US20120128701A1 - Compositions and methods for the removal of biofilms - Google Patents

Compositions and methods for the removal of biofilms Download PDF

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US20120128701A1
US20120128701A1 US13/229,575 US201113229575A US2012128701A1 US 20120128701 A1 US20120128701 A1 US 20120128701A1 US 201113229575 A US201113229575 A US 201113229575A US 2012128701 A1 US2012128701 A1 US 2012128701A1
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hmg
polypeptide
biofilm
protein
isolated
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Steven D. Goodman
Lauren O. Bakaletz
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University of Southern California USC
Nationwide Childrens Hospital Inc
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University of Southern California USC
Nationwide Childrens Hospital Inc
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Priority to US14/885,800 priority patent/US10595530B2/en
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    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01N—PRESERVATION OF BODIES OF HUMANS OR ANIMALS OR PLANTS OR PARTS THEREOF; BIOCIDES, e.g. AS DISINFECTANTS, AS PESTICIDES OR AS HERBICIDES; PEST REPELLANTS OR ATTRACTANTS; PLANT GROWTH REGULATORS
    • A01N37/00—Biocides, pest repellants or attractants, or plant growth regulators containing organic compounds containing a carbon atom having three bonds to hetero atoms with at the most two bonds to halogen, e.g. carboxylic acids
    • A01N37/44—Biocides, pest repellants or attractants, or plant growth regulators containing organic compounds containing a carbon atom having three bonds to hetero atoms with at the most two bonds to halogen, e.g. carboxylic acids containing at least one carboxylic group or a thio analogue, or a derivative thereof, and a nitrogen atom attached to the same carbon skeleton by a single or double bond, this nitrogen atom not being a member of a derivative or of a thio analogue of a carboxylic group, e.g. amino-carboxylic acids
    • A01N37/46—N-acyl derivatives
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides
    • A61K38/16—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • A61K38/17—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • A61K38/1703—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates
    • A61K38/1709—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P1/00—Drugs for disorders of the alimentary tract or the digestive system
    • A61P1/02—Stomatological preparations, e.g. drugs for caries, aphtae, periodontitis
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P27/00—Drugs for disorders of the senses
    • A61P27/16—Otologicals
    • 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
    • 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
    • A61P37/00—Drugs for immunological or allergic disorders
    • A61P37/02—Immunomodulators
    • A61P37/04—Immunostimulants
    • 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
    • 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

  • This invention generally relates to the methods and compositions to lessen and/or cure clinical or industrial bacterial biofilms.
  • Biofilms Bacteria persisting in a biofilm in the human body cause about two-thirds of all chronic/recurrent diseases. These biofilms are comprised of bacteria protected by an outer “slime” that is often comprised primarily of DNA which prevents the innate and adaptive immune systems, antibiotics and other antibacterial agents from gaining access to the bacteria inside the biofilm. Biofilms make it extremely difficult to clear the infection from the body. Furthermore, biofilms can act as a reservoir for future acute infections often with lethal consequences.
  • At least one protein from the DNABII family of proteins is found in all known eubacteria and are naturally found outside of the bacterial cell. While they elicit a strong innate immune response, host subjects fail to naturally produce specific antibody to family members as a result of infection.
  • the major problem with bacterial biofilms is the inability of the host immune system and/or antibiotics and other antimicrobials to gain access to the bacteria protected within the biofilm.
  • Biofilms are present in an industrial setting as well.
  • biofilms are implicated in a wide range of petroleum process problems, from the production field to the gas station storage tank.
  • sulfate reducing biofilm bacteria produce hydrogen sulfide (soured oil).
  • biofilm activity develops slimes which impede filters and orifices.
  • Biofilm and biofilm organisms also cause corrosion of pipeline and petroleum process equipment.
  • biofilms are found in or on any surface that supports microbial growth, e.g., in drains, on food preparation surfaces, in toilets and in swimming pools and spas.
  • Biofilms are implicated in a wide range of water processes, both domestic and industrial. They can grow on the surface of process equipment and impede the performance of the equipment, such as degradation of heat transfer or plugging of filters and membranes. Biofilms growing on cooling tower fill can add enough weight to cause collapse of the fill. Biofilms cause corrosion of even highly specialized stainless steels. Biofilms in a water process can degrade the value of a final product. Biofilms growing in drinking water distribution systems can harbor potential pathogenic organisms, corrosive organisms or bacteria that degrade the aesthetic quality of the water.
  • polypeptides that have one or more HMG-box domains(s), such as HMGB1 can interfere with the structure of extracellular DNA scaffold inside biofilms. By competing with microbial proteins that bind to the DNA scaffold in the biofilm, these polypeptides destabilize the biofilm, leading to destruction and removal of the biofilm by the host immune system.
  • HMG-box domain(s) enable a protein to bind non-B-type DNA conformations such as kinked or unwound DNA structures.
  • HMG-box domain containing proteins such as HMGB1, HMGB2, HMGB3 and HMGB4, serve important intracellular functions.
  • HMGB1 for instance, binds to DNA structures that are “pre-bent” and is believed to function in many types of DNA metabolism, e.g., RAG1/2 mediated immunoglobulin recombination.
  • HMGB1 proteins are known to be found extracellularly and are released by necrotic but not apoptotic cells as part of the innate immune system.
  • HMGB1 when added to bacterial biofilm communities, altered DNA based lattice in the biofilms.
  • the altered DNA based lattice can then allow access of the host immune system to the biofilm, permitting the host immune system to clear the biofilm.
  • a HMG-box domain containing polypeptide can be used as a therapeutic to destabilize the extracellular DNA shroud of bacterial biofilms. Bacteria that cannot form functional biofilms are more readily cleared by the remainder of the host's immune system.
  • one embodiment of the present disclosure provides a method for inhibiting, competing or titrating the binding of a DNABII polypeptide or protein to a microbial DNA, comprising contacting the DNABII polypeptide or protein or the microbial DNA with a polypeptide comprising an HMG-box domain, thereby inhibiting, competing or titrating the binding of the DNABII protein or polypeptide to the microbial DNA.
  • Another embodiment of the present disclosure provides a method for inhibiting, preventing or breaking down a microbial biofilm, comprising contacting the biofilm with a polypeptide comprising an HMG-box domain, thereby inhibiting, preventing or breaking down the microbial biofilm.
  • the contacting is in vitro or in vivo.
  • Yet another embodiment of the present disclosure provides a method of inhibiting, preventing or breaking down a biofilm in a subject, comprising administering to the subject an effective amount of a polypeptide comprising an HMG-box domain, thereby inhibiting, preventing or breaking down the microbial biofilm.
  • polypeptide comprising an HMG-box domain comprises one or more of:
  • the polypeptide comprising an HMG-box domain comprises an isolated or recombinant protein HMGB1, a polypeptide that is at least about 70% identical to HMGB1 or a fragment thereof that comprises one or more HMG-box domains.
  • the isolated or recombinant protein is a mammalian protein.
  • the mammalian protein is a human protein.
  • Any of the above method can further comprise administering to the subject an effective amount of one or more of an antimicrobial, an antigenic peptide or an adjuvant.
  • the subject in one aspect, is a non-human animal or a human patient.
  • the polypeptide is administered by a method comprising topically, transdermally, sublingually, rectally, vaginally, ocularly, subcutaneous, intramuscularly, intraperitoneally, urethrally, intranasally, by inhalation or orally.
  • the subject is a pediatric patient and the polypeptide is administered in a formulation for the pediatric patient.
  • the biofilm can comprise microbial DNA from a microorganism identified in Table 1.
  • the polypeptide is administered locally to the microbial infection.
  • the present disclosure provides a method for inducing or providing an immune response in a subject in need thereof, comprising administering to the subject an effective amount of a polypeptide comprising an HMG-box domain.
