METHODS OF USE & COMPOSITIONS OF IBD, IBS, & ANTINEOPLASTIC MICROBIAL THERAPEUTICS

Abstract

This invention relates to the medical use of pathogen associated molecular pattern (PAMP) displaying immunostimulatory microbial immuno-adjuvants [MIAs], as therapeutics when used in combination with check point inhibitors to treat various types of cancer and to methods of treatment which involve treating a subject with these compounds and compound mixtures and process methods for identifying and optimally composing them for their therapeutic use in cancer treatment. It also relates to the use of inhibitors of these PAMP displaying immunostimulatory microbial immuno-adjuvants [MIAs], as therapeutics when used to treat inflammatory bowel disease (IBD) including Crohn's Disease and ulcerative colitis and irritable bowel syndrome (IBS) and process methods for identifying and optimally composing them for their therapeutic use in IBD and IBS.

Claims

1. A method for the treatment or prophylaxis of neoplastic cancerous disease comprising administering one or more active agents selected from the group consisting of one or more Pathogen Associate Molecular Pattern (PAMP) displaying compounds or pharmaceutically acceptable salts thereof, PAMP recognizing antibodies, PAMP displaying enteral and injectable lipopolysaccharides (LPSs), and mixtures thereof as microbial immuno-adjuvants to increase both the range of tumor types treated by check point inhibitors and the percentage of patients with a specific tumor type responding to check point inhibitor therapy.

2-8. (canceled)

9. The method of claim 1, wherein the cancerous disease is selected from the group consisting of metastatic melanoma, lung cancer, renal cancer, breast cancer, colorectal cancer, gastric cancer, prostate cancer, bladder cancer, ovarian cancer, hematologic malignancies, pancreatic cancer, brain cancer, head & neck cancer, esophogeal cancer, hepatic cancer, and sarcomas.

10. A method of using PAMP identifying small molecular motifs in bioinformatic analysis, the method comprising (a) using data from both whole genome shotgun DNA sequencing and, transcriptomics and proteomics, (b) identifying PAMP displaying products that can be recognized by pattern recognition receptors (PRRs) and serve as microbial immune-adjuvants (MIAs) in cancer treatment when used in conjunction with check point inhibitors.

11. The method of claim 10 wherein the PAMP displaying products identified in step (b) serve as microbial immune-adjuvants (MIAs) in cancer treatment when used in conjunction with check point inhibitors.

12. The method of claim 10 wherein the PAMP displaying products identified in step (b) are useful for immunological stimulation in the cancer setting,

13. The method of claim 12, wherein the PAMP displaying products concomitantly serve as a means of targeting PAMPs to be blocked, deleted, or downregulated by identified compounds to use in the treatment of inflammatory bowel disease (IBD) and inflammatory bowel syndrome (IBS).

14. A method comprising administering of one or more of a moiety selected from the group consisting of attenuated versions of identified endotoxins and attenuated versions of identified exotoxins, that display one or more PAMPs, to treat a condition selected from the group consisting of cancer, IBD, and IBS.

15. The method of claim 14 wherein the attenuated versions of identified endotoxins are selected from Botox (onobutulinumtoxiaA).

16. The method of claim 14 further comprising the administration of check point inhibitors to induce an immunostimulatory response in immune cells, and wherein the condition is cancer.

17. The method of claim 14 wherein the PAMPSs have close homologies to tumor-specific molecular patterns (TSMPs) and wherein the condition is cancer.

18. The method of claim 17 further comprising the administration of check point inhibitors to induce an immunostimulatory response in immune cells and to target and treat the cancer.

19. The method of claim 14, wherein the moiety blocks, deletes, or downregulates the immunostimulatory response in immune in the treatment of flares and symptomatology associated with IBD and IBS.

Description

DETAILED DESCRIPTION OF THE INVENTION

[0031] All publications, patents and patent applications, including any drawings and appendices therein are incorporated by reference in their entirety for all purposes to the same extent as if each individual publication, patent or patent application, drawing, or appendix was specifically and individually indicated to be incorporated by reference in its entirety for all purposes.

[0032] Where appropriate, any one or more of the other active agents may be in the form of a pharmaceutically acceptable salt.

[0033] Suitable pharmaceutically acceptable salts include, but are not limited to, salts of pharmaceutically acceptable inorganic acids such as hydrochloric, sulfuric, phosphoric, nitric, carbonic, boric, sulfuric, and hydrobromic acids, or salts of pharmaceutically acceptable organic acids such as acetic, propionic, butyric, tartaric, maleic, hydroxymaleic, fumaric, malic, citric, lactic, mucic, gluconic, benzoic, succinic, oxalic, phenylacetic, methanesulphonic, toluenesulphonic, benzenesulphonic, salicylic, sulphanilic, aspartic, glutamic, edetic, stearic, palmitic, oleic, lauric, pantothenic, tannic, ascorbic and valeric acids.

