Compositions and methods for treating inflammatory bowel disease

Abstract

Aspects of the present disclosure relate to compositions and methods for treating one or more inflammatory bowel diseases ("IBD"), such as ulcerative colitis ("UC") and / or Crohn's disease. Some embodiments relate to a pharmaceutical dosage form comprising a core comprising an inhibitor of a protease (e.g., a bacterial protease) and a controlled release coating applied to an outer surface of the core. In some cases, the protease inhibitor is a gligliptin or a pharmaceutically acceptable salt thereof. In some cases, the controlled release coating is configured to release the protease inhibitor in the large intestine (e.g., colon) and / or small intestine of a subject administered the pharmaceutical dosage form. Some embodiments relate to methods of treating one or more IBDs comprising delivering a therapeutically effective amount of an inhibitor of a protease (e.g., bacterial protease) to the large intestine (e.g., colon) and / or the small intestine of a subject.

Description

Related applications

[0001] This application claims the benefit of U.S. Provisional Application No. 63 / 510,884, entitled “COMPOSITIONS AND METHODS FOR TREATING ULCERATIVE COLITIS,” filed June 28, 2023, and U.S. Provisional Application No. 63 / 510,885, entitled “COMPOSITIONS AND METHODS FOR TREATING INFLAMMATORY BOWEL DISEASE,” filed June 28, 2023, the entire contents of each of which are incorporated herein by reference. Background Technology

[0002] Inflammatory bowel disease (“IBD”) is a disease characterized by chronic inflammation of the gastrointestinal tract (“GI”). One type of IBD is ulcerative colitis (“UC”), which causes ulcers on the lining of the large intestine (e.g., colon) and / or rectum. Another type of IBD is Crohn's disease, which can cause inflammation in any part of the gastrointestinal tract. IBD can cause symptoms such as diarrhea, abdominal pain, rectal bleeding, weight loss, anemia, and fatigue, and can be associated with a decline in quality of life. In some cases, IBD can lead to complications requiring hospitalization and / or surgery.

[0003] Millions of people worldwide are affected by IBD each year. In 2017, more than 6.8 million cases of IBD were found globally, with the highest prevalence in the United States. Therefore, there is a continued need to develop safe and effective treatments for IBD. Summary of the Invention

[0004] This disclosure relates to compositions and methods for treating inflammatory bowel diseases (e.g., ulcerative colitis, Crohn's disease). The subject matter of this invention relates in some cases to associated products, alternative solutions to specific problems, and / or a variety of different uses of one or more systems and / or articles.

[0005] In some embodiments, a composition comprising an inhibitor of a protease is provided. In some embodiments, the composition comprises an inhibitor of a bacterial protease (e.g., one or more inhibitors). In some embodiments, the composition comprises an inhibitor of a bacterial protease and an excipient. In some embodiments, a composition comprising two or more protease inhibitors (e.g., 2, 3, 4, 5, or 5-10 inhibitors) is provided. In some embodiments, a composition comprising two or more bacterial protease inhibitors (e.g., 2, 3, 4, 5, or 5-10 inhibitors) is provided.

[0006] In some aspects, a pharmaceutical dosage form is described. In some embodiments, the pharmaceutical dosage form comprises a core containing an inhibitor of a protease. In some embodiments, the protease inhibitor comprises a gliptin or a pharmaceutically acceptable salt thereof.

[0007] In some aspects, compositions comprising two or more gliptin drugs (e.g., 2, 3, 4, 5, or 5-10 drugs) are provided. In some aspects, pharmaceutical dosage forms comprising two or more gliptin drugs (e.g., 2, 3, 4, 5, or 5-10 drugs) are provided.

[0008] In some embodiments, the drug formulation includes a controlled-release coating applied to the outer surface of the core. In some embodiments, the controlled-release coating is configured to release an inhibitor of a protease in the large and / or small intestine of a subject who has been administered the drug formulation.

[0009] In some aspects, a method for treating inflammatory bowel disease is described. In some embodiments, the method includes delivering a therapeutically effective amount of a protease inhibitor to the large and / or small intestine of a subject. In some embodiments, the protease inhibitor comprises a gliptin or a pharmaceutically acceptable salt thereof.

[0010] In some aspects, a method for treating inflammatory bowel disease is described. In some embodiments, the method includes determining the abundance of bacterial proteases in a sample obtained from a subject. In some embodiments, the method includes delivering a therapeutically effective amount of an inhibitor of the bacterial protease to the large intestine and / or small intestine of the subject. In some embodiments, the protease inhibitor comprises a gliptin or a pharmaceutically acceptable salt thereof.

[0011] Other advantages and novel features of the invention will become apparent from the following detailed description of various non-limiting embodiments of the invention when considered in conjunction with the accompanying drawings. In the event of any conflicting and / or inconsistent disclosures in this specification and in documents incorporated by reference, this specification shall prevail. Attached Figure Description

[0012] Non-limiting embodiments of the present invention will be described by way of example with reference to the accompanying drawings, which are schematic and not intended to be drawn to scale. In the drawings, each identical or nearly identical component shown is represented by a single number. For clarity, not every component is labeled in every drawing, nor is every component of every embodiment of the invention shown, where illustration is not necessary to enable those skilled in the art to understand the invention. In the drawings: Figure 1 The effects of recombinant proteases on intestinal barrier integrity are shown according to some implementation schemes. Figure 1The graphs show the transepithelial resistance ("TEER") (Ω) over time (hours) for T84 intestinal cells without dipeptidyl peptidase-4 ("DPP-4") (labeled "cell control"), intestinal cells without DPP-4 but containing a protease inhibitor (labeled "cell control + protease inhibitor"), intestinal cells containing DPP-4 (labeled "DPP-4"), and intestinal cells containing both DPP-4 and a protease inhibitor (labeled "DPP-4 + protease inhibitor"). The protease inhibitor is a 1x Roche cOmplete™ EDTA-free protease inhibitor mixture.

[0013] Figure 2 This illustrates, according to some implementation schemes, the use of wild-type Bacteroides commonis containing DPP-4 (… B. Vulgatus) (Left) and (Right) Bacteroides with DPP-4 gene removal, chart showing the percentage of intestinal cell adhesion and invasion.

[0014] Figure 3 The graph shows the percentage inhibition of Bacteroides vulgaris DPP-4 by six gliptins: sitagliptin, linagliptin, ticagliptin, trogliptin, ocagliptin, and vildagliptin, according to some embodiments.

[0015] Figure 4 The chemical structures of sitagliptin, vildagliptin, octagliptin, and ticagliptin are shown according to some embodiments.

[0016] Figure 5 The inhibitory effects of vildagliptin and saxagliptin on different orthologs of DPP-4 (two forms encoded in the genome of Bacteroides vulgaris (BVU3876 and BVU1991), an ortholog from Bacteroides polymorpha (BT4193), and human DPP-4) are shown according to some embodiments.

[0017] Figure 6 The graph shows the disease activity index of sitagliptin administered orally or rectally according to some implementation schemes. Detailed Implementation

[0018] This disclosure relates to compositions and methods for treating one or more inflammatory bowel diseases (“IBD”), such as ulcerative colitis (“UC”) and / or Crohn’s disease. Some embodiments relate to a pharmaceutical dosage form comprising a core containing an inhibitor of a protease (e.g., a bacterial protease) and a controlled-release coating applied to the outer surface of the core. In some cases, the protease inhibitor is a gliptin or a pharmaceutically acceptable salt thereof. In some cases, the controlled-release coating is configured to release the protease inhibitor in the large intestine (e.g., colon) and / or small intestine (e.g., distal ileum) of a subject to which the pharmaceutical dosage form has been administered. Some embodiments relate to a method of treating one or more IBDs, the method comprising delivering a therapeutically effective amount of an inhibitor of a protease (e.g., a bacterial protease) to the large intestine (e.g., colon) and / or small intestine (e.g., distal ileum) of a subject.

[0019] The term "gliptins" generally refers to a class of compounds that inhibit human dipeptidyl peptidase-4 ("DPP-4" or "DPP-IV"), an enzyme that degrades a variety of substrates, including glucagon-like peptide-1 ("GLP-1") and glucagon-like peptide-2 ("GLP-2"). GLP-1 and GLP-2 are hormones secreted by intestinal endocrine cells and have multiple functions. For example, GLP-2 has various cell-protective, repair, and energy-conserving functions, including but not limited to increasing the barrier function of the intestinal epithelium, regulating gastric motility and gastric acid secretion, stimulating crypt cell proliferation, and inhibiting apoptosis in intestinal epithelial cells and crypt compartments. GLP-1 also performs multiple functions, including but not limited to promoting insulin secretion and inhibiting gastric emptying, gastric acid secretion, and gastric motility. Several gliptins, including sitagliptin, saxagliptin, linagliptin, and alogliptin, have been approved by the U.S. Food and Drug Administration ("FDA") for oral administration to treat type 2 diabetes.

[0020] Five major binding subsites have been identified within DPP-4: the broad S2 subsite, the S1 subsite, the S2 subsite, the S1' subsite, and the S2' subsite. These are targets for the development of gliptin drugs (Mathur et al.). Molecules, 2023, 28(5860). Each subsite plays a different role in the inhibitory activity of the binding molecule. Specifically, occupancy of the S1 and S2 subsites is necessary for inhibition, and further interaction with the S1', S2', and S2 extensive subsites increases potency. Therefore, in some embodiments, the glibenclamide of this disclosure interacts with or associates with the S1 and S2 subsites of DPP-4. In some embodiments, the glibenclamide of this disclosure interacts with or associates with the S1, S2, and S2 extensive subsites of DPP-4. In some embodiments, the glibenclamide of this disclosure interacts with or associates with the S1, S2, and S2' subsites of DPP-4. In some embodiments, the glibenclamide of this disclosure interacts with or associates with the S1, S2, and S1' subsites of DPP-4. In some embodiments, the glibenclamide of this disclosure interacts with or associates with the S1, S2, and S1' and S2' subsites of DPP-4. In some embodiments, the gliptin drugs of this disclosure interact or associate with the S1, S2 subsites, the broad S2 subsite, and the S1' and S2' subsites of DPP-4.

[0021] Examples of gliptin drugs include, but are not limited to, sitagliptin, ticagliptin, octagliptin, vildagliptin, saxagliptin, alogliptin, linagliptin, giglitazone, alagliptin, treagliptin, iverogliptin, gogliptin, dugliptin, repagliptin, and pulugliptin or their derivatives or combinations thereof.

[0022] Surprisingly, the inventors of this disclosure have discovered that administration of glibenclamide drugs containing one or more inhibitors of proteases (e.g., bacterial proteases, such as bacterial DPP-4) or pharmaceutically acceptable salts thereof can promote the treatment and / or prevention of IBD (e.g., UC, Crohn's disease). In some cases, the overproduction of certain proteases by certain microorganisms in the gut microbiome may be associated with increased IBD activity. For example, it has been found that 40% of patients with clinically active UC have excessive amounts of certain proteases expressed by certain bacteria in their gut microbiome. Despite receiving conventional drug treatment, a significant proportion of these patients exhibit persistent disease activity. As described herein, the inventors have recognized and understood that administration of one or more protease inhibitors (e.g., glibenclamide drugs or pharmaceutically acceptable salts thereof) to subjects diagnosed with IBD (e.g., UC, Crohn's disease) or at risk of developing IBD can advantageously prevent, reduce, or stop one or more symptoms of IBD in said subjects.

[0023] definition The terms “inhibition,” “inhibiting,” “inhibit,” or “inhibitor” refer to the ability of a compound to reduce, slow down, stop, or prevent the activity of a specific biological process in a cell (e.g., protease activity (e.g., bacterial DPP-4)) relative to a control. As used herein, in the context of an enzyme, such as a bacterial protease (e.g., DPP-4), the term “inhibit” or “inhibition” refers to a reduction in enzyme activity. In some embodiments, the term refers to a reduction in the level of enzyme activity, such as DPP-4 activity, to a level that is statistically significantly lower than an initial level, which may be, for example, a baseline level of enzyme activity. In some embodiments, the term refers to a level where the enzyme activity (e.g., DPP-4, bacterial DPP-4) is reduced to less than 75%, less than 50%, less than 40%, less than 30%, less than 25%, less than 20%, less than 10%, less than 9%, less than 8%, less than 7%, less than 6%, less than 5%, less than 4%, less than 3%, less than 2%, less than 1%, less than 0.5%, less than 0.1%, less than 0.01%, less than 0.001%, or less than 0.0001% of its initial level, which may be, for example, the baseline level of enzyme activity. In some embodiments, the inhibitor is a grisalis-like drug.