  • the administration is local to where the immune response is desired.
  • polypeptide comprising an HMG-box domain comprises one or more of:
  • the polypeptide comprising an HMG-box domain comprises an isolated or recombinant protein HMGB1, a polypeptide that is at least about 70% identical to HMGB1 or a fragment thereof that comprises one or more HMG-box domains.
  • the isolated or recombinant protein can be a mammalian protein or in a particular aspect, a human protein.
  • the subject in some aspects, is a non-human animal or a human patient.
  • kits comprising any one or more agent of the group
  • kits further comprises one or more of an adjuvant, an antigenic peptide or an antimicrobial.
  • kit further comprises a carrier selected from the group of a liquid carrier, a pharmaceutically acceptable carrier, a solid phase carrier, a pharmaceutically acceptable carrier, an implant, a stent, a paste, a gel, a dental implant or a medical implant.
  • polypeptide that is at least about 70% identical to any of (a), (b), (c) or (d) in the manufacture of a medicament for breaking down a biofilm or inhibiting, preventing or treating a microbial infection that produces a biofilm.
  • FIG. 1 are Western blot gel pictures each with a different antibody indicating the recognized proteins.
  • Polyclonal antisera to HMGB1 fail to crossreact with DNABII proteins members and polyclonal antisera to DNABII family members fail to crossreact with HMGB1.
  • FIG. 2 are Western blot gel pictures showing the binding specificity of goat anti-human HMGB1 antibodies and that HMGB1 is found in naive serum.
  • FIG. 3 presents confocal microscopy images of 40h in vitro NTHI biofilms not treated (left) or treated (right) with anti-HMGB1 antibodies at 24 hours.
  • the images show that reduction of HMGB1 found in naive serum by the antibody caused enhanced biofilm growth, shown as thicker biofilm at lower right as compared to a thinner one at lower left.
  • FIG. 4 includes gel images showing detection of HMGB1 in mammalian na ⁇ ve serum by Western blot.
  • the arrows indicate the detected HMGB1 in each sample. Note that HMGB1 had a His tag. Doublet observed in HMGB1 lanes was also present in example blot on specification sheet.
  • FIG. 5 presents confocal microscopy images of NTHI biofilms treated with different concentrations of HMGB1 and shows that HMGB1 dose-dependently inhibited biofilm formation.
  • Control in sterile medium sBHI (BHI with 2 mg heme/mL and 2 mg b-NAD/mL).
  • FIG. 6 presents dual labeling images of HMBG1 and IHF in bronchoalveolar lavage (BAL): A, labeling of HMGB1 with Alexafluor 488 conjugated antibodies; B, labeling of IHF with Alexafluor 594 conjugated antibodies; C, merged image of (A) and (B) showing localization of both antibodies.
  • DAPI was psuedocolored white in all images.
  • FIG. 7 presents microscopy images showing HMGB1 and IHF labeling of biomass formed by NTHI in the middle ear of a chinchilla.
  • the images are from serial sections of an OCT embedded biomass co-labeled for HMGB1 and IHF using goat anti-HMGB1 (diluted 1:25) and rabbit anti-IHF (diluted 1:200). Labeling was detected using Donkey anti-Goat AlexaFluor 488 and Donkey anti-rabbit AlexaFluor 594. dsDNA was stained with DAPI and pseudocolored white.
  • FIG. 8 shows that HMGB1 was detected periodically along the length of dsDNA strands. It was also found to be in close proximity of IHF at junctions.
  • FIG. 9 presents different z-plane images of the same section of the slide.
  • HMGB1 and IHF are both detected at the junction of strands of dsDNA and are in close proximity.
  • FIG. 10 presents an electromobility shift assay of HMGB1 bound to synthetic DNA Holliday junctions. Images show that HMGB1 failed to stabilize Holliday junction structural integrity with increasing temperature.
  • a polypeptide includes a plurality of polypeptides, including mixtures thereof.
  • compositions and methods include the recited elements, but do not exclude others.
  • Consisting essentially of when used to define compositions and methods, shall mean excluding other elements of any essential significance to the combination for the intended use. Thus, a composition consisting essentially of the elements as defined herein would not exclude trace contaminants from the isolation and purification method and pharmaceutically acceptable carriers, such as phosphate buffered saline, preservatives and the like.
  • Consisting of shall mean excluding more than trace elements of other ingredients and substantial method steps for administering the compositions of this invention. Embodiments defined by each of these transition terms are within the scope of this invention.
  • a “biofilm” intends a thin layer or an organized community of microorganisms that at times can adhere to the surface of a structure, that may be organic or inorganic, together with the polymers; such as DNA; that they secrete and/or release.
  • the biofilms are very resistant to microbiotics and antimicrobial agents. They live on gingival tissues, teeth and restorations, causing caries and periodontal disease, also known as periodontal plaque disease. They also cause chronic middle ear infections. Biofilms can also form on the surface of dental implants, stents, catheter lines and contact lenses. They grow on pacemakers, heart valve replacements, artificial joints and other surgical implants.
  • a “DNABII polypeptide or protein” intends a DNA binding protein or polypeptide that is composed of DNA-binding domains and thus have a specific or general affinity for DNA. In one aspect, they bind DNA in the minor grove.
  • Non-limiting examples of DNABII proteins are an integration host factor (IHF) protein and a histone-like protein from E. coli strain U93 (HU).
  • IHF protein is a bacterial protein that is used by bacteriophages to incorporate their DNA into the host bacteria. These are DNA binding proteins that function in genetic recombination as well as in transcription and translational regulation. They also bind extracellular microbial DNA.
  • the genes that encode the IHF protein subunits in E. coli are himA (Genbank accession No.: POA6X7.1) and himD (POA6Y1.1) genes. Homologs for these genes are found in other organisms, and peptides corresponding to these genes from other organisms can be found in Table 1.
  • HMGB1 is a high mobility group box (HMGB) 1 protein that is reported to bind to and distort the minor groove of DNA and is an example of an interfering agent. Recombinant or isolated protein and polypeptide are commercially available from Atgenglobal, ProSpecBio, Protein1 and Abnova.
  • HU or “histone-like protein from E. coli strain U93” refers to a class of heterodimeric proteins typically associated with E. coli . HU proteins are known to bind DNA junctions. Related proteins have been isolated from other microorganisms. The complete amino acid sequence of E. coli HU was reported by Laine et al. (1980) Eur. J. Biochem. 103(3):447-481. Antibodies to the HU protein are commercially available from Abcam.
  • Microorganism intends single or double stranded DNA from a microorganism that produces a biofilm.
  • “Inhibiting, preventing or breaking down” a biofilm intends the prophylactic or therapeutic reduction in the structure of a biofilm.
  • the terms “inhibiting, competing or titrating” intend a reduction in the formation of the DNA/protein matrix (for example as shown in FIG. 1 ) that is a component of a microbial biofilm.
  • a “bent polynucleotide” intends a double strand polynucleotide that contains a small loop on one strand which does not pair with the other strand and any polynucleotide where the end to end distance is reduced beyond natural thermal fluctations i.e. that is bending beyond the persistence length of 150 bp for native B-form double stranded DNA.
  • the loop is from 1 base to about 20 bases long, or alternatively from 2 bases to about 15 bases long, or alternatively from about 3 bases to about 12 bases long, or alternatively from about 4 bases to about 10 bases long, or alternatively has about 4, 5, or 6, or 7, or 8, or 9 or 10 bases.
  • a “subject” of diagnosis or treatment is a cell or an animal such as a mammal or a human.
  • Non-human animals subject to diagnosis or treatment and are those subject to infections or animal models, for example, simians, murines, such as, rats, mice, chinchilla, canine, such as dogs, leporids, such as rabbits, livestock, sport animals and pets.