[0034] It is intended that the aspects and embodiments of this invention encompasses LPS, attenuated toxin, and/or any other active agent in all solid forms, including amorphous forms, as well as crystalline forms, and polymorphs thereof.

[0035] Throughout this specification the term ‘in combination’ means that one or more other actives are both administered to the patient over the same period of treatment. They may be administered together, i.e. at the same time. In this case they may be administered in a single formulation, (e.g. as a single tablet or capsule or sachet) or in separate formulations administered simultaneously or nearly simultaneously. Alternatively, they may be administered at separate times of day.

[0036] The combinations of the invention provide benefits which are at least additive compared to the use of either agent alone. In many embodiments, the combinations are something more than additive, e.g. synergistic, compared to the use of either agent alone.

[0037] The definition of the term ‘treatment’ in this specification encompasses prophylaxis and prevention (i.e. reducing or eliminating the risk of contracting the disease). As well as meaning curing a person of the disease, ‘treatment’ also includes preventing the onset of symptoms, controlling (e.g. by slowing or eliminating) progression of disease, preventing the spread of the disease to other parts of the body and/or to other persons, reducing the spread of the disease and other facets of medical practice which will be readily understood by the person skilled in the art to fall within the meaning of the term ‘treatment’.

[0038] Throughout the description and claims of this specification, the words “comprise” and “contain” and variations of them mean “including but not limited to”, and they are not intended to (and do not) exclude other moieties, additives, components, integers or steps. Throughout the description and claims of this specification, the singular encompasses the plural unless the context otherwise requires. In particular, where the indefinite article is used, the specification is to be understood as contemplating plurality as well as singularity, unless the context requires otherwise.

Formulations

[0039] For the above-mentioned therapeutic uses the dosage administered will, of course, vary with the compound employed, the mode of administration, the treatment desired and the disorder indicated.

[0040] The pharmaceutical compositions may be administered systemically, e.g. by oral administration in the form of tablets, capsules, syrups, powders or granules; or by parenteral administration in the form of a sterile solution, suspension or emulsion for injection (including intravenous, subcutaneous, intramuscular, intravascular or infusion); or by rectal administration in the form of suppositories.

[0041] For oral administration, one or more active agents may be admixed with an adjuvant or a carrier, for example, lactose, saccharose, sorbitol, mannitol; a starch, for example, potato starch, corn starch or amylopectin; a cellulose derivative; a binder, for example, gelatine or polyvinylpyrrolidone; and/or a lubricant, for example, magnesium stearate, calcium stearate, polyethylene glycol, a wax, paraffin, and the like, and then compressed into tablets. If coated tablets are required, the cores, prepared as described above, may be coated with a concentrated sugar solution which may contain, for example, gum arabic, gelatine, talcum and titanium dioxide. Alternatively, the tablet may be coated with a suitable polymer dissolved in a readily volatile organic solvent.

[0042] For the preparation of soft gelatine capsules, one or more active agents may be admixed with, for example, a vegetable oil or polyethylene glycol. Hard gelatine capsules may contain granules of the compound using either the above-mentioned excipients for tablets. Also liquid or semisolid formulations of the compound of the invention may be filled into hard gelatine capsules. Liquid preparations for oral application may be in the form of syrups or suspensions, for example, solutions containing the compound of the invention, the balance being sugar and a mixture of ethanol, water, glycerol and propylene glycol. Optionally such liquid preparations may contain colouring agents, flavouring agents, sweetening agents (such as saccharine), preservative agents and/or carboxymethylcellulose as a thickening agent or other excipients known to those skilled in art.

[0043] For intravenous (parenteral) administration, one or more active agents may be administered as a sterile aqueous or oily solution. Parenteral formulations are particularly suitable for patients suffering from a severe infections. The person skilled in the art would be well aware of what differentiates a serious infection from a non-serious infection. By way of example, severe infections include those which render the patient unable to take the active agents orally, e.g. infections which render the patient unconscious, emetic, weak, delirious etc.