[0024] The term "small molecule" refers to a molecule with a relatively low molecular weight, whether naturally occurring or artificially produced (e.g., through chemical synthesis). Typically, a small molecule is an organic compound (e.g., it contains carbon). Small molecules may contain multiple carbon-carbon bonds, stereocenters, and other functional groups (e.g., amines, hydroxyl groups, carbonyl groups, and heterocycles). In some embodiments, the molecular weight of the small molecule is not more than about 1,000 g / mol, not more than about 900 g / mol, not more than about 800 g / mol, not more than about 700 g / mol, not more than about 600 g / mol, not more than about 500 g / mol, not more than about 400 g / mol, not more than about 300 g / mol, not more than about 200 g / mol, or not more than about 100 g / mol. In some embodiments, the molecular weight of the small molecule is at least about 100 g / mol, at least about 200 g / mol, at least about 300 g / mol, at least about 400 g / mol, at least about 500 g / mol, at least about 600 g / mol, at least about 700 g / mol, at least about 800 g / mol, or at least about 900 g / mol or at least about 1,000 g / mol. Combinations of the above ranges (e.g., at least about 200 g / mol and not exceeding about 500 g / mol) are also possible. In some embodiments, the small molecule is a therapeutically active agent, such as a drug (e.g., a molecule approved by the U.S. Food and Drug Administration as provided in the U.S. Federal Regulations (CFR)). The small molecule may also be complexed with one or more metal atoms and / or metal ions. Preferred small molecules are biologically active because they produce biological effects (e.g., inhibition of proteases) in microorganisms of the gut microbiome (e.g., bacteria), preferably bacteria of the genus Bacteroides, more preferably bacteria of the genus Bacteroides, and / or in animals (preferably mammals, more preferably humans). Small molecules include, but are not limited to, radionuclides, imaging agents, and pharmaceutical active ingredients or agents (e.g., bacterial protease inhibitors, gliptins). In some embodiments, the small molecule is a drug. Preferably, but not necessarily, the drug is one that has been deemed safe and effective for human or animal use by an appropriate government or regulatory agency. For example, the FDA according to 21 CFR... Sections 330.5, 331 to 361, and 440 to 460 (incorporated hereby by reference) list drugs approved for human use; FDA regulations are based on 21 CFR. Drugs listed in 500 to 589 (incorporated herein by reference) are for veterinary use. All listed drugs are considered acceptable for use in accordance with this disclosure.

[0025] The definitions of specific functional groups and chemical terms are described in more detail below. Chemical elements are identified according to the periodic table, CAS version, Handbook of Chemistry and Physics, 75th edition, inside cover, and specific functional groups are generally defined as described therein. Furthermore, the general principles of organic chemistry, as well as specific functional groups and reactivity, are described in Thomas Sorrell's... Organic Chemistry , University Science Books, Sausalito, 1999; Michael B. Smith, March's Advanced Organic Chemistry , 7th edition, John Wiley &Sons, Inc., New York, 2013; Richard C. Larock, Comprehensive Organic Transformations , John Wiley & Sons, Inc., New York, 2018; and Carruthers, Some Modern Methods of Organic Synthesis, 3rd ed. Cambridge University Press, Cambridge, 1987.

[0026] The compounds described herein may contain one or more asymmetric centers and therefore may exist in a variety of stereoisomeric forms, such as enantiomers and / or diastereomers. For example, the compounds described herein may be in the form of individual enantiomers, diastereomers, or geometric isomers, or may be in the form of mixtures of stereoisomers, including racemic mixtures and mixtures rich in one or more stereoisomers. Isomers can be isolated from mixtures by methods known to those skilled in the art, including chiral high-performance liquid chromatography (HPLC) and the formation and crystallization of chiral salts; or preferred isomers can be prepared by asymmetric synthesis. See, for example, Jacques et al. Enantiomers, Racemates and Resolutions (Wiley Interscience, New York, 1981); Wilen et al., Tetrahedron 33:2725 (1977); Eliel, EL Stereochemistry of Carbon Compounds (McGraw-Hill, NY,1962); and Wilen, SH Tables of Resolving Agents and Optical ResolutionsPage 268 (E.L. Eliel, Univ. of Notre Dame Press, Notre Dame, IN 1972). This disclosure also covers compounds as single isomers substantially free of other isomers, and compounds as mixtures of various isomers, alternatively.

[0027] In the formula, the key It's a single key, indicated by a dashed line. It is a single key or does not exist, and the key or It is either a single bond or a double bond.

[0028] When a range of values ​​(“range”) is listed, each value within the range and its subranges are included. Unless otherwise provided, a range includes the values ​​at both ends of the range. For example, “C” 1-6 "Alkyl" encompasses C1, C2, C3, C4, C5, C6, C 1-6 C 1-5 C 1-4 C 1-3 C 1-2 C 2-6 C 2-5 C 2-4 C 2-3 C 3-6 C 3-5 C 3-4 C 4-6 C 4-5 and C 5-6 alkyl.

[0029] The term "aliphatic group" refers to alkyl, alkenyl, ynyl, and carbocyclic groups. Similarly, the term "heteroaliphatic group" refers to heteroalkyl, heteroalkenyl, heteroynyl, and heterocyclic groups.

[0030] The term "alkyl" refers to a group consisting of a straight-chain or branched saturated hydrocarbon group having 1 to 20 carbon atoms ("C"). 1-20 Alkyl group”. Unless otherwise stated, each instance of an alkyl group is independently unsubstituted (“unsubstituted alkyl”) or substituted with one or more substituents (e.g., halogens, such as F) (“substituted alkyl”).

[0031] The term "haloalkyl" is a substituted alkyl group in which one or more hydrogen atoms are independently replaced by a halogen (e.g., fluorine, bromine, chlorine, or iodine). "Hyperhaloalkyl" is a subset of haloalkyl groups and refers to an alkyl group in which all hydrogen atoms are independently replaced by a halogen (e.g., fluorine, bromine, chlorine, or iodine). In some embodiments, the haloalkyl moiety has 1 to 20 carbon atoms ("C"). 1-20(Haloalkyl). In some embodiments, all hydrogen atoms of the haloalkyl group are independently replaced by fluorine to provide a "perfluoroalkyl". In some embodiments, all hydrogen atoms of the haloalkyl group are independently replaced by chlorine to provide a "perchloroalkyl".

[0032] The term "heteroalkyl" refers to an alkyl group that further comprises at least one heteroatom selected from oxygen, nitrogen, or sulfur (e.g., 1, 2, 3, or 4 heteroatoms), said heteroatom being located within the parent chain (e.g., inserted between adjacent carbon atoms in the parent chain) and / or at one or more end positions of the parent chain. In some embodiments, heteroalkyl refers to a saturated group ("heteroalkyl group") having 1 to 20 carbon atoms and 1 or more heteroatoms within the parent chain. 1-20 alkyl").

[0033] The term "alkenyl" refers to a group of straight-chain or branched hydrocarbons having 1 to 20 carbon atoms and one or more carbon-carbon double bonds (e.g., 1, 2, 3 or 4 double bonds).

[0034] The term "heteroalkenyl" refers to an alkenyl group that also includes at least one heteroatom selected from oxygen, nitrogen, or sulfur (e.g., 1, 2, 3, or 4 heteroatoms), said heteroatom being located within the parent chain (e.g., inserted between adjacent carbon atoms in the parent chain) and / or at one or more end positions of the parent chain. In some embodiments, heteroalkenyl refers to a group having 1 to 20 carbon atoms, at least one double bond, and one or more heteroatoms within the parent chain ("heteroalkenyl group"). 1-20 (alkenyl").

[0035] The term "carbocyclic" or "carbocyclic" refers to a non-aromatic ring system having 3 to 14 ring carbon atoms ("C"). 3-14A heterocyclic group consisting of a carbonyl group and a non-aromatic cyclic hydrocarbon group with zero heteroatoms. The term "heterocyclic group" or "heterocyclic" refers to a group having a 3- to 14-membered non-aromatic ring system having a ring carbon atom and 1 to 4 ring heteroatoms, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur ("3- to 14-membered heterocyclic group"). In heterocyclic groups containing one or more nitrogen atoms, the bonding point can be a carbon or nitrogen atom, where the valence allows. Heterocyclic groups can be monocyclic ("monocyclic heterocyclic group") or polycyclic (e.g., fused, bridged, or spirocyclic systems, such as bicyclic systems ("bicyclic heterocyclic group") or tricyclic systems ("tricyclic heterocyclic group")), and can be saturated or may contain one or more... Carbon-carbon double or triple bonds. A heterocyclic polycyclic system may include one or more heteroatoms in one or two rings. "Hypercyclic group" also includes ring systems in which the heterocyclic ring as defined above is fused with one or more carbocyclic groups, with the connection point on the carbocyclic or heterocyclic ring; or includes ring systems in which the heterocyclic ring as defined above is fused with one or more aryl or heteroaryl groups, with the connection point on the heterocyclic ring, and in such cases, the number of ring members continues to represent the number of ring members in the heterocyclic ring system. Unless otherwise indicated, each instance of a heterocyclic group is independently unsubstituted ("unsubstituted heterocyclic group") or substituted with one or more substituents ("substituted heterocyclic group").

[0036] In some embodiments, the heterocyclic group is a 5-10 membered nonaromatic ring system having a cyclic carbon atom and 1-4 cyclic heteroatoms, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur (“5-10 membered heterocyclic group”). In some embodiments, the heterocyclic group is a 5-6 membered nonaromatic ring system having a cyclic carbon atom and 1-4 cyclic heteroatoms, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur (“5-6 membered heterocyclic group”).

[0037] The term "aryl" refers to a monocyclic or polycyclic (e.g., bicyclic or tricyclic) 4n+2 aromatic ring system (e.g., having 6, 10, or 14 shared π electrons in a ring array) that provides 6-14 ring carbon atoms and zero heteroatoms ("C") in the aromatic ring system. 6-14 Aryl group (“C6 aryl”; for example, phenyl). In some embodiments, the aryl group has six ring carbon atoms (“C6 aryl”; for example, phenyl).

[0038] "Aryl" is a subset of "alkyl" and refers to an alkyl group that has been substituted with an aryl group, wherein the connecting point is on the alkyl part.

[0039] The term "heteroaryl" refers to a 5-14 membered monocyclic or polycyclic (e.g., bicyclic, tricyclic) 4n+2 aromatic ring system (e.g., having 6, 10, or 14 shared π electrons in a ring array), wherein the aromatic ring system provides a cyclic carbon atom and 1-4 cyclic heteroatoms, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur ("5-14 membered heteroaryl"). In heteroaryls containing one or more nitrogen atoms, the linkage can be a carbon or nitrogen atom, where the valence allows. Heteroaryl polycyclic ring systems may contain one or more heteroatoms in one or two rings. In some embodiments, the heteroaryl is a 5-10 membered aromatic ring system, wherein the aromatic ring system provides a cyclic carbon atom and 1-4 cyclic heteroatoms, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur ("5-10 membered heteroaryl"). In some embodiments, the heteroaryl group is a 5-6 membered aromatic ring system provided with a cyclic carbon atom and 1-4 cyclic heteroatoms, wherein each heteroatom is independently selected from nitrogen, oxygen and sulfur (“5-6 membered heteroaryl”).

[0040] The term “halogen” or “halogen” refers to fluorine (fluorinated, -F), chlorine (chlorinated, -Cl), bromine (brominated, -Br), or iodine (iodinated, -I).

[0041] The term "hydroxyl" or "hydroxyl group" refers to the -OH group. The term "amino group" refers to the -NH2 group. The term "substituted amino group" can be extended to refer to a monosubstituted amino group, a disubstituted amino group, or a trisubstituted amino group. In some embodiments, "substituted amino group" is a monosubstituted amino group or a disubstituted amino group.