  • protein refers to a compound of two or more subunit amino acids, amino acid analogs or peptidomimetics.
  • the subunits may be linked by peptide bonds. In another embodiment, the subunit may be linked by other bonds, e.g., ester, ether, etc.
  • a protein or peptide must contain at least two amino acids and no limitation is placed on the maximum number of amino acids which may comprise a protein's or peptide's sequence.
  • amino acid refers to either natural and/or unnatural or synthetic amino acids, including glycine and both the D and L optical isomers, amino acid analogs and peptidomimetics.
  • isolated or recombinant refers to molecules separated from other DNAs or RNAs, respectively that are present in the natural source of the macromolecule as well as polypeptides.
  • isolated or recombinant nucleic acid is meant to include nucleic acid fragments which are not naturally occurring as fragments and would not be found in the natural state.
  • isolated is also used herein to refer to polynucleotides, polypeptides and proteins that are isolated from other cellular proteins and is meant to encompass both purified and recombinant polypeptides.
  • the term “isolated or recombinant” means separated from constituents, cellular and otherwise, in which the cell, tissue, polynucleotide, peptide, polypeptide, protein, antibody or fragment(s) thereof, which are normally associated in nature.
  • an isolated cell is a cell that is separated from tissue or cells of dissimilar phenotype or genotype.
  • An isolated polynucleotide is separated from the 3′ and 5′ contiguous nucleotides with which it is normally associated in its native or natural environment, e.g., on the chromosome.
  • a non-naturally occurring polynucleotide, peptide, polypeptide, protein, antibody or fragment(s) thereof does not require “isolation” to distinguish it from its naturally occurring counterpart.
  • an equivalent intends at least about 70% homology or identity, or alternatively about 80% homology or identity and alternatively, at least about 85%, or alternatively at least about 90%, or alternatively at least about 95% or alternatively 98% percent homology or identity and exhibits substantially equivalent biological activity to the reference protein, polypeptide or nucleic acid.
  • the term intends a polynucleotide that hybridizes under conditions of high stringency to the reference polynucleotide or its complement.
  • a polynucleotide or polynucleotide region (or a polypeptide or polypeptide region) having a certain percentage (for example, 80%, 85%, 90% or 95%) of “sequence identity” to another sequence means that, when aligned, that percentage of bases (or amino acids) are the same in comparing the two sequences.
  • the alignment and the percent homology or sequence identity can be determined using software programs known in the art, for example those described in Current Protocols in Molecular Biology (Ausubel et al., eds. 1987) Supplement 30, section 7.7.18, Table 7.7.1.
  • default parameters are used for alignment.
  • a preferred alignment program is BLAST, using default parameters.
  • “Homology” or “identity” or “similarity” refers to sequence similarity between two peptides or between two nucleic acid molecules. Homology can be determined by comparing a position in each sequence which may be aligned for purposes of comparison. When a position in the compared sequence is occupied by the same base or amino acid, then the molecules are homologous at that position. A degree of homology between sequences is a function of the number of matching or homologous positions shared by the sequences. An “unrelated” or “non-homologous” sequence shares less than 30% identity or alternatively less than 25% identity, less than 20% identity, or alternatively less than 10% identity with one of the sequences of the present invention.
  • “Homology” or “identity” or “similarity” can also refer to two nucleic acid molecules that hybridize under stringent conditions to the reference polynucleotide or its complement.
  • Hybridization refers to a reaction in which one or more polynucleotides react to form a complex that is stabilized via hydrogen bonding between the bases of the nucleotide residues.
  • the hydrogen bonding may occur by Watson-Crick base pairing, Hoogstein binding, or in any other sequence-specific manner.
  • the complex may comprise two strands forming a duplex structure, three or more strands forming a multi-stranded complex, a single self-hybridizing strand, or any combination of these.
  • a hybridization reaction may constitute a step in a more extensive process, such as the initiation of a PCR reaction, or the enzymatic cleavage of a polynucleotide by a ribozyme.
  • Examples of stringent hybridization conditions include: incubation temperatures of about 25° C. to about 37° C.; hybridization buffer concentrations of about 6 ⁇ SSC to about 10 ⁇ SSC; formamide concentrations of about 0% to about 25%; and wash solutions from about 4 ⁇ SSC to about 8 ⁇ SSC.
  • Examples of moderate hybridization conditions include: incubation temperatures of about 40° C. to about 50° C.; buffer concentrations of about 9 ⁇ SSC to about 2 ⁇ SSC; formamide concentrations of about 30% to about 50%; and wash solutions of about 5 ⁇ SSC to about 2 ⁇ SSC.
  • Examples of high stringency conditions include: incubation temperatures of about 55° C.
  • hybridization incubation times are from 5 minutes to 24 hours, with 1, 2, or more washing steps, and wash incubation times are about 1, 2, or 15 minutes.
  • SSC is 0.15 M NaCl and 15 mM citrate buffer. It is understood that equivalents of SSC using other buffer systems can be employed.
  • the terms “treating,” “treatment” and the like are used herein to mean obtaining a desired pharmacologic and/or physiologic effect.
  • the effect may be prophylactic in terms of completely or partially preventing a disorder or sign or symptom thereof and/or may be therapeutic in terms of a partial or complete cure for a disorder and/or adverse effect attributable to the disorder.
  • To “prevent” intends to prevent a disorder or effect in vitro or in vivo in a system or subject that is predisposed to the disorder or effect.
  • An example of such is preventing the formation of a biofilm in a system that is infected with a microorganism known to produce one.
  • “Pharmaceutically acceptable carriers” refers to any diluents, excipients or carriers that may be used in the compositions of the invention.
  • Pharmaceutically acceptable carriers include ion exchangers, alumina, aluminum stearate, lecithin, serum proteins, such as human serum albumin, buffer substances, such as phosphates, glycine, sorbic acid, potassium sorbate, partial glyceride mixtures of saturated vegetable fatty acids, water, salts or electrolytes, such as protamine sulfate, disodium hydrogen phosphate, potassium hydrogen phosphate, sodium chloride, zinc salts, colloidal silica, magnesium trisilicate, polyvinyl pyrrolidone, cellulose-based substances, polyethylene glycol, sodium carboxymethylcellulose, polyacrylates, waxes, polyethylene-polyoxypropylene-block polymers, polyethylene glycol and wool fat.
  • Suitable pharmaceutical carriers are described in Remington's Pharmaceutical Sciences, Mack Publishing Company, a standard reference text in this field. They are preferably selected with respect to the intended form of administration, that is, oral tablets, capsules, elixirs, syrups and the like and consistent with conventional pharmaceutical practices.
  • administering can be effected in one dose, continuously or intermittently throughout the course of treatment. Methods of determining the most effective means and dosage of administration are known to those of skill in the art and will vary with the composition used for therapy, the purpose of the therapy, the target cell being treated and the subject being treated. Single or multiple administrations can be carried out with the dose level and pattern being selected by the treating physician. Suitable dosage formulations and methods of administering the agents are known in the art. Route of administration can also be determined and method of determining the most effective route of administration are known to those of skill in the art and will vary with the composition used for treatment, the purpose of the treatment, the health condition or disease stage of the subject being treated and target cell or tissue. Non-limiting examples of route of administration include oral administration, nasal administration, injection and topical application.
  • the term “effective amount” refers to a quantity sufficient to achieve a beneficial or desired result or effect. In the context of therapeutic or prophylactic applications, the effective amount will depend on the type and severity of the condition at issue and the characteristics of the individual subject, such as general health, age, sex, body weight, and tolerance to pharmaceutical compositions. In the context of an immunogenic composition, in some embodiments the effective amount is the amount sufficient to result in a protective response against a pathogen. In other embodiments, the effective amount of an immunogenic composition is the amount sufficient to result in antibody generation against the antigen. In some embodiments, the effective amount is the amount required to confer passive immunity on a subject in need thereof.