Treatment of Cancer

[0044] The present invention includes MIA products associated with PAMPs and used in conjunction with check point inhibitors to treat cancers that include, but are not limited to, metastatic melanoma, lung cancer, renal cancer, breast cancer, colorectal cancer, gastric cancer, prostate cancer, bladder cancer, ovarian cancer, hematologic malignancies, pancreatic cancer, brain cancer, head & neck cancer, esophogeal cancer, hepatic cancer, and sarcomas. It also includes MIA products with tumor specific molecular patterns (TSMPs).

[0045] In the present invention, the administered companion regimen to checkpoint inhibitors for cancer is a mixture of two or more toxins, attenuated toxins, and regions of toxins displaying immunostimulatory PAMPS selected from those produced by specific strains of bacterial organisms selected from the group consisting of Fusobacterium species (including F. nucleatum and F. necrophorum), Helicobacter species (including Helicobacter Pylon), Prevotella species, Bacteroides species (including B. thetaiotamicron and B. fragilis), Clostridium species (including C. difficile, C. perfringens, and C. botulinum), Porphymonas species, Escherichia species (including E. coli), Vibrio species (including V. cholerae), Campylobacter species (including C. jejuni), Salmonella species (including S. enterica and serovar S. Typhi), Enterobacter species (including E. aerogenes and E. cloacae), Shigella species (including S. dysenteriae, S. flexneri, and S. sonnei), Bifidobacterium species (including B. infantis), Lactobacillus species (including hydrogen peroxide producing strains of L. acidophilus, L. jensenii, and L. catenaforme), Bacillus species (including B. subtilus and B. licheniformis), Peptococcus species, Peptostreptococcus species, Streptococcus species (including S. pyogenes), Actinomyces species, Staphylococcus species (including S. aureus), Enterococcus species (including Enterococcus faecalis), and Listeria species (including L. monocytogenes).

[0046] In the present invention, the administered companion regimen to checkpoint inhibitors for cancer is a mixture of two or compounds produced by hydrogen peroxide, nitric oxide, and reactive oxygen species (ROS) producing bacterial cells displaying immunostimulatory PAMPS selected from those produced by specific strains of bacterial organisms selected from the group consisting of Fusobacterium species (including F. nucleatum and F. necrophorum), Helicobacter species (including Helicobacter pylon), Prevotella species, Bacteroides species (including B. thetaiotamicron and B. fragilis), Clostridium species (including C. difficile, C. perfringens, and C. botulinum), Porphymonas species, Escherichia species (including E. coli), Vibrio species (including V. cholerae), Campylobacter species (including C. jejuni), Salmonella species (including S. enterica and serovar S. Typhi), Enterobacter species (including E. aerogenes and E. cloacae), Shigella species (including S. dysenteriae, S. flexneri, and S. sonnei), Bifidobacterium species (including B. infantis), Lactobacillus species (including hydrogen peroxide producing strains of L. acidophilus, L. jensenii, and L. catenaforme), Bacillus species (including B. subtilus and B. licheniformis), Peptococcus species, Peptostreptococcus species, Streptococcus species (including S. pyogenes), Actinomyces species, Staphylococcus species (including S. aureus), Enterococcus species (including Enterococcus faecalis), and Listeria species (including L. monocytogenes).

[0047] In the present invention, the PAMPs are produced by therapeutically administered (enteral and parenteral formulations) lipopolysaccharides (LPS) derived from cellular components of bacteria selected from the group consisting of Fusobacterium species (including F. nucleatum and F. necrophorum), Helicobacter species (including Helicobacter Pylon), Prevotella species, Bacteroides species (including B. thetaiotamicron and B. fragilis), Clostridium species (including C. difficile, C. perfringens, and C. botulinum), Porphymonas species, Escherichia species (including E. coli), Vibrio species (including V. cholerae), Campylobacter species (including C. jejuni), Salmonella species (including S. enterica and serovar S. Typhi), Enterobacter species (including E. aerogenes and E. cloacae), Shigella species (including S. dysenteriae, S. flexneri, and S. sonnei), Bifidobacterium species (including B. infantis), Lactobacillus species (including hydrogen peroxide producing strains of L. acidophilus, L. jensenii, and L. catenaforme), Bacillus species (including B. subtilus and B. licheniformis), Peptococcus species, Peptostreptococcus species, Streptococcus species (including S. pyogenes), Actinomyces species, Staphylococcus species (including S. aureus), Enterococcus species (including Enterococcus faecalis), and Listeria species (including L. monocytogenes).