[0042] As used herein, the term "salt" means any and all salts and encompasses pharmaceutically acceptable salts. Salts include ionic compounds produced by the neutralization reaction of acids and bases. A salt is composed of one or more cations (positively charged ions) and one or more anions (negative ions), such that the salt is electrically neutral (has no net charge). Salts of the compounds disclosed herein include those derived from inorganic and organic acids and bases. Examples of acid addition salts are salts formed by amino groups with inorganic acids (such as hydrochloric acid, hydrobromic acid, phosphoric acid, sulfuric acid, and perchloric acid) or with organic acids (such as acetic acid, oxalic acid, maleic acid, tartaric acid, citric acid, succinic acid, or malonic acid), or salts formed by other methods known in the art (such as ion exchange). Other salts include adipate, alginate, ascorbate, aspartate, benzenesulfonate, benzoate, hydrogen sulfate, borate, butyrate, camphorate, camphorsulfonate, citrate, cyclopentanepropionate, disglucuronate, dodecyl sulfate, ethanesulfonate, formate, fumarate, glucohepanoate, glyceryl phosphate, glucuronate, hemisulfate, heptaate, hexanoate, hydroiodate, 2-hydroxy-ethanesulfonate, lacturonate, lactate, laurate, lauryl sulfate, malate, maleate, malonate, methanesulfonate, 2-naphthalenesulfonate, nicotinate, nitrate, oleate, oxalate, palmitate, dihydroxynaphthalate, pectate, persulfate, 3-phenylpropionate, phosphate, picrate, neopentanoate, propionate, stearate, succinate, sulfate, tartrate, thiocyanate, p-toluenesulfonate, undecanoate, valerate, hippurate, etc. Salts derived from suitable bases include alkali metal salts, alkaline earth metal salts, ammonium salts, and N salts. + (C 1-4 Alkyl)4 salts. Representative alkali metal or alkaline earth metal salts include sodium, lithium, potassium, calcium, magnesium, etc. Other salts include ammonium, quaternary ammonium, and amine cations formed using counterions such as halide, hydroxide, carboxyl, sulfate, phosphate, nitrate, lower alkyl sulfonate, and aryl sulfonate ions.

[0043] The term "pharmaceutically acceptable salt" refers to those salts that, to the extent of reasonable medical judgment, are suitable for use in contact with the tissues of humans and lower animals without undue toxicity, irritation, anaphylactic reactions, etc., and in proportion to a reasonable benefit / risk ratio. Pharmaceutically acceptable salts are well known in the art. For example, Berge et al. described pharmaceutically acceptable salts in detail in J. Pharmaceutical Sciences, 1977, 66, 1-19, which is incorporated herein by reference.

[0044] Pharmaceutically acceptable salts of the compounds disclosed herein include those derived from suitable inorganic and organic acids and bases. Examples of pharmaceutically acceptable non-toxic acid addition salts are salts formed by amino groups with inorganic acids (such as hydrochloric acid, hydrobromic acid, phosphoric acid, sulfuric acid, and perchloric acid) or with organic acids (such as acetic acid, oxalic acid, maleic acid, tartaric acid, citric acid, succinic acid, or malonic acid), or salts formed by other methods known in the art (such as ion exchange). Other pharmaceutically acceptable salts include adipate, alginate, ascorbate, aspartate, benzenesulfonate, benzoate, hydrogen sulfate, borate, butyrate, camphorate, camphorsulfonate, citrate, cyclopentanepropionate, disaccharide, dodecyl sulfate, ethanesulfonate, formate, fumarate, glucono-heptahydrate, glyceryl phosphate, gluconate, hemisulfate, heptahydrate, hexanoate, hydroiodate, 2-hydroxy-ethanesulfonate, lacturonate, lactate, laurate, lauryl sulfate, malate, maleate, malonate, methanesulfonate, 2-naphthalenesulfonate, nicotinate, nitrate, oleate, oxalate, palmitate, dihydroxynaphthalate, pectate, persulfate, 3-phenylpropionate, phosphate, picrate, neopentanoate, propionate, stearate, succinate, sulfate, tartrate, thiocyanate, p-toluenesulfonate, undecanoate, valerate, etc. Salts derived from suitable bases include alkali metal salts, alkaline earth metal salts, ammonium salts, and N salts. + (C 1-4 Alkyl)4 salts. Representative alkali metal or alkaline earth metal salts include sodium, lithium, potassium, calcium, magnesium, etc. Other pharmaceutically acceptable salts include, where appropriate, non-toxic ammonium, quaternary ammonium, and amine cations formed using counterions such as halide, hydroxide, carboxyl, sulfate, phosphate, nitrate, lower alkyl sulfonate, and aryl sulfonate ions.

[0045] The term "solvent" refers to a compound or its salt that typically associates with a solvent via a solvent decomposition reaction. This physical association can include hydrogen bonding. Common solvents include water, methanol, ethanol, acetic acid, DMSO, THF, diethyl ether, etc. The compounds described herein can be prepared, for example, in crystalline form and can be solvated. Suitable solvates include pharmaceutically acceptable solvates, as well as stoichiometric and non-stoichiometric solvates. In some cases, solvates will be separable, for example when one or more solvent molecules are incorporated into the lattice of a crystalline solid. "Solvent" includes both solution phases and separable solvates. Representative solvates include hydrates, ethanolides, and methanolides.

[0046] The term "hydrate" refers to a compound that associates with water. Typically, the number of water molecules in a hydrate of a compound is in a definite ratio to the number of compound molecules in the hydrate. Therefore, a hydrate of a compound can be represented, for example, by the general formula R•xH₂O, where R is the compound and x is a number greater than 0. A given compound can form more than one type of hydrate, including, for example, monohydrates (x is 1), lower hydrates (x is a number greater than 0 and less than 1, such as hemihydrates (R•0.5H₂O)), and polyhydrates (x is a number greater than 1, such as dihydrates (R•2H₂O) and hexahydrates (R•6H₂O)).

[0047] The term "tautomer" or "tautomerizing" refers to two or more interconvertible compounds resulting from at least one formal migration of hydrogen atoms and at least one change in valence (e.g., single to double, triple to single, or vice versa). The exact proportions of tautomers depend on several factors, including temperature, solvent, and pH. Tautomerization (i.e., the reaction that provides tautomer pairs) can be catalyzed by acids or bases. Exemplary tautomerizations include ketone to enol, amide to imide, lactam to lactimide, enamine to imide, and enamine to (different enamines) tautomerization.

[0048] It should also be understood that compounds with the same molecular formula but different atomic bonding properties or sequences, or different spatial arrangements of their atoms, are called "isomers". Isomers with different spatial arrangements of their atoms are called "stereoisomers".

[0049] Stereoisomers that are not mirror images of each other are called "diastereomers," while stereoisomers that are non-overlapping mirror images of each other are called "enantiomers." When a compound has an asymmetry center, for example, if it is bonded to four different groups, it may have a pair of enantiomers. Enantiomers can be characterized by the absolute configuration of their asymmetry center and described by the R-sequence and S-sequence rules of Cahn and Prelog, or by the way the molecule rotates around the plane of polarization and is specified as dextrorotatory or levorotatory (i.e., (+) isomers or (-) isomers, respectively). Chiral compounds can exist as individual enantiomers or mixtures thereof. A mixture containing equal proportions of enantiomers is called a "racemic mixture."

[0050] The term "crystallization" or "crystalline form" refers to a solid form that exhibits essentially three-dimensional order. In some embodiments, the crystalline form of a solid is a solid form that is not substantially amorphous. In some embodiments, the X-ray powder diffraction (XRPD) pattern of the crystalline form includes one or more well-defined peaks.

[0051] The term "amorphous" or "amorphous form" refers to a solid form ("solid form") that substantially lacks three-dimensional order. In some embodiments, the amorphous form of a solid is a substantially non-crystalline solid form. In some embodiments, Cu is used. Kα The amorphous X-ray powder diffraction (XRPD) pattern includes a broad scattering band with peaks at 2θ, for example, from 20° to 70° (inclusive). In some embodiments, the amorphous XRPD pattern also includes one or more peaks attributed to the crystal structure. In some embodiments, the maximum intensity of any one of the one or more peaks attributed to the crystal structure observed at 2θ from 20° to 70° (inclusive) is no more than 300 times, no more than 100 times, no more than 30 times, no more than 10 times, or no more than 3 times the maximum intensity of the broad scattering band. In some embodiments, the amorphous XRPD pattern does not include peaks attributed to the crystal structure.

[0052] The term "cocrystal" refers to a crystal structure comprising at least two different components (e.g., the compounds and acids disclosed herein), each of which is independently an atom, ion, or molecule. In some embodiments, none of the components are solvents. In some embodiments, at least one component is a solvent. Cocrystals of the compounds and acids disclosed herein differ from salts formed from the compounds and acids disclosed herein. In salts, the compounds disclosed herein are complexed with the acids in a manner that facilitates proton transfer (e.g., complete proton transfer) from the acid to the compound disclosed herein at room temperature. However, in cocrystals, the compounds disclosed herein are complexed with the acids in a manner that facilitates proton transfer from the acid to the compound disclosed herein at room temperature. In some embodiments, there is no proton transfer from the acid to the compound disclosed herein in the cocrystal. In some embodiments, there is partial proton transfer from the acid to the compound disclosed herein in the cocrystal. Cocrystals can be used to improve the properties of the compounds disclosed herein (e.g., solubility, stability, and ease of formulation).

[0053] The term "polymorph" refers to the crystalline form of a compound (or its salts, hydrates, or solvates). All polymorphs have the same elemental composition. Different crystalline forms typically exhibit different X-ray diffraction patterns, infrared spectra, melting points, densities, hardness, crystal shapes, optical and electrical properties, stability, and solubility. Recrystallization solvents, crystallization rates, storage temperatures, and other factors can cause one crystalline form to dominate. Various polymorphs of a compound can be prepared by crystallization under different conditions.

[0054] The term "prodrug" refers to a compound having a cleavable group and being converted into the compound described herein by solvent decomposition or under physiological conditions, which is pharmaceutically active in vivo. Examples of such compounds include, but are not limited to, choline ester derivatives, N-alkylmorpholine esters, etc. Other derivatives of the compounds described herein are active in both their acidic and acid-derived forms, but generally offer advantages such as solubility, tissue compatibility, or delayed release in mammalian organisms in their acid-sensitive forms (see Bundgard, H., Design of Prodrugs, pp. 7-9, 21-24, Elsevier, Amsterdam 1985). Prodrugs include acid derivatives well known to those skilled in the art, such as esters prepared by reacting a parent acid with a suitable alcohol, or amides, or anhydrides, or mixed anhydrides, prepared by reacting a parent acid compound with a substituted or unsubstituted amine. Simple aliphatic or aromatic esters, amides, and anhydrides derived from acidic groups side-attached to the compounds described herein are specific prodrugs.

[0055] The terms “composition” and “formulation” are used interchangeably.

[0056] Therefore, compositions comprising inhibitors of proteases are provided. In some embodiments, the composition comprises an inhibitor of a bacterial protease. In some embodiments, the composition comprises an inhibitor of a bacterial protease and an excipient. In some embodiments, the composition comprises two or more protease inhibitors (e.g., 2, 3, 4, 5, or 5-10). In some embodiments, the composition comprises two or more bacterial protease inhibitors (e.g., 2, 3, 4, 5, or 5-10). In some embodiments, the excipient comprises an agent that promotes targeted delivery of the protease inhibitor to the intestinal site. In some embodiments, the composition comprises an inhibitor of a bacterial protease and an agent that promotes targeted delivery of the protease inhibitor to the small intestine. In some embodiments, the composition comprises an inhibitor of a bacterial protease and an agent that promotes targeted delivery of the protease inhibitor to the cecum and / or colon.

[0057] In some embodiments, compositions comprising gliptin drugs or pharmaceutically acceptable salts thereof are provided. In some embodiments, compositions comprising two or more gliptin drugs (e.g., 2, 3, 4, 5, or 5-10). In some embodiments, pharmaceutical dosage forms comprising gliptin drugs or pharmaceutically acceptable salts thereof are provided. In some embodiments, pharmaceutical dosage forms comprising two or more gliptin drugs (e.g., 2, 3, 4, 5, or 5-10).

[0058] In some embodiments, the gliptin is selected from sitagliptin, ticagliptin, octagliptin, vildagliptin, saxagliptin, alogliptin, linagliptin, giglitazone, alagliptin, tregliptin, evogliptin, gogliptin, dugliptin, repagliptin, and pulugliptin, or derivatives thereof. In some embodiments, the gliptin is sitagliptin. In some embodiments, the gliptin is vildagliptin. In some embodiments, the gliptin is octagliptin. In some embodiments, the gliptin is ticagliptin.