  • the effective amount will depend on the intended use, the degree of immunogenicity of a particular antigenic compound, and the health/responsiveness of the subject's immune system, in addition to the factors described above. The skilled artisan will be able to determine appropriate amounts depending on these and other factors.
  • the effective amount will depend on the size and nature of the application in question. It will also depend on the nature and sensitivity of the in vitro target and the methods in use. The skilled artisan will be able to determine the effective amount based on these and other considerations.
  • the effective amount may comprise one or more administrations of a composition depending on the embodiment.
  • the agents and compositions can be used in the manufacture of medicaments and for the treatment of humans and other animals by administration in accordance with conventional procedures, such as an active ingredient in pharmaceutical compositions.
  • An agent of the present invention can be administered for therapy by any suitable route of administration. It will also be appreciated that the preferred route will vary with the condition and age of the recipient and the disease being treated.
  • a solid phase support examples include glass, polystyrene, polypropylene, polyethylene, dextran, nylon, amylases, natural and modified celluloses, polyacrylamides, gabbros and magnetite.
  • the nature of the carrier can be either soluble to some extent or insoluble.
  • the support material may have virtually any possible structural configuration so long as the coupled molecule is capable of binding to a polynucleotide, polypeptide or antibody.
  • the support configuration may be spherical, as in a bead or cylindrical, as in the inside surface of a test tube or the external surface of a rod.
  • the surface may be flat such as a sheet, test strip, etc. or alternatively polystyrene beads.
  • suitable carriers for binding antibody or antigen will be able to ascertain the same by use of routine experimentation.
  • an “antibody” includes whole antibodies and any antigen binding fragment or a single chain thereof.
  • the term “antibody” includes any protein or peptide containing molecule that comprises at least a portion of an immunoglobulin molecule. Examples of such include, but are not limited to a complementarity determining region (CDR) of a heavy or light chain or a ligand binding portion thereof, a heavy chain or light chain variable region, a heavy chain or light chain constant region, a framework (FR) region or any portion thereof or at least one portion of a binding protein.
  • CDR complementarity determining region
  • the antibodies can be polyclonal or monoclonal and can be isolated from any suitable biological source, e.g., murine, rat, sheep or canine.
  • Immuno response broadly refers to the antigen-specific responses of lymphocytes to foreign substances. Any substance that can elicit an immune response is said to be “immunogenic” and is referred to as an “immunogen”. All immunogens are antigens, however, not all antigens are immunogenic. An immune response of this invention can be humoral (via antibody activity) or cell-mediated (via T cell activation).
  • the term “inducing an immune response in a subject” is a term well understood in the art and intends that an increase of at least about 2-fold, more preferably at least about 5-fold, more preferably at least about 10-fold, more preferably at least about 100-fold, even more preferably at least about 500-fold, even more preferably at least about 1000-fold or more in an immune response to an antigen (or epitope) can be detected or measured, after introducing the antigen (or epitope) into the subject, relative to the immune response (if any) before introduction of the antigen (or epitope) into the subject.
  • An immune response to an antigen includes, but is not limited to, production of an antigen-specific (or epitope-specific) antibody and production of an immune cell expressing on its surface a molecule which specifically binds to an antigen (or epitope).
  • Methods of determining whether an immune response to a given antigen (or epitope) has been induced are well known in the art.
  • antigen-specific antibody can be detected using any of a variety of immunoassays known in the art, including, but not limited to, ELISA, wherein, for example, binding of an antibody in a sample to an immobilized antigen (or epitope) is detected with a detectably-labeled second antibody (e.g., enzyme-labeled mouse anti-human Ig antibody).
  • ELISA immunoassays known in the art, including, but not limited to, ELISA, wherein, for example, binding of an antibody in a sample to an immobilized antigen (or epitope) is detected with a detectably-labeled second antibody (e.g., enzyme-labeled mouse anti-human Ig antibody).
  • modulate an immune response includes inducing (increasing, eliciting) an immune response; and reducing (suppressing) an immune response.
  • An immunomodulatory method is one that modulates an immune response in a subject.
  • HMG domain or “high mobility group (HMG) box domain” refers to an amino acid sequence that is involved in binding DNA (Stros et al., Cell Mol Life Sci. 64(19-20):2590-606 (2007)).
  • the structure of the HMG-box domain consists of three helices in an irregular array.
  • an HMG-box domain enables a protein to bind non-B-type DNA conformations (kinked or unwound) with high affinity.
  • HMG-box domains can be found in high mobility group proteins, which are involved in the regulation of DNA-dependent processes such as transcription, replication and DNA repair, all of which require changing the conformation of chromatin (Thomas (2001) Biochem. Soc. Trans. 29(Pt 4):395-401).
  • Non-limiting examples of polypeptides comprising an HMG-box domain include HMG1(HMGB1), HMG2(HMGB2), HMGB3 and HMGB4 non-histone components of chromatin; SRY (sex determining region Y protein) involved in differential gonadogenesis; the SOX family of transcription factors (Harley et al. (2003) Endocr. Rev. 24(4):466-87); sequence-specific LEF1 (lymphoid enhancer binding factor 1) and TCF-1 (T-cell factor 1) involved in regulation of organogenesis and thymocyte differentiation (Labbé et al. (2000) Proc. Natl. Acad. Sci. USA.
  • SSRP structure-specific recognition protein SSRP involved in transcription and replication
  • MTF1 mitochondrial transcription factor mitochondrial transcription factor
  • nucleolar transcription factors UBF 1/2 upstream binding factor
  • yeast ARS-binding factor yeast transcription factors 1xr1, Rox1, Nhp6b and Spp41
  • mating type proteins MAT involved in the sexual reproduction of fungi (Barve et al. (2003) Fungal Genet. Biol. 39(2):151-67); and the YABBY plant-specific transcription factors.
  • Exemplary sequences of polypeptides comprising an HMG-box domain include NP — 002119 (human HMGB1), NP — 001124160 (human HMGB2), NP — 005333 (human HMGB3) and NP — 660206 (human HMGB4).
  • An HMGB1 fragment that contains either of these two HMG-box domains for example, also constitutes a polypeptide comprising an HMG-box domain, within the meaning of the present disclosure.
  • a polypeptide comprising an HMG-box domain intends any of the above described proteins, fragments of these proteins that contain one or more of the HMG-box domain or equivalents of these proteins or fragments.
  • an equivalent of a polypeptide refers to a sequence that is at least about 70%, or alternatively at least about 75%, or at least about 80%, or at least about 85%, or at least about 90%, or at least about 95%, or at least about 98% or at least about 99% identical to the reference polypeptide.
  • the equivalent of a polypeptide retains the intended function and/or structural characteristics of the polypeptide, e.g., containing an HMG-box domain.
  • the equivalent polypeptide includes a domain that is at least about 70%, or alternatively at least about 80%, or at least about 85%, or at least about 90%, or at least about 95%, or at least about 98% or at least about 99% identical to the HMG-box domain.
  • such an equivalent domain retains the function and/or structural characteristics of the HMB-box domain, e.g., binding to a HMB-box binding target.
  • the equivalent polypeptide can hybridize with the polypeptide under stringent conditions.
  • polypeptides comprising an HMG-box domain are intended to include wildtype and recombinantly produced polypeptides and proteins from prokaryotic and eukaryotic host cells, as well as muteins, analogs and fragments thereof.
  • the term also includes antibodies and anti-idiotypic antibodies.
  • Such polypeptides can be isolated or produced using the methods identified below.
  • the proteins and polypeptides are obtainable by a number of processes known to those of skill in the art, which include purification, chemical synthesis and recombinant methods.