[0048] In the present invention, the administered companion regimen to checkpoint inhibitors for cancer is a mixture of lipopolysaccharides, and/or regions of lipopolysaccharides displaying immunostimulatory PAMPS derived from those produced by two or more specific strains of bacterial organisms selected from the group consisting of Fusobacterium species (including F. nucleatum and F. necrophorum), Helicobacter species (including Helicobacter pylon), Prevotella species, Bacteroides species (including B. thetaiotamicron and B. fragilis), Clostridium species (including C. difficile, C. perfringens, and C. botulinum), Porphymonas species, Escherichia species (including E. coli), Vibrio species (including V. cholerae), Campylobacter species (including C. jejuni), Salmonella species (including S. enterica and serovar S. Typhi), Enterobacter species (including E. aerogenes and E. cloacae), Shigella species (including S. dysenteriae, S. flexneri, and S. sonnei), Bifidobacterium species (including B. infantis), Lactobacillus species (including hydrogen peroxide producing strains of L. acidophilus, L. jensenii, and L. catenaforme), Bacillus species (including B. subtilus and B. licheniformis), Peptococcus species, Peptostreptococcus species, Streptococcus species (including S. pyogenes), Actinomyces species, Staphylococcus species (including S. aureus), Enterococcus species (including Enterococcus faecalis), and Listeria species (including L. monocytogenes).

[0049] In the present invention, the administered companion regimen to checkpoint inhibitors for cancer is a mixture of antibodies raised against two or more toxins, attenuated toxins, and regions of toxins displaying immunostimulatory PAMPS selected from those produced by specific strains of bacterial organisms selected from the group consisting of Fusobacterium species (including F. nucleatum and F. necrophorum), Helicobacter species (including Helicobacter pylon), Prevotella species, Bacteroides species (including B. thetaiotamicron and B. fragilis), Clostridium species (including C. difficile, C. perfringens, and C. botulinum), Porphymonas species, Escherichia species (including E. coli), Vibrio species (including V. cholerae), Campylobacter species (including C. jejuni), Salmonella species (including S. enterica and serovar S. Typhi), Enterobacter species (including E. aerogenes and E. cloacae), Shigella species (including S. dysenteriae, S. flexneri, and S. sonnei), Bifidobacterium species (including B. infantis), Lactobacillus species (including hydrogen peroxide producing strains of L. acidophilus, L. jensenfi, and L. catenaforme), Bacillus species (including B. subtilus and B. licheniformis), Peptococcus species, Peptostreptococcus species, Streptococcus species (including S. pyogenes), Actinomyces species, Staphylococcus species (including S. aureus), Enterococcus species (including Enterococcus faecalis), and Listeria species (including L. monocytogenes).

[0050] In the present invention, the administered companion regimen to checkpoint inhibitors for cancer is an immunological mixture is of antibodies raised against two or more lipopolysaccharides or regions of lipopolysaccharides displaying immunostimulatory PAMPS selected from those produced by specific strains of bacterial organisms selected from the group consisting of Fusobacterium species (including F. nucleatum and F. necrophorum), Helicobacter species (including Helicobacter pylon), Prevotella species, Bacteroides species (including B. thetaiotamicron and B. fragilis), Clostridium species (including C. difficile, C. perfringens, and C. botulinum), Porphymonas species, Escherichia species (including E. coli), Vibrio species (including V. cholerae), Campylobacter species (including C. jejuni), Salmonella species (including S. enterica and serovar S. Typhi), Enterobacter species (including E. aerogenes and E. cloacae), Shigella species (including S. dysenteriae, S. flexneri, and S. sonnei), Bifidobacterium species (including B. infantis), Lactobacillus species (including hydrogen peroxide producing strains of L. acidophilus, L. jensenii, and L. catenaforme), Bacillus species (including B. subtilus and B. licheniformis), Peptococcus species, Peptostreptococcus species, Streptococcus species (including S. pyogenes), Actinomyces species, Staphylococcus species (including S. aureus), Enterococcus species (including Enterococcus faecalis), and Listeria species (including L. monocytogenes).

Treatment of IBD/IBS

[0051] In the present invention, the administered therapeutic is a toxin or mixture of two or more toxins, attenuated toxins, capable of down-regulating the IBS or IBD immunostimulatory PAMPs, with the toxin or toxins being selected from those produced by specific strains of bacterial organisms selected from the group consisting of Fusobacterium species (including F. nucleatum and F. necrophorum), Helicobacter species (including Helicobacter pylon), Prevotella species, Bacteroides species (including B. thetaiotamicron and B. fragilis), Clostridium species (including C. difficile, C. perfringens, and C. botulinum), Porphymonas species, Escherichia species (including E. coli), Vibrio species (including V. cholerae), Campylobacter species (including C. jejuni), Salmonella species (including S. enterica and serovar S. Typhi), Enterobacter species (including E. aerogenes and E. cloacae), Shigella species (including S. dysenteriae, S. flexneri, and S. sonnei), Bifidobacterium species (including B. infantis), Lactobacillus species (including hydrogen peroxide producing strains of L. acidophilus, L. jensenii, and L. catenaforme), Bacillus species (including B. subtilus and B. licheniformis), Peptococcus species, Peptostreptococcus species, Streptococcus species (including S. pyogenes), Actinomyces species, Staphylococcus species (including S. aureus), Enterococcus species (including Enterococcus faecalis), and Listeria species (including L. monocytogenes).