[0059] In some implementations, gliptin drugs may have formula (I): (I), Or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, cocrystal, tautomer, stereoisomer, isotopically labeled compound or prodrug, wherein: X is NR1 or CR1; Dashed lines indicate either non-existent elements or double bonds; Y does not exist or is -CH2-; R is an optionally substituted alkyl, optionally substituted heteroalkyl, optionally substituted alkenyl, optionally substituted heteroalkenyl, halogen, optionally substituted acyl or carbonyl; n is 0-5, R1 is an alkyl group, an optionally substituted alkyl group, an optionally substituted heteroalkyl group, an optionally substituted alkenyl group or an optionally substituted heteroalkenyl group, an aryl group, an optionally substituted aryl group, an optionally substituted cycloalkyl group, an optionally amine-substituted alkyl group, an optionally hydroxy-substituted alkyl group, an optionally halogen-substituted alkyl group, an optionally amine-substituted aryl group, an optionally hydroxy-substituted aryl group, an optionally halogen-substituted aryl group, an optionally amine-substituted cycloalkyl group, an optionally hydroxy-substituted cycloalkyl group, an optionally halogen-substituted cycloalkyl group.

[0060] In some embodiments, the gliptin includes a central stent comprising a pyrimidine group substituted with two carbonyl groups. In some embodiments, the gliptin includes a central stent of formula (II): (II), or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, cocrystal, tautomer, stereoisomer, isotopically labeled compound, or prodrug thereof, wherein: n is 2 or 3; p is 1 or 2; Each instance of R2 is independently hydrogen, an optionally substituted alkyl group, or an optionally substituted heteroalkyl group; Each instance of R3 is an optionally substituted alkyl or optionally substituted alkenyl group, wherein optionally two instances of R3 form an optionally substituted heterocyclic group with the nitrogen atom to which they are attached; and Each instance of R4 is an optionally substituted alkyl group.

[0061] The inventors further recognize and understand that, in the case of oral administration of protease inhibitors (e.g., bacterial protease inhibitors), it may be necessary for the oral dosage form to include a controlled-release coating to facilitate targeted delivery of the protease inhibitor to a specific location within the gastrointestinal tract (e.g., the colon and / or small intestine). In some cases, targeted delivery of the protease inhibitor to a specific location within the gastrointestinal tract can enhance therapeutic efficacy, reduce systemic drug exposure and associated toxicity, and / or improve drug bioavailability.

[0062] I. Compositions and Dosage Forms In some embodiments, compositions are provided comprising one or more protease inhibitors (e.g., 2, 3, 4, 5, or 5-10 of the gliptins or compounds described herein) or pharmaceutically acceptable salts, solvates, hydrates, polymorphs, cocrystals, tautomers, stereoisomers, isotopically labeled compounds, or prodrugs thereof. In some embodiments, pharmaceutical compositions are provided comprising one or more protease inhibitors (e.g., 2, 3, 4, 5, or 5-10 of the gliptins or compounds described herein) or pharmaceutically acceptable salts, solvates, hydrates, polymorphs, cocrystals, tautomers, stereoisomers, isotopically labeled compounds, or prodrugs thereof, and a pharmaceutically acceptable carrier. In some embodiments, the pharmaceutical compositions described herein further comprise additional pharmaceutical agents. The pharmaceutical compositions described herein can be prepared by any method known in the pharmaceutical art.

[0063] This disclosure provides pharmaceutical compositions comprising a protease inhibitor (e.g., one or more protease inhibitors described herein) or a pharmaceutically acceptable salt thereof, and optionally a pharmaceutically acceptable excipient. In some embodiments, the pharmaceutical compositions described herein comprise a protease inhibitor (e.g., one or more protease inhibitors described herein) or a pharmaceutically acceptable salt thereof, and a pharmaceutically acceptable excipient.

[0064] The inventors have recognized and understand that, in the case of oral administration of protease inhibitors (e.g., human or bacterial protease inhibitors), it may be necessary for the oral dosage form to include a controlled-release coating to facilitate targeted delivery of the protease inhibitor to a specific location (e.g., colon, small intestine) within the subject's gut. In some cases, targeted delivery of the protease inhibitor to a specific location within the gut can enhance therapeutic efficacy, reduce systemic drug exposure and associated toxicity, and / or improve drug bioavailability. In some embodiments, the pharmaceutical compositions described herein comprise a core containing an effective amount of a protease inhibitor (e.g., the active ingredient) and a controlled-release coating applied to the outer surface of the core, wherein the controlled-release coating is configured to release the protease inhibitor in the gut of a subject to which the pharmaceutical dosage form has been administered.

[0065] Pharmaceutical compositions may be prepared, packaged, and / or sold as a single unit dose and / or as multiple single unit doses in batches. A “unit dose” is a discrete amount of a pharmaceutical composition containing a predetermined amount of an active ingredient (e.g., a protease inhibitor). The amount of active ingredient is generally equal to the dose of active ingredient to be administered to a subject and / or a suitable portion of that dose, such as half or one-third of that dose.

[0066] In some embodiments, the composition comprises a protease inhibitor (e.g., one or more protease inhibitors described herein) or a pharmaceutically acceptable salt thereof, and a targeted delivery promoter. In some embodiments, the targeted delivery promoter comprises one or more materials soluble under certain conditions. In some embodiments, the targeted delivery promoter comprises one or more materials soluble under certain pH conditions. In some embodiments, the targeted delivery promoter comprises one or more materials readily degraded by microorganisms.

[0067] In some embodiments, the targeted delivery promoter comprises one or more materials that dissolve under certain pH conditions and / or one or more materials that are readily degraded by microorganisms.

[0068] According to some embodiments, a pharmaceutical dosage form is provided comprising a core containing an inhibitor of a protease (e.g., one or more protease inhibitors). In some embodiments, the core comprises an effective amount of the protease inhibitor (e.g., one or more protease inhibitors) or a pharmaceutically acceptable salt thereof. In some embodiments, the effective amount is a therapeutically effective amount. In some embodiments, the effective amount is a preventatively effective amount. In some embodiments, the therapeutically effective amount of the protease inhibitor is an amount sufficient to alleviate one or more symptoms of inflammatory bowel disease in a subject (e.g., delay or reduce the onset, progression, and / or severity of said one or more symptoms). In some embodiments, the therapeutically effective amount of the protease inhibitor is an amount sufficient to reduce the risk of the subject developing inflammatory bowel disease. In some embodiments, the therapeutically effective amount of the protease inhibitor is an amount sufficient to modulate protease activity in the large intestine (e.g., colon) and / or small intestine (e.g., distal ileum) of a subject. In some embodiments, the therapeutically effective amount of the protease inhibitor is an amount sufficient to modulate (e.g., reduce) protease activity in the large intestine (e.g., colon) and / or small intestine (e.g., distal ileum) of a subject. In some implementations, the therapeutically effective amount of the protease inhibitor is an amount sufficient to modulate (e.g., reduce) the activity of bacterial proteases in the subject's large intestine (e.g., colon) and / or small intestine (e.g., distal ileum).

[0069] In some implementations, the therapeutically effective amount of the protease inhibitor is an amount sufficient to provide the desired side effects in the subject.

[0070] A protease is generally defined as an enzyme that catalyzes the hydrolysis of proteins (e.g., cleaving one or more peptide bonds to break down a protein into smaller polypeptides or individual amino acids). In some embodiments, the protease is a bacterial protease. In some embodiments, the protease is a protease expressed by microorganisms in the gut microbiome. In some embodiments, the protease is a protease expressed by microorganisms in the gut microbiome present in humans. In some embodiments, the protease is a protease expressed by microorganisms in the gut microbiome present in a person with at least one symptom of IBD. In some embodiments, the protease is a protease expressed by microorganisms in the gut microbiome present in a person who does not have diabetes. In some embodiments, the protease is a protease expressed by microorganisms in the gut microbiome present in a person who does not have an inflammatory disease or condition other than IBD. In some embodiments, the protease is a serine protease, a cysteine ​​protease, or a metalloproteinase. In some embodiments, the protease is a serine protease. In some cases, the serine protease is a type S09 protease under the MEROPS classification system (e.g., an S09.13 protease). In some embodiments, the protease is configured to cleave GLP-1 and / or GLP-2. In some embodiments, the protease is configured to preferentially cleave GLP-2 (e.g., the protease has a higher binding affinity for GLP-2 than for GLP-1). In some cases, the protease is dipeptidyl peptidase-4 (“DPP-4”). In some embodiments, the protease is bacterial DPP-4. In some embodiments, the protease is DPP-4 expressed by microorganisms in the gut microbiome. In some embodiments, the protease is DPP-4 expressed by microorganisms present in the gut microbiome of humans. In some embodiments, the protease is DPP-4 expressed by microorganisms present in the gut microbiome of people with at least one symptom of IBD. In some embodiments, the protease is DPP-4 expressed by microorganisms present in the gut microbiome of people who do not have diabetes. In some embodiments, the protease is DPP-4 expressed by microorganisms present in the gut microbiome of people who do not have an inflammatory disease or condition other than IBD.

[0071] In some embodiments, the protease is expressed by microorganisms in the gut microbiome. In some embodiments, the microorganisms are bacteria. In some cases, the bacteria are pathogenic bacteria that disrupt intestinal epithelial permeability and / or otherwise relate to IBD. In some cases, the bacteria are species of Bacteroides. Non-limiting examples of suitable species of Bacteroides include Bacteroides vulgaris (…). B. vulgatus ), Bacteroides multifiliis ( B.dorei ), Bacteroides fragilis ( B. fragilis ), Bacteroides masei ( B. massiliensis ), Bacteroides ovalis ( B. ovatus), Bacteroides multiforme ( B. theta ), Bacteroides monomorpha ( B. uniformis ), fecal Bacteroides ( B. stercoris ), Bacteroides cellulose B. cellulosilyticus ), Bacteroides xylan B. xylanisolvens ) and fecal bacterium ( B. caccae In some cases, the bacteria are *Bacteroides commonis* and / or *Bacteroides multifiliis*. In some cases, the bacteria are *Bacteroides commonis*. In some cases, the genus of the bacteria may be derived from... Phocaeicola It is a genus that has been reclassified from the genus Bacteroides. Phocaeicola Non-restrictive examples of suitable species of the genus include P. vulgatus and P. dorei In some cases, the protease includes DPP-4 expressed by Bacteroides commonis and / or Bacteroides multifiliis.

[0072] Protease inhibitors are generally compounds that reduce or inhibit the activity of proteases. In some embodiments, protease inhibitors reduce or inhibit the activity of bacterial proteases. In some embodiments, protease inhibitors reduce or inhibit the activity of bacterial proteases present in the gut microbiome. In some embodiments, protease inhibitors reduce or inhibit the activity of bacterial proteases present in the gut microbiome of humans. In some embodiments, protease inhibitors reduce or inhibit the activity of bacterial proteases present in the gut microbiome of people with at least one symptom of IBD. In some embodiments, protease inhibitors reduce or inhibit the activity of bacterial proteases present in the gut microbiome of people who do not have diabetes. In some embodiments, protease inhibitors reduce or inhibit the activity of bacterial proteases present in the gut microbiome of people who do not have an inflammatory disease or condition other than IBD. In some embodiments, protease inhibitors comprise glibenclamides or pharmaceutically acceptable salts thereof. Examples of gliptin drugs include, but are not limited to, sitagliptin, ticagliptin, octagliptin, vildagliptin, saxagliptin, alogliptin, linagliptin, giglitazone, alagliptin, treagliptin, evogliptin, gogliptin, dugliptin, neogliptin, repagliptin, cogliptin, fogliptin, and pulugliptin or their derivatives or combinations.

[0073] In some embodiments, the protease inhibitor comprises a glibenclamide that reduces or inhibits the activity of bacterial proteases. In some embodiments, the protease inhibitor comprises a glibenclamide that reduces or inhibits the activity of bacterial proteases present in the gut microbiome. In some embodiments, the protease inhibitor comprises a glibenclamide that reduces or inhibits the activity of bacterial proteases present in the gut microbiome of a human. In some embodiments, the protease inhibitor comprises a glibenclamide that reduces or inhibits the activity of bacterial proteases present in the gut microbiome of a person having at least one symptom of IBD. In some embodiments, the protease inhibitor comprises a glibenclamide that reduces or inhibits the activity of bacterial proteases present in the gut microbiome of a person who does not have diabetes. In some embodiments, the protease inhibitor comprises a glibenclamide that reduces or inhibits the activity of bacterial proteases present in the gut microbiome of a person who does not have an inflammatory disease or condition other than IBD.