  • Polypeptides can be isolated from preparations such as host cell systems. by methods such as immunoprecipitation with antibody and standard techniques such as gel filtration, ion-exchange, reversed-phase and affinity chromatography. For such methodology, see for example Deutscher et al. (1999) Guide To Protein Purification: Methods In Enzymology (Vol. 182, Academic Press). Accordingly, this invention also provides the processes for obtaining these polypeptides as well as the products obtainable and obtained by these processes.
  • polypeptides also can be obtained by chemical synthesis using a commercially available automated peptide synthesizer such as those manufactured by Perkin/Elmer/Applied Biosystems, Inc., Model 430A or 431A, Foster City, Calif., USA.
  • the synthesized polypeptide can be precipitated and further purified, for example by high performance liquid chromatography (HPLC).
  • HPLC high performance liquid chromatography
  • this invention also provides a process for chemically synthesizing the proteins of this invention by providing the sequence of the protein and reagents, such as amino acids and enzymes and linking together the amino acids in the proper orientation and linear sequence.
  • proteins and polypeptides can be obtained by well-known recombinant methods as described, for example, in Sambrook et al. (1989) supra, using the host cell and vector systems described herein.
  • polypeptides of this invention also can be combined with various solid phase carriers, such as an implant, a stent, a paste, a gel, a dental implant or a medical implant or liquid phase carriers, such as beads, sterile or aqueous solutions, pharmaceutically acceptable carriers, suspensions or emulsions.
  • solid phase carriers such as an implant, a stent, a paste, a gel, a dental implant or a medical implant or liquid phase carriers, such as beads, sterile or aqueous solutions, pharmaceutically acceptable carriers, suspensions or emulsions.
  • non-aqueous solvents include propyl ethylene glycol, polyethylene glycol and vegetable oils.
  • the carriers also can include an adjuvant that is useful to non-specifically augment a specific immune response. A skilled artisan can easily determine whether an adjuvant is required and select one.
  • suitable adjuvants include, but are not limited to Freund's Complete and Incomplete, mineral salts and polynucleotides.
  • suitable adjuvants include monophosphoryl lipid A (MPL), mutant derivatives of the heat labile enterotoxin of E. coli , mutant derivatives of cholera toxin, CPG oligonucleotides and adjuvants derived from squalene.
  • One embodiment of the present disclosure provides a method for inhibiting, competing or titrating the binding of a DNABII polypeptide or protein to a microbial DNA, comprising contacting the DNABII polypeptide or protein or the microbial DNA with a polypeptide comprising an HMG-box domain, thereby inhibiting, competing or titrating the binding of the DNABII protein or polypeptide to the microbial DNA.
  • HMGB1 Polypeptides having one or more HMG-box domains are known in the art and further described above.
  • One such example is HMGB1 from eukaryotes, a non-specific DNA binding protein. It was known that HMGB1 is released from cells during necrosis, but not apoptosis, and is also released by macrophage stimulated with endotoxin and proinflammatory cytokines. Released HMGB1 recruits neutrophils and act as a cytokine to promote inflammation. HMGB1 aksi activates dendritic cells and promotes their functional maturation and response to lymph node chemokines.
  • HMGB1 binds in the minor groove of DNA, but is not homologous to DNABII family proteins.
  • the data presented in Example 2 shows that HMGB1 has a high affinity for bent DNA structures and is functionally similar to DNABII.
  • Another embodiment of the present disclosure provides a method for inhibiting, preventing or breaking down a microbial biofilm, comprising contacting the biofilm with a polypeptide comprising an HMG-box domain, thereby inhibiting, preventing or breaking down the microbial biofilm.
  • the contacting is in vitro or in vivo.
  • Yet another embodiment of the present disclosure provides a method of inhibiting, preventing or breaking down a biofilm in a subject, comprising administering to the subject an effective amount of a polypeptide comprising an HMG-box domain, thereby inhibiting, preventing or breaking down the microbial biofilm.
  • polypeptide comprising, or alternatively consisting essentially of, or yet further consisting of an HMG-box domain that also comprises or alternatively consisting essentially of, or yet further consisting of one or more of:
  • polypeptide that is at least about 70%, or alternatively at least about 75%, or at least about 80%, or at least about 85%, or at least about 90%, or at least about 95%, or at least about 98% or at least about 99% identical to any of (a), (b), (c) or (d).
  • the polypeptide comprising an HMG-box domain comprises or alternatively consists essentially of, or yet further consists of an isolated or recombinant protein HMGB1, a polypeptide that is at least about 70%, or at least about 75%, or at least about 80%, or at least about 85%, or at least about 90%, or at least about 95%, or at least about 98% or at least about 99% identical to HMGB1, or a fragment thereof that comprises or alternatively consists essentially of, or yet further consists of one or more HMG-box domains.
  • polypeptide comprising an HMG-box domain comprises or alternatively consists essentially of, or yet further consists of a biological equivalent to any polypeptide recited above.
  • the isolated or recombinant protein is a mammalian protein.
  • the mammalian protein is a human protein.
  • Any of the above method can further comprise or alternatively consists essentially of, or yet further consists of administering to the subject an effective amount of one or more of an antimicrobial, an antigenic peptide or an adjuvant.
  • the subject in one aspect, is a non-human animal or a human patient.
  • the polypeptide is administered by a method comprising topically, transdermally, sublingually, rectally, vaginally, ocularly, subcutaneous, intramuscularly, intraperitoneally, urethrally, intranasally, by inhalation or orally.
  • the subject is a pediatric patient and the polypeptide is administered in a formulation for the pediatric patient.
  • the biofilm can comprise microbial DNA from a microorganism identified in Table 1.
  • the polypeptide is administered locally to the microbial infection.
  • the present disclosure provides a method for inducing or providing an immune response in a subject in need thereof, comprising or alternatively consisting essentially of, or yet further consisting of administering to the subject an effective amount of a polypeptide comprising an HMG-box domain.
  • the administration is local to where the immune response is desired. Examples of polypeptides comprising an HMG-box domain are described above.
  • the isolated or recombinant protein can be a mammalian protein or in a particular aspect, a human protein.
  • the subject in some aspects, is a non-human animal or a human patient.
  • agents and compositions of this invention can be concurrently or sequentially administered with other antimicrobial agents and/or surface antigens.
  • administration is locally to the site of the infection.
  • Other non-limiting examples of administration include by one or more method comprising transdermally, sublingually, rectally, vaginally, ocularly, subcutaneous, intramuscularly, intraperitoneally, intranasally, by inhalation or orally.
  • any of the above described polypeptide comprising or alternatively consisting essentially of, or yet further consisting of an HMG-box domain for the manufacture of a medicament in breaking down a biofilm or inhibiting, preventing or treating a microbial infection that produces a biofilm.
  • the contacting can be performed in vitro or in vivo.
  • the method provides a means to determine efficacy of the agents of this invention prior to animal or clinical studies and can be used to determine if the agents of this invention work synergistically with additional antimicrobials.
  • the method provides a means to determine efficacy of the agents of this invention prior to studies in human patients and can be used to determine if the agents of this invention work synergistically with additional antimicrobials.
  • Microbial infections and disease that can be treated by the methods of this invention include infection by the organisms identified in Table 1, e.g., Streptococcus agalactiae, Neisseria meningitidis, Treponemes, denticola, pallidum, Burkholderia cepacia or Burkholderia pseudomallei .
  • the microbial infection is one or more of Haemophilus influenzae (nontypeable), Moraxella catarrhalis, Streptococcus pneumoniae, Streptococcus pyogenes, Pseudomonas aeruginosa, Mycobacterium tuberculosis .
  • microbial infections may be present in the upper, mid or lower airway (otitis, sinusitis or bronchitis) but also exacerbations of chronic obstructive pulmonary disease (COPD), chronic cough, complications of and/or primary cause of cystic fibrosis (CF) and community acquired pneumonia (CAP).
