (AGT AAC TCC AC);
where X is 9, and where thymine bases (T) may be uracil bases (U).
33. A pharmaceutical composition, comprising a pharmaceutically acceptable carrier and an antisense morpholino oligomer, wherein the antisense morpholino oligomer is composed of morpholino subunits and phosphorus-containing intersubunit linkages joining a morpholino nitrogen of one subunit to a 5'-exocyclic carbon of an adjacent subunit, and having (a) about 10-40 nucleotide bases, and (b) a targeting sequence of sufficient length and complementarity to specifically hybridize to a bacterial mRNA target sequence that encodes a protein associated with a biochemical pathway and/or cellular process, or a ribosoma! RNA (rRMA) target sequence, where the oligomer is conjugated to a cell-penetrating peptide (CPP).
34. The pharmaceutical composition of claim 33, wherein the antisense morpho!ino oligomer is of formula (I):
Figure imgf000082_0001
or a pharmaceutically acceptable salt thereof,
where each Nu is a nucleobase which taken together forms a targeting sequence;
X is an integer from 9 to 38;
T is selected from OH and a moiety of the formula:
R6
O p N(R )2R5
O
where each R4 is independently Ci-C6 alkyl, and R5 is selected from an electron pair and H, and Rs is selected from OH, --N(R7)CH2C a moiety of the formula:
Figure imgf000082_0002
where:
R7 is selected from H and C Cs alkyl, and
R8 is selected from G, -C{0)-R9QH, acyl, trifyl, and 4-methoxytrifyi, where:
R9 is of the formula -(0-alkyl)y- where y is an integer from 3 to 10 and each of the y alky! groups is independently selected from C2-C6 alkyl;
each instance of R1 is -N(R10)2R where each R10 is independently C C6 alkyl, and R11 is selected from an electron pair and H;
R2 is selected from H, G, acyl, trifyl, 4-methoxytrityl, benzoyl, stearoyi, and a moiety of the formula:
Figure imgf000083_0001
where L is selected from -C(0)(CH2)6C(0)- and -C(0)(CH2)2S2(CH2)2C(0)-, and each R12 is of the formula ~{CH2)2OC(0)N(R14)2 where each R14 is of the formula -(CH2)6NHC(=N H)N H2; and
R3 is selected from an electron pair, H, and C C6 alkyl,
where G is a cell penetrating peptide ("CPP") and linker moiety selected from
-C(0)(CH2)5NH-CPP, -C(0)(CH2)2N H-CPP, -C(0)(CH2)2N HC(0)(CH2)5NH -CPP,
and -C(0)CH2NH-CPP, or G is of the formula:
Figure imgf000083_0002
, where the CPP is attached to the linker moiety by an amide bond at the CPP carboxy terminus, with the proviso that only one instance of G is present,
where the targeting sequence specifically hybridizes to a bacterial mRNA target sequence that encodes a protein associated with a biochemical pathway and/or cellular process, or a ribosomal RNA (rRNA) target sequence.
35. A method of reducing expression and activity of a protein associated with a biochemical pathway and/or cellular process in a bacterium, comprising contacting the bacterium with an antisense morpholino oligomer, wherein the antisense morpholino oligomer is composed of morpholino subunits and phosphorus-containing intersubunit linkages joining a morpholino nitrogen of one subunit to a 5'-exocyciic carbon of an adjacent subunit, and having (a) about 10-40 nucleotide bases, and (b) a targeting sequence of sufficient length and complementarity to specifically hybridize to a bacterial mRNA target sequence that encodes a protein associated with a biochemical pathway and/or cellular process, or a ribosomal RNA (rRMA) target sequence, where the oligomer is conjugated to a cell-penetrating peptide (CPP).
The method of claim 35, wherein the antisense morpholino oligomer is of formul
Figure imgf000084_0001
or a pharmaceutically acceptable salt thereof,
where each IMu is a nucleobase which taken together forms a targeting sequence;
X is an integer from 9 to 38;
T is selected from OH and a moiety of the formula:
Figure imgf000084_0002
where each R4 is independently C Cs alkyl, and R5 is selected from an electron pair and H, and R6 is selected from OH, --N(R7)CH2C a moiety of the formula:
Figure imgf000085_0001
where:
R7 is selected from H and CrC6 alkyl, and
Rs is selected from G, -CfQ)"R9OH, acyl, trityl, and 4-methoxytrityl, where:
R9 is of the formula -(0-alkyl)y- where y is an integer from 3 to 10 and each of the y alkyl groups is independently selected from C2-C6 aikyl;
each instance of Rx is -i\l{R10)2Rn where each Rlu is independently C Cs alkyl, and Rxl is selected from an electron pair and H;
R2 is selected from H, G, acyl, trityl, 4-methoxytrityl, benzoyl, stearoyl, and a moiety of the formula:
Figure imgf000085_0002
where L is selected from -C(0)(CH2)6C(0)- and -C(0)(CH2)2S2(CH2)2C(0)- and each R12 is of the formula -fCH2)2OC{0)N(R14)2 where each R14 is of the formula -(CH2)6NHC(=NH)NH2; and
R;! is selected from an electron pair, H, and C C6 alkyl,
where G is a cell penetrating peptide ("CPP") and linker moiety selected from
-C(0)(CH2)5NH-CPP, -C(0)(CH2)2NH-CPP, -C(0)(CH2)2NHC(0)(CH2)5NH-CPP,
and -C(0)CH2NH-CPP, or G is of the formula:
Figure imgf000085_0003
, where the CPP is attached to the linker moiet by an amide bond at the CPP carboxy terminus, with the proviso that only one instance of G is present, where the targeting sequence specifically hybridizes to a bacterial mRNA target sequence that encodes a protein associated with a biochemical pathway and/or cellular process, or a ribosomal R!MA (rRIMA) target sequence.
37. The method of claim 35 or 36, where the bacterium is in a subject, and the method comprises administering the antisense oligomer to the subject.
38. The method of any one of the preceding claims, where the bacterium is selected from the genera Klebsiella, Pseudomonas, Acinetobacter, and Escherichia.
39. The method of any one of the preceding claims, where the bacterium is selected from an antibiotic-resistant strain of Klebsiella, Pseudomonas, Acinetobacter, or Escherichia and a multi -drug resistant ( DR) strain of Klebsiella, Pseudomonas, Acinetobacter, or Escherichia,
40. The method of any one of the preceding claims, where the bacterium is selected from Klebsiella pneumoniae, Pseudomonas aeruginosa, Acinetobacter baumannii, and Escherichia coli.
41. The method of any one of the preceding claims, comprising administering the oligomer separately or concurrently with an antimicrobial agent, optionally where administration of the oligomer increases susceptibility of the bacterium to the antimicrobial agent.
42. The method of 41, where the antimicrobial agent is selected from one or more of a β-!actam antibiotic, an aminoglycoside antibiotic, and a polymyxin.
43. The method of claim 41 or 42, where the combination of oligomer and the antimicrobial agent increases the susceptibility of the bacterium to the antibiotic relative to the oligomer and/or the microbial agent alone.
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