[0074] In some embodiments, the composition comprises a therapeutically effective amount of a protease inhibitor or a pharmaceutically acceptable salt thereof. In some embodiments, the composition comprises a therapeutically effective amount of more than one (e.g., 2, 3, 4, 5, or 5-10) protease inhibitors or a pharmaceutically acceptable salt thereof. In some embodiments, the pharmaceutical dosage form comprises a core containing a therapeutically effective amount of a protease inhibitor or a pharmaceutically acceptable salt thereof. In some embodiments, the pharmaceutical dosage form comprises a core containing a therapeutically effective amount of more than one (e.g., 2, 3, 4, 5, or 5-10) protease inhibitors or a pharmaceutically acceptable salt thereof. In some embodiments, the therapeutically effective amount of the protease inhibitor is sufficient to reduce one or more symptoms of IBD (e.g., UC, Crohn's disease) in a subject (e.g., delaying or reducing the onset, progression, and / or severity of said one or more symptoms). In some embodiments, the therapeutically effective amount of the protease inhibitor is sufficient to reduce the risk of the subject developing IBD (e.g., UC, Crohn's disease). In some embodiments, the therapeutically effective amount of the protease inhibitor is an amount sufficient to promote wound healing in the large intestine (e.g., colon) and / or small intestine (e.g., distal ileum) of the subject. In some embodiments, the effective amount is an amount that effectively inhibits the activity of the protease by at least about 10%, at least about 20%, at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, at least about 95%, or at least about 98%. In some implementations, the therapeutically effective dose of the protease inhibitor is in the range of about 1 mg to 2000 mg (e.g., 1 mg to 10 mg, 1 mg to 50 mg, 1 mg to 100 mg, 10 mg to 50 mg, 10 mg to 100 mg, 50 mg to 100 mg, 100 mg to 150 mg, 100 mg to 200 mg, 150 mg to 200 mg, 200 mg to 250 mg, 250 mg to 300 mg, 300 mg to 400 mg, 400 mg to 500 mg, 500 mg to 750 mg, 750 mg to 1000 mg, 1000 mg to 1250 mg, 1250 mg to 1500 mg, 1500 mg to 2000 mg).In some implementations, the therapeutically effective dose of the protease inhibitor is about 1 mg, about 5 mg, about 10 mg, about 15 mg, about 20 mg, about 25 mg, about 30 mg, about 35 mg, about 40 mg, about 45 mg, about 50 mg, about 55 mg, about 60 mg, about 65 mg, about 70 mg, about 75 mg, about 80 mg, about 85 mg, about 90 mg, about 95 mg, about 100 mg, about 105 mg, about 110 mg, about 115 mg, about 120 mg, about 125 mg, about 130 mg, about 135 mg, about 140 mg, about 145 mg, about 150 mg, about 155 mg, about 160 mg, about 165 mg, about 170 mg, about 175 mg, about 180 mg, about 185 mg, about 190 mg, about 195 mg, or about 200 mg. The dosage ranges described herein provide guidance for administering the provided pharmaceutical compositions to adults. The amount to be administered to, for example, children or adolescents, may be determined by a medical practitioner or person skilled in the art, and may be less than or the same as the amount administered to adults.

[0075] In some embodiments, the composition comprises one or more pharmaceutically acceptable excipients. In some embodiments, the core of the pharmaceutical dosage form comprises one or more pharmaceutically acceptable excipients. In some cases, one or more pharmaceutically acceptable excipients include one or more pharmaceutically acceptable carriers, buffers, salts, inert diluents or fillers, binders, stabilizers, emulsifiers, disintegrants, diluents, lubricants, additives, preservatives, flavor masking agents, colorants, adjuvants, dispersants and / or granulators, surfactants and / or oils and / or other agents. Non-limiting examples of suitable pharmaceutically acceptable excipients include sugars (e.g., sucrose, lactose), polysaccharides (e.g., cellulose and its derivatives, starch, dextran), sugar alcohols (e.g., xylitol, sorbitol, mannitol), gelatin, polymers (e.g., polyvinylpyrrolidone, polyethylene glycol, polyacrylate), colloidal silica, calcium carbonate, calcium phosphate, calcium hydroxide, magnesium stearate, sodium lauryl sulfate, and sodium acetate. Excipients such as cocoa butter and suppository waxes, colorants, coating agents, sweeteners, flavoring agents, and aroma agents may also be present in the composition. The relative amounts of the active ingredient, pharmaceutically acceptable excipients, and / or any other ingredients in the pharmaceutical compositions described herein will vary depending on the identity, body type, and / or disease of the subject being treated, and further depending on the route of administration of the composition. The composition may contain between 0.1% and 100% (w / w) of the active ingredient.

[0076] In some embodiments, the composition comprises a protease inhibitor and a carrier. In some embodiments, the composition comprises a protease inhibitor and a carrier that is not absorbed by intestinal cells. In some embodiments, the composition comprises a protease inhibitor and a carrier that is minimally absorbed by intestinal cells. For example, in some aspects, the composition comprises a protease inhibitor and a carrier in which about 99% of said amount of carrier is not absorbed into the bloodstream. In some aspects, the composition comprises a protease inhibitor and a carrier in which about 50%, about 51%, about 55%, about 60%, about 65%, about 70%, about 75%, about 80%, about 85%, about 90%, about 95%, about 98%, about 99%, or about 100% of said amount of carrier is not absorbed into the bloodstream.

[0077] In some embodiments, the composition comprises a protease inhibitor and a carrier that is not absorbed across the intestinal wall of the subject. In some embodiments, the composition comprises a protease inhibitor and a carrier, with approximately 51% to approximately 99% of the carrier not absorbed across the intestinal wall of the subject. In some embodiments, the composition comprises a protease inhibitor and a carrier, with approximately 1%, approximately 5%, approximately 10%, approximately 15%, approximately 20%, approximately 25%, approximately 30%, approximately 35%, approximately 40%, approximately 45%, or approximately 49% of the carrier being absorbed into the bloodstream of the subject. In some embodiments, the composition comprises a protease inhibitor and a carrier that allows the protease inhibitor to target the gut microbiome. In some embodiments, the composition comprises a protease inhibitor and a carrier that allows the protease inhibitor to specifically target the gut microbiome present in the subject and does not allow the protease inhibitor to target the bloodstream of the subject. In some embodiments, the carrier that allows the protease inhibitor to specifically target the gut microbiome present in the subject and does not allow the protease inhibitor to target the bloodstream of the subject comprises a polymer. In some embodiments, the carrier that allows the protease inhibitor to specifically target the gut microbiome and does not allow the protease inhibitor to target the bloodstream comprises a polymer containing polyvinylpyrrolidone. In some embodiments, the carrier that specifically targets the protease inhibitor to the gut microbiome and does not target the protease inhibitor to the blood comprises a polymer hydrogel, such as a polyvinylpyrrolidone (PVP) hydrogel. In some embodiments, the carrier that specifically targets the protease inhibitor to the gut microbiome and does not target the protease inhibitor to the blood comprises a polymer, such as a PVP hydrogel loaded with a protease inhibitor. The term "loaded" as used herein refers to an interaction between two molecules (e.g., a polymer and a protease inhibitor). The interaction can be based on hydrophilic interactions, such as charge interactions, or hydrophobic interactions. In some embodiments, the composition comprising a polymer (e.g., a PVP hydrogel loaded with a protease inhibitor) targets the protease inhibitor to a location in the gut. In some embodiments, the composition comprising a polymer (e.g., a PVP hydrogel loaded with a protease inhibitor) targets the protease inhibitor to a location in the gut with an alkaline pH. For example, a polymer-containing carrier (e.g., a PVP hydrogel loaded with a protease inhibitor) can enable the protease inhibitor to target the distal ileum and / or colon, wherein an alkaline pH reduces hydrogen bonds within the polymer (e.g., the PVP hydrogel) and hydrogen bonds between the polymer (e.g., the PVP hydrogel) and the protease inhibitor, thereby achieving the release of the protease inhibitor in the distal ileum and / or colon. In some embodiments, the polymer-containing carrier (e.g., a PVP polymer) associates with the protease inhibitor via a linker. In some embodiments, the polymer-containing carrier (e.g., a PVP polymer) associates with the protease inhibitor via a non-digestible linker.In some embodiments, the protease inhibitor is dispersed in a polymer (e.g., a PVP polymer). In some embodiments, the protease inhibitor is present in, for example, the core of a tablet and a polymer, such as a PVP polymer surrounding the tablet core.

[0078] In some embodiments, the composition comprises the pH-sensitive material and / or the microbial-sensitive material described herein. In some embodiments, the composition comprises the pH-sensitive material and / or the microbial-sensitive material and / or a carrier. In some embodiments, the composition comprises the pH-sensitive material and / or the microbial-sensitive material and / or a carrier containing a polymer. In some embodiments, the composition comprises the pH-sensitive material and / or the microbial-sensitive material and / or a carrier containing a PVP polymer. In some embodiments, the composition comprises the pH-sensitive material and / or the microbial-sensitive material and / or a carrier, wherein the carrier contains a PVP polymer loaded with a protease inhibitor. In some embodiments, the core comprises the pH-sensitive material and / or the microbial-sensitive material described herein. In some embodiments, the composition comprises one or more nanoparticles (e.g., lipid nanoparticles, polymer nanoparticles). In some embodiments, the core comprises one or more nanoparticles (e.g., lipid nanoparticles, polymer nanoparticles).

[0079] In some embodiments, the composition comprises tablets, gelcaps, capsules, lozenges, pods, or other suitable solid forms. In some embodiments, the core comprises tablets, gelcaps, capsules, lozenges, pods, or other suitable solid forms. In some embodiments, the composition comprises capsules (e.g., hard-shell capsules) containing one or more protease inhibitors in powder form. In some embodiments, the pharmaceutical dosage form comprises capsules (e.g., hard-shell capsules) containing one or more protease inhibitors in powder form.

[0080] In some embodiments, the composition comprises a capsule (e.g., a soft-shell capsule) containing one or more protease inhibitors in liquid form (e.g., a solution or suspension of one or more protease inhibitors). In some embodiments, the pharmaceutical dosage form comprises a capsule (e.g., a soft-shell capsule) containing one or more protease inhibitors in liquid form (e.g., a solution or suspension of one or more protease inhibitors).

[0081] In some embodiments, the composition comprises a controlled-release coating. In some embodiments, the pharmaceutical dosage form comprises a controlled-release coating applied to the outer surface of the core. In some cases, the controlled-release coating provides the core with targeted delivery to desired locations within the gastrointestinal tract, such as one or more portions of the large intestine (e.g., colon) and / or small intestine (e.g., distal ileum) of a subject to which the pharmaceutical dosage form has been administered. In some embodiments, the controlled-release coating is configured to release the composition in the large intestine (e.g., colon) of a subject. In some embodiments, the controlled-release coating is configured to release the core in the large intestine (e.g., colon) of a subject. In some cases, the controlled-release coating is configured to release the composition in the small intestine of a subject. In some cases, the controlled-release coating is configured to release the composition in the distal ileum of a subject. In some cases, the controlled-release coating is configured to release the core in the small intestine of a subject.

[0082] In some embodiments, the controlled-release coating comprises a single layer. In some embodiments, the controlled-release coating consists of a single layer. In some embodiments, the controlled-release coating comprises multiple layers. The multiple layers may include two, three, four, five, or more layers. In some cases, two or more of the multiple layers contain the same material. In some cases, two or more of the multiple layers contain different materials.