  • COPD chronic obstructive pulmonary disease
  • COPD chronic cough
  • CF cystic fibrosis
  • CAP community acquired pneumonia
  • Infections might also occur in the oral cavity (caries, periodontitis) and caused by Streptococcus mutans, Porphyromonas gingivalis, Aggregatibacter actinomycetemcomitans . Infections might also be localized to the skin (abscesses, ‘staph’ infections, impetigo, secondary infection of burns, Lyme disease) and caused by Staphylococcus aureus, Staphylococcus epidermidis, Pseudomonas aeruginosa and Borrelia burdorferi . Infections of the urinary tract (UTI) can also be treated and are typically caused by Escherichia coli .
  • Infections of the gastrointestinal tract are typically caused by Salmonella enterica serovar, Vibrio cholerae and Helicobacter pylori .
  • Infections of the genital tract include and are typically caused by Neisseria gonorrhoeae .
  • Infections can be of the bladder or of an indwelling device caused by Enterococcus faecalis .
  • Infections associated with implanted prosthetic devices, such as artificial hip or knee replacements or dental implants or medical devices such as pumps or monitoring systems, typically caused by a variety of bacteria, can be treated by the methods of this invention. These devices can be coated or conjugated to an agent as described herein.
  • Infections caused by Streptococcus agalactiae are the major cause of bacterial septicemia in newborns. Such infections can also be treated by the methods of this invention. Likewise, infections caused by Neisseria meningitidis which can cause meningitis can also be treated.
  • routes of administration applicable to the methods of the invention include intranasal, intramuscular, intratracheal, subcutaneous, intradermal, topical application, intravenous, rectal, nasal, oral and other enteral and parenteral routes of administration. Routes of administration may be combined, if desired, or adjusted depending upon the agent and/or the desired effect.
  • An active agent can be administered in a single dose or in multiple doses.
  • Embodiments of these methods and routes suitable for delivery include systemic or localized routes.
  • routes of administration suitable for the methods of the invention include, but are not limited to, enteral, parenteral or inhalational routes.
  • Parenteral routes of administration other than inhalation administration include, but are not limited to, topical, transdermal, subcutaneous, intramuscular, intraorbital, intracapsular, intraspinal, intrasternal and intravenous routes, i.e., any route of administration other than through the alimentary canal.
  • Parenteral administration can be conducted to effect systemic or local delivery of the inhibiting agent. Where systemic delivery is desired, administration typically involves invasive or systemically absorbed topical or mucosal administration of pharmaceutical preparations.
  • the compounds of the invention can also be delivered to the subject by enteral administration.
  • Enteral routes of administration include, but are not limited to, oral and rectal (e.g., using a suppository) delivery.
  • Methods of administration of the active through the skin or mucosa include, but are not limited to, topical application of a suitable pharmaceutical preparation, transcutaneous transmission, transdermal transmission, injection and epidermal administration.
  • a suitable pharmaceutical preparation for transdermal transmission, absorption promoters or iontophoresis are suitable methods.
  • Iontophoretic transmission may be accomplished using commercially available “patches” that deliver their product continuously via electric pulses through unbroken skin for periods of several days or more.
  • the active will be administered orally on a continuous, daily basis, at least once per day (QD) and in various embodiments two (BID), three (TID) or even four times a day.
  • the therapeutically effective daily dose will be at least about 1 mg, or at least about 10 mg, or at least about 100 mg or about 200—about 500 mg and sometimes, depending on the compound, up to as much as about 1 g to about 2.5 g.
  • Dosing of can be accomplished in accordance with the methods of the invention using capsules, tablets, oral suspension, suspension for intra-muscular injection, suspension for intravenous infusion, gel or cream for topical application or suspension for intra-articular injection.
  • compositions described herein can be determined by standard pharmaceutical procedures in cell cultures or experimental animals, for example, to determine the LD50 (the dose lethal to 50% of the population) and the ED50 (the dose therapeutically effective in 50% of the population).
  • the dose ratio between toxic and therapeutic effects is the therapeutic index and it can be expressed as the ratio LD50/ED50.
  • Compositions which exhibit high therapeutic indices are preferred. While compounds that exhibit toxic side effects may be used, care should be taken to design a delivery system that targets such compounds to the site of affected tissue in order to minimize potential damage to uninfected cells and, thereby, reduce side effects.
  • the data obtained from the cell culture assays and animal studies can be used in formulating a range of dosage for use in humans.
  • the dosage of such compounds lies preferably within a range of circulating concentrations that include the ED50 with little or no toxicity.
  • the dosage may vary within this range depending upon the dosage form employed and the route of administration utilized.
  • the therapeutically effective dose can be estimated initially from cell culture assays.
  • a dose can be formulated in animal models to achieve a circulating plasma concentration range that includes the IC50 (i.e., the concentration of the test compound which achieves a half-maximal inhibition of symptoms) as determined in cell culture.
  • IC50 i.e., the concentration of the test compound which achieves a half-maximal inhibition of symptoms
  • levels in plasma may be measured, for example, by high performance liquid chromatography.
  • an effective amount of a composition sufficient for achieving a therapeutic or prophylactic effect ranges from about 0.000001 mg per kilogram body weight per administration to about 10,000 mg per kilogram body weight per administration.
  • the dosage ranges are from about 0.0001 mg per kilogram body weight per administration to about 100 mg per kilogram body weight per administration.
  • Administration can be provided as an initial dose, followed by one or more “booster” doses.
  • Booster doses can be provided a day, two days, three days, a week, two weeks, three weeks, one, two, three, six or twelve months after an initial dose.
  • a booster dose is administered after an evaluation of the subject's response to prior administrations.
  • treatment of a subject with a therapeutically effective amount of the therapeutic compositions described herein can include a single treatment or a series of treatments.
  • compositions and related methods of the present invention may be used in combination with the administration of other therapies. These include, but are not limited to, the administration of DNase enzymes, antibiotics, antimicrobials, or other antibodies.
  • the methods and compositions include a deoxyribonuclease (DNase) enzyme that acts synergistically with a composition of this disclosure, e.g., a DNase.
  • DNase is any enzyme that catalyzes the cleavage of phosphodiester linkages in the DNA backbone.
  • DNase enzymes that are known to target not only cruciform structures, but also a variety of secondary structure of DNA include DNAse I, T4 EndoVII and T7 Endo I.
  • the effective amount of anti-DNABII antibody needed to destabilize the biofilm is reduced when combined with a DNase.
  • the DNase can be added directly to the assay or in a suitable buffer known to stabilize the enzyme.
  • the effective unit dose of DNase and the assay conditions may vary, and can be optimized according to procedures known in the art.
  • the methods and compositions can be combined with antibiotics and/or antimicrobials.
  • Antimicrobials are substances that kill or inhibit the growth of microorganisms such as bacteria, fungi, or protozoans.
  • biofilms are generally resistant to the actions of antibiotics, compositions and methods described herein can be used to sensitize the infection involving a biofilm to traditional therapeutic methods for treating infections.
  • the use of antibiotics or antimicrobials in combination with methods and compositions described herein allow for the reduction of the effective amount of the antimicrobial and/or biofilm reducing agent.
  • antimicrobials and antibiotics useful in combination with methods of the current invention include amoxicillin, amoxicillin-clavulanate, cefdinir, azithromycin, and sulfamethoxazole-trimethoprim.
  • the therapeutically effective dose of the antimicrobial and/or antibiotic in combination with the biofilm reducing agent can be readily determined by traditional methods.
  • the dose of the antimicrobial agent in combination with the biofilm reducing agent is the average effective dose which has been shown to be effective in other bacterial infections, for example, bacterial infections wherein the etiology of the infection does not include a biofilm.