Methods of Bioinformatics and Process of PAMP Expressing Product Development

[0052] The bioinformatics of the present invention employs a base of whole genome shotgun sequencing analysis of metagenomic data that uses iterative scanning of small motifs, including 12 amino-acid (36 bp) motifs, that are then compared for a comprehensive taxonomy against all 280,000 named organisms in public databases and are benchmarked against other pipelines (e.g., MetaPhlan, Phylosift, GOTTCHA and Kraken). These analyses enable the identification of the motifs in PAMPs through proteomic and transcriptomics by mapping genes encoding endotoxins and exotoxins to those molecules and the LPSs associated with different bacterial strains and can map near homologous TSMPs.

[0053] The present invention includes combinations of MIAs that are therapeutically beneficial in cancer and will be demonstrated as non-naturally occurring and involving inventive steps as contemplated in the intellectual property scheme described in Exhibit 1: Novel IP Regime: Patenting Microbial Ecologies.

[0054] Table 1 gives a summary of various bacterial organisms and in which clinical sites they are observed.

TABLE-US-00001 TABLE 1 Clinical sites of infection Soft Intra- Organism GI Oral Respiratory tissue Pelvic abdominal Gram-negative organisms Bacteroides fragilis +++ + +++ ++ +++ Bacteroides thetaiotamicron +++ ++ +++ Campylobacter jejuni +++ + ++ Clostridium botulinum +++ ++ Clostridium difficile +++ + Clostridium perfringens +++ + Enterobacter aerogenes +++ +++ Enterobacter cloacae +++ +++ Escherichia coli +++ ++ +++ Fusobacterium gonidiaformans + ++ Fusobacterium necrophorum + + +++ ++ + ++ Fusobacterium nucleatum + ++ +++ ++ + ++ Helicobacter pylori +++ + Parabacteroides distasonis ++ +++ Porphyromonas asaccharolytica ++ ++ ++ Porphyromonas gingivali + +++ + + + Porphyromonas uenonis + ++ Prevotella amnii +++ +++ Prevotella bivia +++ + +++ + Prevotella disiens +++ +++ Prevotella melaninogenica +++ + ++ ++ +++ Prevotella timonensis +++ + +++ Megasphaera 1&2 +++ Salmonella enterica +++ ++ +++ Salmonella Typhi +++ ++ +++ Shigella dysenteriae +++ +++ Shigella flexneri +++ +++ Shigella sonnei +++ +++ Vibrio cholerae +++ + ++ Gram-positive organisms Actinomyces israelii + + + + Actinomyces neuii ssp neuii + + + + + Actinomyces odontolyticus + ++ + ++ + + Actinomyces radingae + ++ + + + + Actinomyces turicensis + ++ + ++ ++ ++ Enterococcus faecalis +++ ++ ++ ++ Listeria monocytogenes +++ + +++ Peptostreptococcus anaerobius + ++ ++ Staphylococcus aureus + +++ +++ +++ Streptococcus pyogenes + ++ +++ ++ +, infrequent; ++, sometimes; +++, frequently

[0055] Features, integers, characteristics, compounds, chemical moieties or groups described in conjunction with a particular aspect, embodiment or example of the invention are to be understood to be applicable to any other aspect, embodiment or example described herein unless incompatible therewith. All of the features disclosed in this specification (including any accompanying claims, abstract and drawings), and/or all of the steps of any method or process so disclosed, may be combined in any combination, except combinations where at least some of such features and/or steps are mutually exclusive. The invention is not restricted to the details of any foregoing embodiments. The invention extends to any novel one, or any novel combination, of the features disclosed in this specification (including any accompanying claims, abstract and drawings, such as attached FIG. 1 Syntheses), or to any novel one, or any novel combination, of the steps of any method or process so disclosed.

[0056] The reader's attention is directed to all papers and documents which are filed concurrently with or previous to this specification in connection with this application and which are open to public inspection with this specification, and the contents of all such papers and documents are incorporated herein by reference.