[0083] In some implementations, one or more layers of the controlled-release coating comprise one or more pH-sensitive materials. A pH-sensitive material is generally a material configured to dissolve at pH values ​​above or below a threshold pH. In healthy individuals, pH values ​​are typically lower in the stomach (e.g., 0.95 to 3.5), increasing from the proximal small intestine (e.g., 5.5 to 7.0) to the distal ileum (e.g., 6.5 to 7.5), decreasing in the cecum (e.g., 5.5 to 7.0), and then increasing in the colon (e.g., 6.0 to 7.5). In individuals with IBD, gastric and / or colonic pH values ​​may be higher or lower than in healthy individuals, particularly in the stomach, distal ileum, cecum, and right colon, where pH values ​​in IBD patients may be higher than in healthy individuals (see, for example, Press et al., Aliment. Pharmacol. Ther. 1998, 12: 672-78). In some embodiments, the pH-sensitive material is configured to resist dissolution at the relatively low pH of the stomach and to dissolve at the relatively high pH of the colon and / or small intestine. In some embodiments, the pH-sensitive material is configured to dissolve at pH values ​​of 5.5 or higher, 6.0 or higher, 6.5 or higher, 7.0 or higher, or 7.5 or higher. In some embodiments, the pH-sensitive material is configured to dissolve at pH 5.5, at about pH 5.6, at about pH 5.7, at about pH 5.8, at about pH 5.9, at about pH 6.0, at about pH 6.1, at about pH 6.2, at about pH 6.3, at about pH 6.4, at about pH 6.5, at about pH 6.6, at about pH 6.7, at about pH 6.8, at about pH 6.9, at about pH 7.0, at about pH 7.1, at about pH 7.2, at about pH 7.3, at about pH 7.4, or at about pH 7.5. In some embodiments, a pH of 7.5 or higher includes pH values ​​of about 7.6, about 7.7, about 7.8, about 7.9, about 8.0, about 8.1, about 8.2, about 8.3, about 8.4, about 8.5, about 8.6, about 8.7, about 8.8, about 8.9, or about 9.0. In some embodiments, the pH-sensitive material is configured to dissolve at pH values ​​higher than 7.1. In some embodiments, the pH-sensitive material is configured to dissolve at pH values ​​higher than 7.2. In some embodiments, the pH-sensitive material is configured to dissolve at pH values ​​higher than 7.3. In some embodiments, the pH-sensitive material is configured to dissolve at pH values ​​higher than 7.4. In some embodiments, the pH-sensitive material is configured to dissolve at pH values ​​higher than 7.5. In some embodiments, the pH-sensitive material is configured to dissolve at a pH value of about 7.1.In some embodiments, the pH-sensitive material is configured to dissolve at a pH of about 7.2. In some embodiments, the pH-sensitive material is configured to dissolve at a pH of about 7.3. In some embodiments, the pH-sensitive material is configured to dissolve at a pH of about 7.4. In some embodiments, the pH-sensitive material is configured to dissolve at a pH of about 7.5.

[0084] In some embodiments, the pH-sensitive material is configured to dissolve at a pH of about 7.2 to about 7.5. In some embodiments, the pH-sensitive material is configured to dissolve at a pH of about 7.3 to about 7.5. In some embodiments, the pH-sensitive material is configured to dissolve at a pH of about 7.4 to about 7.5. In some embodiments, the pH-sensitive material is configured to dissolve at a pH of about 7.2 to about 7.4. In some embodiments, the pH-sensitive material is configured to dissolve at a pH of about 7.2 to about 7.3.

[0085] In some embodiments, the composition comprises more than one pH-sensitive material. In some embodiments, the composition comprises a first pH-sensitive material configured to dissolve at a first pH and a second pH-sensitive material configured to dissolve at a second pH. In some embodiments, the composition further comprises a third pH-sensitive material dissolved at a third pH. In some embodiments, the composition further comprises a fourth pH-sensitive material dissolved at a fourth pH. In some embodiments, the composition further comprises a fifth pH-sensitive material dissolved at a fifth pH. For example, the composition can target a protease inhibitor to the cecum or right colon, wherein the composition comprises a first material configured to dissolve at about pH 7.5, initially reaching about pH 7.5 when intestinal contents reach the distal ileum; and a second material configured to dissolve at about pH 5.5, reaching about pH 5.5 when intestinal contents reach the cecum.

[0086] In some embodiments, the composition comprises a material configured to dissolve at a pH higher than 7.5 (e.g., pH 7.6), which may be the pH in the distal ileum of a subject with IBD. In some embodiments, the composition comprises a first material configured to dissolve at a pH higher than 7.5 (e.g., pH 7.6), which may be the pH in the distal ileum of a subject with IBD; and a second material configured to dissolve at a pH higher than 7.5 (e.g., pH 7.6), which may be the pH in the colon of a subject with IBD. In some embodiments, the composition comprises an agent that increases the pH in the intestinal region. In some embodiments, the composition comprises a pH-sensitive material configured to dissolve at a pH of 7.5 or higher. In some embodiments, the composition comprises a pH-sensitive material configured to dissolve at pH of about 7.6, about 7.7, about 7.8, about 7.9, about 8.0, about 8.1, about 8.2, about 8.3, about 8.4, about 8.5, about 8.6, about 8.7, about 8.8, about 8.9, or about 9.0. In some embodiments, the composition comprises an agent that increases the pH in the intestinal location, and the composition further comprises a pH-sensitive material configured to dissolve at pH of about 7.6, about 7.7, about 7.8, about 7.9, about 8.0, about 8.1, about 8.2, about 8.3, about 8.4, about 8.5, about 8.6, about 8.7, about 8.8, about 8.9, or about 9.0.

[0087] In some embodiments, the composition comprises multiple layers. In some embodiments, the composition comprises a core containing a polymer (e.g., a PVP polymer loaded with a protease inhibitor). In some embodiments, the composition further comprises a first layer added to the outer surface of the core, the first layer comprising a pH-sensitive material configured to dissolve at pH values ​​of about 7.6, about 7.7, about 7.8, about 7.9, about 8.0, about 8.1, about 8.2, about 8.3, about 8.4, about 8.5, about 8.6, about 8.7, about 8.8, about 8.9, or about 9.0. In some embodiments, the composition further comprises a second layer added to the outer surface of the first layer, the second layer comprising an agent that increases the pH in the intestinal location. In some embodiments, the second layer is configured to dissolve at a pH value present in the distal ileum. In some embodiments, the second layer is configured to dissolve at a pH value present in the cecum. In some embodiments, the second layer is configured to dissolve at a pH value present in the colon. In some embodiments, when the second layer dissolves in the distal ileum, cecum, or colon, the agent contained in the second layer increases the pH in the distal ileum, cecum, or colon to about 7.6, about 7.7, about 7.8, about 7.9, about 8.0, about 8.1, about 8.2, about 8.3, about 8.4, about 8.5, about 8.6, about 8.7, about 8.8, about 8.9, or about 9.0. In some embodiments, a first layer of pH-sensitive material, dissolved at pH of about 7.6, about 7.7, about 7.8, about 7.9, about 8.0, about 8.1, about 8.2, about 8.3, about 8.4, about 8.5, about 8.6, about 8.7, about 8.8, about 8.9, or about 9.0, is dissolved in the distal ileum, cecum, or colon, thereby releasing a core containing a PVP polymer loaded with protease inhibitors.

[0088] In some embodiments, one or more pH-sensitive materials comprise a pH-sensitive polymer. In certain cases, the pH-sensitive polymer comprises one or more monomers selected from: methacrylic acid, methyl methacrylate, methyl acrylate, ethyl acrylate, acrylic acid, dimethylaminoethyl methacrylate, butyl methacrylate, and N-isopropylacrylamide. Non-limiting examples of suitable pH-sensitive polymers include copolymers of methacrylic acid and methyl methacrylate, copolymers of methacrylic acid and ethyl acrylate, methyl acrylate, copolymers of methyl methacrylate and methacrylic acid, aminoalkyl methacrylate copolymers, cellulose acetate phthalate (“CAP”), hydroxypropyl methylcellulose phthalate (“HPMCP”), hydroxypropyl methylcellulose acetate succinate (“HPMC-AS”), poly(N-isopropylacrylamide”) (“PNI-PAM”), and EUDRAGIT. ® S, EUDRAGIT ® FS, EUDRAGIT ® L and Kollicoat ® MAE 100P.

[0089] In some embodiments, the composition comprises one or more microbial-sensitive materials. In some cases, one or more layers of the controlled-release coating comprise microbial-sensitive materials. In some cases, the microbial-sensitive materials are readily degraded by one or more microorganisms residing in a part of the gastrointestinal tract (e.g., the colon). Non-limiting examples of suitable microbial-sensitive materials include amylose, lactulose, amylopectin, pectin, guar gum, locust bean gum, inulin, chitosan, arabinogalactan, agave fructan, alginate, chondroitin sulfate, dextran, and cyclodextrin.

[0090] In some embodiments, the composition comprises a pH-sensitive material and / or a microbial-sensitive material. In some embodiments, the composition comprises more than one pH-sensitive material and / or more than one microbial-sensitive material. In some embodiments, the controlled-release coating comprises a layer containing both a pH-sensitive material and a microbial-sensitive material. In some embodiments, the controlled-release coating comprises a layer containing a pH-sensitive material and / or a layer containing a microbial-sensitive material. In some embodiments, the controlled-release coating comprises one or more layers containing a pH-sensitive material and one or more layers containing a microbial-sensitive material. In some embodiments, the controlled-release coating comprises one or more layers containing a first pH-sensitive material and one or more layers containing a second pH-sensitive material. In some cases, the controlled-release coating comprises one, two, three, four, five, or more pH-sensitive materials. In some embodiments, the controlled-release coating comprises one or more layers containing a first microbial-sensitive material and one or more layers containing a second microbial-sensitive material. In some examples, the controlled-release coating comprises one, two, three, four, five, or more microbial-sensitive materials.

[0091] In some embodiments, the composition comprises a controlled-release coating. In some embodiments, the composition comprises more than one controlled-release coating. In some embodiments, the composition comprises one layer of a controlled-release coating. In some embodiments, the composition comprises more than one layer of a controlled-release coating. In some embodiments, the composition comprises one layer of a controlled-release coating containing a pH-sensitive material. In some embodiments, the composition comprises one layer of a controlled-release coating containing a microbial-sensitive material. In some embodiments, the composition comprises one layer of a controlled-release coating containing a pH-sensitive material and one layer of a controlled-release coating containing a microbial-sensitive material.

[0092] In some embodiments, the composition comprises more than one layer of controlled-release coating containing a pH-sensitive material. In some embodiments, the composition comprises more than one layer of controlled-release coating containing a microbial-sensitive material. In some embodiments, the composition comprises more than one layer of controlled-release coating containing both pH-sensitive and microbial-sensitive materials.

[0093] In some embodiments, the composition comprises one, two, three, four, five, or more layers of a controlled-release coating containing a pH-sensitive material. In some embodiments, the composition comprises one, two, three, four, five, or more layers of a controlled-release coating containing a microbial-sensitive material. In some embodiments, the composition comprises one, two, three, four, five, or more layers of a controlled-release coating containing a pH-sensitive material and / or one, two, three, four, five, or more layers of a controlled-release coating containing a pH-sensitive material. In some embodiments, the composition comprises one, two, three, four, five, or more layers of a controlled-release coating containing a pH-sensitive material and / or one, two, three, four, five, or more layers of a controlled-release coating containing a pH-sensitive material and / or a carrier as described herein. In some embodiments, the carrier containing the polymer is contained within one, two, three, four, five, or more layers of a controlled-release coating containing a pH-sensitive material, and / or within one, two, three, four, five, or more layers of a controlled-release coating containing a pH-sensitive material. In some embodiments, the carrier containing the PVP polymer is contained within one, two, three, four, five, or more layers of a controlled-release coating containing a pH-sensitive material, and / or within one, two, three, four, five, or more layers of a controlled-release coating containing a pH-sensitive material. In some embodiments, the carrier containing the PVP polymer associated with a protease inhibitor (e.g., a bacterial protease inhibitor) is contained within one, two, three, four, five, or more layers of a controlled-release coating containing a pH-sensitive material, and / or within one, two, three, four, five, or more layers of a controlled-release coating containing a pH-sensitive material.

[0094] In some embodiments, the composition comprises a layer containing a controlled-release coating of a pH-sensitive material configured to dissolve at the pH of the distal ileum and a layer containing a controlled-release coating of a microbial-sensitive material readily degraded by one or more microorganisms residing in the cecum and / or colon.

[0095] In some embodiments, the composition comprises a layer containing a controlled-release coating of a pH-sensitive material configured to dissolve at the pH of the proximal small intestine, and a layer containing a controlled-release coating of a microbial-sensitive material readily degraded by one or more microorganisms residing in the small intestine. In some embodiments, the composition comprises a layer containing a controlled-release coating of a pH-sensitive material configured to dissolve at the pH of the proximal small intestine, and a layer containing a microbial-sensitive material readily degraded by one or more microorganisms residing in the ileum.