  • the dose is 0.1, 0.15, 0.2, 0.25, 0.30, 0.35, 0.40, 0.45, 0.50, 0.55, 0.60, 0.65, 0.70, 0.75, 0.8, 0.85, 0.9, 0.95, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.0, 2.5, 3.0 or 5 times the average effective dose.
  • the antibiotic or antimicrobial can be added prior to, concurrent with, or subsequent to the addition of the anti-DNABII antibody.
  • the methods and compositions can be combined with antibodies that treat the bacterial infection.
  • an antibody useful in combination with the methods and compositions described herein is an antibody directed against an unrelated outer membrane protein (e.g., OMP P5). Treatment with this antibody alone does not debulk a biofilm in vitro. Combined therapy with this antibody and a biofilm reducing agent results in a greater effect than that which could be achieved by either reagent used alone at the same concentration.
  • Other antibodies that may produce a synergistic effect when combined with a biofilm reducing agent or methods to reduce a biofilm include anti-rsPilA, anti-OMP26, anti-OMP P2, and anti-whole OMP preparations.
  • compositions and methods described herein can be used to sensitize the bacterial infection involving a biofilm to common therapeutic modalities effective in treating bacterial infections without a biofilm but are otherwise ineffective in treating bacterial infections involving a biofilm.
  • the compositions and methods described herein can be used in combination with therapeutic modalities that are effective in treating bacterial infections involving a biofilm, but the combination of such additional therapy and biofilm reducing agent or method produces a synergistic effect such that the effective dose of either the biofilm reducing agent or the additional therapeutic agent can be reduced.
  • the combination of such additional therapy and biofilm reducing agent or method produces a synergistic effect such that the treatment is enhanced.
  • An enhancement of treatment can be evidenced by a shorter amount of time required to treat the infection.
  • the additional therapeutic treatment can be added prior to, concurrent with, or subsequent to methods or compositions used to reduce the biofilm, and can be contained within the same formulation or as a separate formulation.
  • kits containing the agents and instructions necessary to perform the in vitro and in vivo methods as described herein also are claimed. Accordingly, the invention provides kits for performing these methods which may include a biological agent of this invention as well as instructions for carrying out the methods of this invention such as collecting tissue and/or performing the screen and/or analyzing the results and/or administration of an effective amount of biological agent as defined herein. These can be used alone or in combination with other suitable antimicrobial agents.
  • the present disclosure provides a kit comprising a polypeptide comprising an HMG-box domain and instructions for use in breaking down a biofilm or inhibiting, preventing or treating a microbial infection that produces a biofilm.
  • a kit comprising a polypeptide comprising an HMG-box domain and instructions for use in breaking down a biofilm or inhibiting, preventing or treating a microbial infection that produces a biofilm. Examples of polypeptides comprising an HMG-box domain are described above.
  • the kit further comprises one or more of an adjuvant, an antigenic peptide or an antimicrobial.
  • the kit further comprises a carrier selected from the group of a liquid carrier, a pharmaceutically acceptable carrier, a solid phase carrier, a pharmaceutically acceptable carrier, an implant, a stent, a paste, a gel, a dental implant or a medical implant.
  • FIG. 1 these antibodies are specific to the corresponding proteins.
  • FIG. 2 further shows that the goat anti-human HMGB1 antibodies are specific to the human HMGB1 protein and the binding is in a dose-dependent manner.
  • HMGB1 protein binds to DNA scaffold in microbial biofilms permitting immune response from the host leading to destruction and removal of the biofilm.
  • HMGB1 Competes with HU and IHF for Binding to Biofilm DNA
  • HMGB1 has high affinity for bent DNA structures and competes with HU and IHF for binding to the DNA in biofilm leading to reduction of biofilm growth.
  • biofilms generated by Nontypable Haemophilus influenzae were treated with na ⁇ ve serum alone, which contained HMGB1, or with serum containing anti-HMGB1 antibody.
  • NTHI Nontypable Haemophilus influenzae
  • FIG. 3 reduction of HMGB1 by the antibody caused enhanced biofilm growth, shown as thicker biofilm at lower right as compared to a thinner one at lower left. Therefore, less competition from HMGB1 for HU and IHF binding sites on the biofilm DNA strengthens the biofilm.
  • FIG. 4 confirms that HMGB1 protein exists in mammalian na ⁇ ve serum and the HMGB1 protein from human, rabbit and goat can all be recognized by the prepared goat anti-human HMGB1 antibodies.
  • the estimated concentrations of HMGB1 in each serum sample were about 0.8 ⁇ g, 0.8 and 2.8 ⁇ g per 80 ⁇ g total protein, respectively.
  • HMGB1 dose-dependently inhibits biofilm formation. For instance, compared to NTHI in sterile medium sBHI (BHI with 2 mg heme/mL and 2 mg b-NAD/mL) that grew up to 22.5 ⁇ M of thickness at 40 hours, 0.075 ⁇ g/ml, 0.75 ⁇ g/ml and 7.5 ⁇ g/ml HMGB1 treatment at 24 hours reduced the biofilm thickness to 21.5 ⁇ m, 20.0 ⁇ m, and 16.5 ⁇ m, respectively ( FIG. 5 ). This indicates that HMGB1 competes for the same binding target as HU and IHF.
  • HMGB1 and IHF were co-localized in an OCT (Optimal Cutting Temperature medium, available commercially from Fisher Scientific Cat. No. 14-373-65) embedded human bronchoalveolar lavage (BAL).
  • OCT Optimal Cutting Temperature medium, available commercially from Fisher Scientific Cat. No. 14-373-65
  • BAL embedded human bronchoalveolar lavage
  • FIG. 8 A further enlarged image in FIG. 8 shows that HMGB1 was periodically along the length of dsDNA strands and in close proximity of IHF at junctions.
  • FIG. 9 different z-plane images of the same section of the slide show that HMGB1 and IHF are both detected at the junction of strands of dsDNA and are in close proximity.
  • HMGB1 competes with IHF and HU for binding to the same target on biofilm DNA.
  • proteins containing a HMG-box domain is useful in inhibiting the formation and growth of biofilm and thus useful in treating diseases and conditions characterized by biofilms.
  • Middle ear infection or otitis media, OM
  • OM Middle ear infection
  • the socioeconomic burden of OM is also great, with cost estimates between $5-6 billion in the United States alone annually.
  • All three of the predominant bacterial pathogens of OM are known to form biofilms both in vitro and in vivo and recently, clinicians have come to appreciate that the chronicity and recurrence of OM is due, at least in part, to the formation of bacterial biofilms within the middle ear cavity.
  • chinchilla model of OM juvenile chinchillas are first given a viral ‘cold’, followed a week later by their being challenged intranasally with an inoculum of viable bacteria. Similar to the human condition wherein “my child has a cold and a week later gets an ear infection” chinchillas will also develop a bacterial OM approximately one week after a challenge, and while experiencing the viral upper respiratory tract infection. Once bacteria gain access to the middle ear (either via ascension of the Eustachian tube or following direct challenge to the middle ear space), they will form a robust biofilm.
  • Applicants thus contemplate and indeed have already used chinchilla models to demonstrate the protective efficacy of the compositions and methods as described herein, which results in rapid resolution of existing biofilms.
  • This model is also useful for therapeutic approaches via either passive delivery of anti-DNABII antibody or via delivery of a small molecule or other agent known to bind to IHF or other DNABII family members.
  • a number of oral bacteria have been implicated in the pathogenesis of inflammatory diseases such as periodontitis and peri-implantitis, which destroy alveolar bone and gingiva. Investigations of the pathogenesis of these bacteria are hampered by lack of effective animal models.