[0096] In some embodiments, the composition comprises a first layer containing a controlled-release coating of a microbial-sensitive material readily degraded by one or more microorganisms residing in the small intestine, and a second layer containing a pH-sensitive material configured to dissolve in the ileum. In some embodiments, the composition comprises a first layer containing a microbial-sensitive material readily degraded by one or more microorganisms residing in the small intestine, a second layer containing a pH-sensitive material configured to dissolve in the ileum, and a third layer containing a microbial-sensitive material readily degraded by one or more microorganisms residing in the colon. In some embodiments, the composition further comprises a carrier comprising a polymer, such as a PVP polymer associated with a protease inhibitor (e.g., a bacterial protease inhibitor).

[0097] In some embodiments, the composition comprises a first layer containing a controlled-release coating of a pH-sensitive material configured to dissolve in the ileum and a second layer containing a controlled-release coating of a microbial-sensitive material readily degraded by one or more microorganisms residing in the colon.

[0098] In some embodiments, the composition comprises a first layer containing a controlled-release coating of a pH-sensitive material configured to dissolve in the proximal small intestine and a second layer containing a controlled-release coating of a second pH-sensitive material configured to dissolve in the distal ileum of the subject.

[0099] In some embodiments, the composition comprises one or more hydrophilic layers and one or more lipophilic layers. In some embodiments, the composition comprises one or more layers formed by an aqueous solution and one or more layers formed by an organic solution. In some embodiments, the composition comprises one or more hydrophilic layers and does not comprise a lipophilic layer. In some embodiments, the composition comprises one or more layers formed by an aqueous solution and does not comprise one or more layers formed by an organic solution.

[0100] In some cases, the controlled-release coating comprises one or more hydrophilic layers and one or more lipophilic layers. In some cases, the controlled-release coating comprises one or more layers formed by an aqueous solution and one or more layers formed by an organic solution. In some embodiments, the controlled-release coating comprises one or more hydrophilic layers and one or more lipophilic layers. In some embodiments, the controlled-release coating comprises one or more layers formed by an aqueous solution and one or more layers formed by an organic solution. In some embodiments, the controlled-release coating comprises one or more hydrophilic layers and does not comprise a lipophilic layer. In some embodiments, the controlled-release coating comprises one or more layers formed by an aqueous solution and does not comprise one or more layers formed by an organic solution.

[0101] In some embodiments, the controlled-release coating comprises a ruptureable membrane. In some embodiments, the controlled-release coating comprises a hydrogel stopper configured to swell and rupture the coating upon exposure to moisture. In some cases, the hydrogel stopper may be covered with a cap comprising a pH-sensitive material and / or a microbial-sensitive material.

[0102] In some embodiments, the composition comprises the protease inhibitor described herein and a carrier. In some embodiments, the composition comprises the protease inhibitor described herein and a liquid or gel carrier. Non-limiting examples of suitable liquid or gel carriers include water, aqueous saline solutions, ethanol solutions, glucose solutions, glycerol solutions, and oils, including but not limited to petroleum (e.g., mineral oil), vegetable oils (e.g., peanut oil, soybean oil, sesame oil), animal oils, and synthetic oils.

[0103] In some embodiments, the composition is formulated as a solution, emulsion, or suspension. In some embodiments, the composition is formulated as a solution, emulsion, or suspension for oral administration. In some embodiments, the composition is formulated as a solution, emulsion, or suspension for rectal administration. In some embodiments, the composition is formulated as an aqueous solution, alcoholic solution, emulsion, gel, cream, and / or ointment. In some embodiments, the composition is formulated as an aqueous solution, alcoholic solution, emulsion, gel, cream, and / or ointment for rectal administration. In some embodiments, the composition is formulated as an aqueous solution, alcoholic solution, emulsion, gel, cream, and / or ointment for oral administration.

[0104] In some embodiments, the pharmaceutical composition is formulated as a solution for intravenous administration. In some embodiments, the pharmaceutical composition is formulated as an aqueous solution for intravenous administration. In some embodiments, the composition is formulated as a solution for intraperitoneal, intramuscular, subcutaneous, intravenous, or intrathecal administration. In some embodiments, the composition is formulated as a solution for intraperitoneal, intramuscular, subcutaneous, intravenous, or intrathecal injection. In some embodiments, the composition is formulated for intraperitoneal, intramuscular, subcutaneous, intravenous, or intrathecal infusion.

[0105] In some aspects, the pharmaceutical dosage form comprises the protease inhibitors described herein (e.g., gliptins or pharmaceutically acceptable salts thereof) and a liquid or gel carrier. In some embodiments, the pharmaceutical dosage form is formulated as a solution, emulsion, or suspension for oral administration. In some embodiments, the pharmaceutical dosage form is formulated as an aqueous solution, alcoholic solution, emulsion, gel, cream, and / or ointment for rectal administration. In some embodiments, rectal administration is achieved by using an enema, suppository, tube, or aerosol with an appendage inserted into the anus. In some embodiments, the pharmaceutical dosage form is formulated as an injection for intraperitoneal, intramuscular, subcutaneous, intravenous, or intrathecal administration. Non-limiting examples of suitable liquid or gel carriers include water, aqueous saline solutions, ethanol solutions, glucose solutions, glycerol solutions, and oils, including but not limited to petroleum (e.g., mineral oil), vegetable oils (e.g., peanut oil, soybean oil, sesame oil), animal oils, and synthetic oils.

[0106] II. Instructions for Use Some aspects relate to a method for treating IBD. IBD can be ulcerative colitis and / or Crohn's disease. In some embodiments, the method includes delivering a therapeutically effective amount of an inhibitor of a protease (or a pharmaceutically acceptable salt thereof) to the large intestine (e.g., colon) and / or small intestine of a subject.

[0107] The protease inhibitor can be any protease inhibitor described herein. In some embodiments, a method is provided that includes delivering an inhibitor of a protease to a subject in need. In some embodiments, a method is provided that includes delivering two or more (e.g., 2, 3, 4, 5, or 5-10) protease inhibitors to a subject in need. In some embodiments, a method is provided that includes administering an inhibitor of a protease to a subject in need. In some embodiments, a method is provided that includes administering two or more (e.g., 2, 3, 4, 5, or 5-10) protease inhibitors to a subject in need. In some embodiments, a method is provided that includes delivering an inhibitor of a bacterial protease to a subject in need. In some embodiments, a method is provided that includes delivering two or more (e.g., 2, 3, 4, 5, or 5-10) bacterial protease inhibitors to a subject in need. In some embodiments, a method is provided that includes administering an inhibitor of a bacterial protease to a subject in need. In some embodiments, a method is provided comprising administering two or more (e.g., 2, 3, 4, 5, or 5-10) bacterial protease inhibitors to a subject in need. In some embodiments, the protease is a serine protease, a cysteine ​​protease, or a metalloproteinase. In some embodiments, the protease is a serine protease (e.g., S09 protease). In some embodiments, the protease is configured to cleave GLP-1 and / or GLP-2. In some embodiments, the protease is configured to preferentially cleave GLP-2. In some cases, the protease is dipeptidyl peptidase-4 (“DPP-4”).

[0108] In some implementations, the protease is expressed by microorganisms (e.g., bacteria) in the gut microbiome. In some cases, the bacteria are species of the genus *Bacteroides*. Non-limiting examples of suitable species of *Bacteroides* include *Bacteroides vulgaris*, *Bacteroides davidiana*, *Bacteroides fragilis*, *Bacteroides masae*, *Bacteroides ovata*, *Bacteroides pleomorphica*, *Bacteroides monomorphica*, *Bacteroides fecalis*, *Bacteroides celluloseolyticus*, *Bacteroides xylanolyticus*, and *Bacteroides fecalis*. In some cases, the bacteria are *Bacteroides vulgaris* and / or *Bacteroides davidiana*. In some cases, the bacteria are *Bacteroides vulgaris*. In some cases, the genus of the bacteria may be derived from... Phocaeicola It is a genus that has been reclassified from the genus Bacteroides. Phocaeicola Non-restrictive examples of suitable species of the genus include P. vulgatus and P. dorei In some cases, the protease includes DPP-4 expressed by Bacteroides commonis and / or Bacteroides multifiliis.

[0109] In some embodiments, the protease inhibitor comprises a gliptin drug or a pharmaceutically acceptable salt thereof. Non-limiting examples of suitable gliptin drugs include sitagliptin, ticagliptin, ocagliptin, vildagliptin, saxagliptin, alogliptin, linagliptin, giglitazone, alagliptin, treagliptin, evogliptin, gogliptin, dugliptin, neogliptin, repagliptin, cogliptin, fogliptin, and pulugliptin or derivatives or combinations thereof (see, for example, K. Wang, Science 2023, 381, 501; A. Wang, BMC Pharmacology 2012, 12(2), pp. 1-11; L. Keller, Nature Chem. Biology 2023, 19: 1469-79; Q. Liao Hindawi J. Chem (2019, pp. 1-8). In some embodiments, a suitable glibenclamide is a glibenclamide that inhibits bacterial proteases. In some embodiments, a suitable glibenclamide is a glibenclamide that inhibits bacterial proteases present in the microbiome of a subject with IBD. In some embodiments, a suitable glibenclamide is a glibenclamide that inhibits bacterial proteases present in the microbiome of a subject without diabetes. In some embodiments, a suitable glibenclamide is a glibenclamide that inhibits bacterial proteases present in the microbiome of a subject without inflammatory diseases or conditions other than IBD. In some embodiments, the protease inhibitor comprises a prodrug of the glibenclamide or a pharmaceutically acceptable salt thereof.

[0110] In some implementations, the subject is a mammalian subject. In some implementations, the subject is a human subject. In some implementations, the subject is a non-human animal subject. Examples of suitable non-human animal subjects include, but are not limited to, non-human primates, dogs, cats, sheep, cattle, pigs, horses, mice, rats, and rabbits. The subject can be male or female. In some cases, the subject is an adult (e.g., 18 years of age or older). In some cases, the subject is a child (e.g., 17 years of age or younger).

[0111] In some embodiments, the subject has been diagnosed with IBD (e.g., UC, Crohn's disease). In some embodiments, the subject exhibits one or more symptoms of IBD (e.g., UC, Crohn's disease). In some embodiments, the subject is at risk of developing IBD (e.g., UC, Crohn's disease). In some embodiments, the subject does not have diabetes. In some embodiments, the subject is not at risk of developing diabetes. In some embodiments, the subject does not have any inflammatory disease or condition other than IBD. In some embodiments, the subject is not at risk of developing any inflammatory disease or condition other than IBD.

[0112] In some implementations, the subject has not received another IBD treatment. In some implementations, the subject has received another IBD treatment. In some implementations, the subject is receiving another IBD treatment concurrently. In some implementations, the subject is refractory to another IBD treatment. In some implementations, the other IBD treatment includes aminosalicylate, corticosteroids, immunosuppressants, biologics, anti-tumor necrosis factor agents, or combinations of two or more of these.

[0113] In some embodiments, a therapeutically effective amount of the protease inhibitor is sufficient to alleviate one or more symptoms of IBD (e.g., UC, Crohn's disease) in a subject (e.g., delaying or reducing the onset, progression, and / or severity of said one or more symptoms). In some embodiments, a therapeutically effective amount of the protease inhibitor is sufficient to reduce the risk of the subject developing IBD (e.g., UC, Crohn's disease). In some embodiments, a therapeutically effective amount of the protease inhibitor is sufficient to promote wound healing in the subject's large intestine (e.g., colon) and / or small intestine.

[0114] In some embodiments, the method includes delivering a therapeutically effective amount of a protease inhibitor or a pharmaceutically acceptable salt thereof to the large intestine (e.g., colon) and / or small intestine of a subject. In some embodiments, the method includes administering a composition comprising a protease inhibitor and / or a carrier by oral, rectal, enteral, parenteral (e.g., intravenous, intramuscular, subcutaneous, intrathecal), nasal, transgenitourinary, local, and / or intraperitoneal administration. In some embodiments, the method includes administering a composition comprising a protease inhibitor and / or a carrier by oral, rectal, or enteral administration. In some embodiments, "enteral" administration includes administration to an intestinal location other than the mouth. In some embodiments, enteral administration includes administration via an enteral catheter. In some embodiments, enteral administration includes administration to the small intestine via an enteral catheter. In some embodiments, enteral administration includes administration to the large intestine (e.g., colon) via an enteral catheter. In some embodiments, enteral administration includes rectal administration.