  • One of the challenges of investigating the pathogenicity of specific bacteria is the difficulty of establishing a biofilm when exogenous bacteria are introduced into the oral cavity of animals. Though animal models of periodontitis have been developed, cultivable bacteria are rarely recovered from the oral cavity of inoculated animals. Developing an effective animal model which can assess the pathogenicity of specific bacteria will greatly aid in elucidating their pathogenic mechanisms.
  • machined titanium dental implants (1.2 ⁇ 4.5 mm) can be modified by grit blasting with A103 (100 ⁇ m) and HCl etching (pH 7.8 for 20 min at 80° C.).
  • Machined and nano-textured implants can be incubated in TSB medium inoculated with D7S clinical strain of Aggregatibacter actinomycetemcomitans (Aa) for 1 to 3 days at 37° C.
  • the bacterial biofilm on the implants can be analyzed by SEM, as well as by confocal laser scanning microscopy following staining with LIVE/DEAD® BacLightTM.
  • Implants with and without established Aa biofilm are transmucosally placed into the alveolar bone of female rats between premolar and incisor region of the maxillae.
  • bacterial samples are collected from saliva and the oral surfaces of implants after 2 days. Aa was detected by culture, as well as by PCR analysis.
  • Lyme disease is the most common tick-borne disease in the United States. Reported cases have more than doubled between 1992 and 2006, with approximately 29,000 new cases confirmed in 2008. Estimates are that the actual number of cases of Lyme disease may exceed that reported by a factor of 6-12 in endemic areas. By definition, these endemic areas are expanding as populations continue to move from cities to suburban and rural areas and whitetail deer (which carry the tick species Ixodes ) increasingly roam these areas. Lyme disease is caused by the microorganism Borrelia burgdorferi , a spirochete. B. burgdorferi is transmitted via the bite of the Ixodes tick and subsequently disseminates, via the bloodstream, to other tissues and organs.
  • C3H/HeN mice are injected with spirochetes via dorsal subcutaneous and intraperitoneal injection, or via intravenous injection. Blood and biopsy specimens are recovered at approximately 7 days post infection for evaluation of microbial burden and assessment of pathology in tissues and organs.
  • the methods and compositions of this invention are contemplated to develop both therapeutic as well as preventative strategies for reduction and/or elimination of the resulting B. burgdorferi biofilms which form subsequent to challenge and are believed to contribute to both the pathogenesis and chronic nature of the disease.
  • Cystic fibrosis is an autosomal recessive disease due to mutations in a gene that encodes the CF transmembrane conductance regulator (called CFTR) anion channel.
  • CFTR CF transmembrane conductance regulator
  • the pigs can be immunized with the interfering agents to either 1) immunize these CF pigs with a polypeptide or other immunogenic agent thereby inducing the formation of antibodies which will eradicate bacterial biofilms in the lungs, to deliver anti-IHF (or other interfering agent) to the lungs of these animals by nebulization to assess the amelioration of the signs of disease and associated pathologies.
  • TB tuberculosis
  • SPF guinea pigs are maintained in a barrier colony and infected via aerosolized spray to deliver ⁇ 20 cfu of M. tuberculosis strain Erdman K01 bacilli into their lungs. Animals are sacrificed with determination of bacterial load and recovery of tissues for histopathological assessment on days 25, 50, 75, 100, 125 and 150 days post-challenge. Unlike mice which do not develop classic signs of TB, guinea pigs challenged in this manner develop well-organized granulomas with central necrosis, a hallmark of human disease.
  • guinea pigs develop severe pyogranulomatous and necrotizing lymphadenitis of the draining lymph nodes as part of the primary lesion complex.
  • Use of this model will provide a pre-clinical screen to confirm and identify therapeutic as well as preventative strategies for reduction and/or elimination of the resulting M. tuberculosis biofilms which have been observed to form in the lungs of these animals subsequent to challenge and are believed to contribute to both the pathogenesis and chronicity of the disease.
  • epidermidis amount to $2 billion annually in the United States. In addition to S. epidermidis, E. faecalis and S. aureus are also contaminations found on indwelling medical devices. There are several animal models of catheter-associated S. epidermidis infections including rabbits, mice, guinea pigs and rats all of which are used to study the molecular mechanisms of pathogenesis and which lend themselves to studies of prevention and/or therapeutics. Rat jugular vein catheters have been used to evaluate therapies that interfere with E. faecalis, S. aureus and S. epidermidis biofilm formation.
  • Biofilm reduction is often measured three ways—(i) sonicate catheter and calculate CFUs, (ii) cut slices of catheter or simply lay on a plate and score, or (iii) the biofilm can be stained with crystal violet or another dye, eluted, and OD measured as a proxy for CFUs.
  • Immunogenic compositions may be administered to a human and animal subjects in the presence of adjuvants such as but not limited to aluminum salts and liposomes. Those skilled in the art will understand that any number of pharmaceutically acceptable adjuvants can also be used. Immunogenic compositions may be administered to a human or animal subjects intramuscularly, subdermally, intranasally, or through any other suitable route. Immunogenic compositions may be prepared in a manner consistent with the selected mode of administration. Immunogenic compositions may take the form of polypeptides, nucleic acids, or a combination thereof, and may comprise full-length or partial antigens.
  • immunogenic compositions may take the form of APCs pulsed with a particular antigen, or APCs transfected with one or more polynucleotides encoding a particular antigen.
  • Administration may comprise a single dose of an immunogenic composition, or an initial administration, followed by one or more booster doses.
  • Booster doses may be provided a day, two days, three days, a week, two weeks, three weeks, one, two, three, six or twelve months, or at any other time point after an initial dose.
  • a booster dose may be administered after an evaluation of the subject's antibody titer.
  • Methods described herein may be used to confer passive immunity on a non-immune subject. Passive immunity against a given antigen may be conferred through the transfer of antibodies or antigen binding fragments that specifically recognize or bind to a particular antigen.
  • Antibody donors and recipients may be human or non-human subjects.
  • the antibody composition may comprise an isolated or recombinant polynucleotide encoding an antibody or antigen binding fragment that specifically recognizes or binds to a particular antigen.
  • Immunogenic compositions may be prepared in a manner consistent with the selected mode of administration.
  • Compositions may comprise whole antibodies, antigen binding fragments, polyclonal antibodies, monoclonal antibodies, antibodies generated in vivo, antibodies generated in vitro, purified or partially purified antibodies, or whole serum.
  • Administration may comprise a single dose of an antibody composition, or an initial administration followed by one or more booster doses.
  • Booster doses may be provided a day, two days, three days, a week, two weeks, three weeks, one, two, three, six or twelve months, or at any other time point after an initial dose.
  • a booster dose may be administered after an evaluation of the subject's antibody titer.

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US11564982B2 (en) 2017-01-04 2023-01-31 Research Institute At Nationwide Children's Hospital DNABII vaccines and antibodies with enhanced activity
US12098188B2 (en) 2017-01-04 2024-09-24 Research Institute At Nationwide Children's Hospital Antibody fragments for the treatment of biofilm-related disorders
US12419944B2 (en) 2017-01-04 2025-09-23 Research Institute At Nationwide Children's Hospital DNABII vaccines and antibodies with enhanced activity
US11746136B2 (en) 2017-03-15 2023-09-05 Research Institute At Nationwide Children's Hospital Composition and methods for disruption of bacterial biofilms without accompanying inflammation
US11090034B2 (en) * 2018-06-12 2021-08-17 Terumo Cardiovascular System Corporation Circular retractor for cardiovascular valve procedures
US12365710B2 (en) 2018-10-05 2025-07-22 Research Institute At Nationwide Children's Hospital HMGB1 protein derivatives for the removal of biofilms
US12453747B2 (en) 2019-06-03 2025-10-28 Research Institute At Nationwide Children's Hospital Prebiotic formulations for prevention of sepsis and necroenterocolitis induced neurodevelopmental deficiencies

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