[0115] In some embodiments, methods of delivering a therapeutically effective amount of a protease inhibitor or a pharmaceutically acceptable salt thereof to the large intestine (e.g., colon) and / or small intestine of a subject include administration of a pharmaceutical composition comprising a protease inhibitor via oral, rectal, enteral, parenteral (e.g., intravenous, intramuscular, subcutaneous, intrathecal), nasal, transgenitourinary, local, and / or intraperitoneal administration. In some embodiments, the pharmaceutical composition is formulated for delivery of the protease inhibitor to the intestine of a subject. In some embodiments, the pharmaceutical composition is formulated for delivery of the protease inhibitor to the large intestine of a subject. In some embodiments, the pharmaceutical composition is formulated for delivery of the protease inhibitor to the colon of a subject. In some embodiments, the pharmaceutical composition is formulated for delivery of the protease inhibitor to the small intestine of a subject.

[0116] In some embodiments, the composition is in solid form. In some embodiments, the pharmaceutical composition is in solid form. In some embodiments, the solid form includes tablets, capsules, lozenges, pills, powders, granules, small capsules, or other suitable solid forms. In some cases, the solid form contains a core as described herein. In such solid dosage forms, the core comprises an active ingredient mixed with at least one inert, pharmaceutically acceptable excipient or carrier such as sodium citrate or dicalcium phosphate and / or the following substances: (a) fillers or extenders such as starch, lactose, sucrose, glucose, mannitol, and silica; (b) binders such as, for example, carboxymethyl cellulose, alginate, gelatin, polyvinylpyrrolidone, sucrose, and gum arabic; (c) humectants such as glycerin; (d) disintegrants such as agar, calcium carbonate, potato or cassava starch, alginate, certain silicates, and sodium carbonate; (e) solution blockers such as paraffin; (f) absorption enhancers such as quaternary ammonium compounds; (g) wetting agents such as, for example, cetyl alcohol and glyceryl monostearate; (h) absorbents such as kaolin and bentonite clay; and (i) lubricants such as talc, calcium stearate, magnesium stearate, solid polyethylene glycol, sodium lauryl sulfate, and mixtures thereof. In the case of capsules, tablets, and pills, the dosage form may contain a buffer. In some cases, the solid form contains a controlled-release coating as described herein. In some embodiments, the solid form is formulated for oral administration. In some cases, the solid form is formulated as a suppository (e.g., for rectal administration).

[0117] In some cases, the solid form comprises a controlled-release coating as described herein. In some embodiments, the solid form is formulated for oral administration. In some cases, the solid form is formulated as a suppository (e.g., for rectal administration).

[0118] In some embodiments, the composition has a liquid or gel form. In some embodiments, the liquid or gel form includes solutions, emulsions, or suspensions formulated for oral, rectal, enteral, parenteral (e.g., intravenous, intramuscular, subcutaneous, intrathecal), nasal, genitourinary, topical, and / or intraperitoneal administration. In some embodiments, the pharmaceutical composition has a liquid or gel form. In some cases, the liquid or gel form includes solutions, emulsions, or suspensions formulated for oral, rectal, enteral, parenteral (e.g., intravenous, intramuscular, subcutaneous, intrathecal), nasal, genitourinary, topical, and / or intraperitoneal administration. In some embodiments, the liquid or gel form is formulated as a solution, emulsion, or suspension for oral administration. In some embodiments, the liquid or gel form is formulated as an enema for rectal administration. In some embodiments, the liquid or gel form is formulated as an injection for intraperitoneal, intramuscular, subcutaneous, intravenous, or intrathecal administration.

[0119] In some embodiments, the liquid or gel form comprises a liquid or gel carrier. Non-limiting examples of suitable liquid or gel carriers include water, salt solutions, glucose solutions, glycerol solutions, and oils, including but not limited to petroleum (e.g., mineral oil), vegetable oils (e.g., peanut oil, soybean oil, sesame oil), animal oils, and oils of synthetic origin.

[0120] In some embodiments, the composition is formulated as a spray. In some embodiments, the pharmaceutical composition is formulated as a spray (e.g., for nasal administration).

[0121] In some embodiments, the composition is administered for an extended period. In some embodiments, the pharmaceutical composition is administered for a period of at least 1 month, at least 3 months, at least 6 months, at least 9 months, at least 1 year, at least 3 years, at least 5 years, at least 10 years, or at least 20 years. In some embodiments, the pharmaceutical composition is applied over a period of 1 to 3 months, 1 to 6 months, 1 to 9 months, 1 month to 1 year, 1 month to 3 years, 1 month to 5 years, 1 month to 10 years, 1 month to 20 years, 3 to 6 months, 3 to 9 months, 3 months to 1 year, 3 months to 3 years, 3 months to 5 years, 3 months to 10 years, 3 months to 20 years, 6 to 9 months, 6 months to 1 year, 6 months to 3 years, 6 months to 5 years, 6 months to 10 years, 6 months to 20 years, 9 months to 1 year, 9 months to 3 years, 9 months to 5 years, 9 months to 10 years, 9 months to 20 years, 1 to 3 years, 1 to 5 years, 1 to 10 years, 1 to 20 years, 3 to 5 years, 3 to 10 years, 3 to 20 years, 5 to 10 years, 5 to 20 years, or 10 to 20 years. In some embodiments, the pharmaceutical composition is administered to the subject daily, weekly, monthly, or at shorter or longer intervals. In some embodiments, shorter intervals include administration every 23 hours, every 22 hours, every 21 hours, every 20 hours, every 19 hours, every 18 hours, every 17 hours, every 16 hours, every 15 hours, every 14 hours, every 13 hours, every 12 hours, every 11 hours, every 10 hours, every 9 hours, every 8 hours, every 7 hours, every 6 hours, every 5 hours, every 4 hours, every 3 hours, every 2 hours, or every 1 hour. In some embodiments, the pharmaceutical composition is administered to the subject every other day, every two days, every four days, every five days, every six days, every seven days, every eight days, every nine days, every ten days, every eleven days, every twelve days, every thirteen days, every two weeks, or every three weeks. In some implementations, longer intervals of administration include administration every 5 weeks, every 6 weeks, every 7 weeks, every 8 weeks, every 9 weeks, every 10 weeks, every 11 weeks, every 12 weeks, every 13 weeks, every 14 weeks, every 15 weeks, every 16 weeks, every 17 weeks, every 18 weeks, every 19 weeks, every 20 weeks, every 21 weeks, every 22 weeks, every 23 weeks, every 24 weeks, every 25 weeks, every 26 weeks, every 27 weeks, every 28 weeks, every 29 weeks, every 30 weeks, every 31 weeks, every 32 weeks, every 33 weeks, every 34 weeks, every 35 weeks, every 36 weeks, every 37 weeks, every 38 weeks, every 39 weeks, every 40 weeks, every 41 weeks, every 42 weeks, every 43 weeks, every 44 weeks, every 45 weeks, every 46 weeks, every 47 weeks, every 48 weeks, every 49 weeks, every 50 weeks, every 51 weeks, or every 52 weeks. In some implementations, the drug composition is administered to the subject until one or more symptoms of IBD (e.g., ulcerative colitis, Crohn's disease) are relieved.The pharmaceutical dosage forms described herein can be administered simultaneously, before, or after one or more other pharmaceutical agents, and the therapeutic agents can be used as, for example, combination therapy. Pharmaceutical agents include therapeutically active agents. Pharmaceutical agents also include preventatively active agents. Pharmaceutical agents include small organic molecules such as pharmaceutical compounds (e.g., compounds approved by the U.S. Food and Drug Administration for human or veterinary use, as provided in Federal Regulations (CFRs)), peptides, proteins, carbohydrates, monosaccharides, oligosaccharides, polysaccharides, nucleoproteins, mucins, lipoproteins, synthetic polypeptides or proteins, small molecules linked to proteins, glycoproteins, steroids, nucleic acids, DNA, RNA, nucleotides, nucleosides, oligonucleotides, antisense oligonucleotides, lipids, hormones, vitamins, and cells. In some embodiments, the additional pharmaceutical agent is an agent that can be used to treat and / or prevent diseases (e.g., inflammatory bowel disease). Other examples of agents include, but are not limited to: aminosalicylates (e.g., sulfasalazine or 5-aminosalicylate or portions thereof, including mesalazine, olsalazine, and balsalazine), glucocorticoids (e.g., prednisolone, ileal budesonide, budesonide MMX, and beclomethasone dipropionate), immunomodulators (e.g., azathioprine, 6-mercaptopurine, cyclosporine, or methotrexate), anti-TNF antibodies (e.g., infliximab, adalimumab, cetuzumab, or golimumab), anti-integrin antibodies (e.g., natezumab or vedolzumab), anti-interleukin antibodies (utecumab, lisanjizumab, or mijizumab), Janus kinase (JAK) inhibitors (e.g., tofacitinib, filagrinib, or utpatinib), or sphingosine-1-phosphate (S1p) modulators (e.g., ozamod or ectremod).

[0122] Each additional agent may be administered at the dosage and / or schedule determined for this agent. Additional agents may also be administered together with each other and / or with the compounds or compositions described herein at a single dose or composition, or separately at different doses or compositions. Specific combinations employed in the regimen will take into account the compatibility of the compounds described herein with one or more additional agents and / or the desired therapeutic and / or preventative effects to be achieved. Generally, the combination of one or more additional agents is intended to be used at levels not exceeding those used individually. In some embodiments, the combined level will be lower than those used individually.

[0123] Some aspects relate to methods for treating IBD (e.g., UC, Crohn's disease), methods comprising determining the abundance of bacterial proteases in a sample obtained from a subject, and delivering a therapeutically effective amount of an inhibitor of said bacterial proteases to the subject's large intestine (e.g., colon) and / or small intestine. In some embodiments, the method of treating IBD comprises administering a therapeutically effective amount of a bacterial protease inhibitor to a subject identified as having a high level of bacterial proteases in the intestine to the subject's large intestine (e.g., colon) and / or small intestine. The bacterial protease can be any bacterial protease described herein. The bacterial protease inhibitor can be any protease inhibitor described herein (e.g., gliptin or a pharmaceutically acceptable salt thereof). The subject can be any subject described herein.

[0124] In some embodiments, determining the abundance of bacterial proteases in a sample obtained from a subject involves obtaining the sample from the subject. In some embodiments, the sample represents a characteristic of the subject's gastrointestinal tract. In some cases, the sample is a fecal sample. In some cases, the sample is a gastrointestinal sample collected from the gastrointestinal tract (e.g., lower gastrointestinal tract, upper gastrointestinal tract). Gastrointestinal samples can be obtained during any suitable procedure, including but not limited to colonoscopy, endoscopy, swab sampling, or brushing a portion of the gastrointestinal tract. In some cases, the sample is a serum sample.

[0125] In some embodiments, determining the abundance of bacterial proteases includes determining the abundance of one or more genes present in a sample from a subject. In some embodiments, determining the abundance of one or more genes present in a sample includes extracting DNA and / or RNA from at least a portion of the sample. Any nucleic acid extraction method known in the art can be used. In some embodiments, determining the abundance of one or more genes present in a sample further includes amplifying at least a portion of the DNA and / or RNA to generate multiple amplicones. Any nucleic acid amplification method known in the art can be used. Non-limiting examples of suitable nucleic acid amplification methods include polymerase chain reaction (PCR) and isothermal amplification methods (e.g., loop-mediated isothermal amplification (LAMP), rolling circle amplification (RCA), nucleic acid sequence-based amplification (NASBA)). In some embodiments, determining the abundance of one or more genes present in a sample includes performing a quantitative nucleic acid amplification method. A non-limiting example of a suitable quantitative nucleic acid amplification method is quantitative PCR (qPCR). In some embodiments, determining the abundance of one or more genes present in a sample further includes sequencing one or more amplicones. Any suitable nucleic acid sequencing method can be used. In some embodiments, the nucleic acid sequencing method is a long-read sequencing method. In some embodiments, the nucleic acid sequencing method is a short-read sequencing method. In some implementations, nucleic acid sequencing methods are next-generation sequencing methods. In some implementations, nucleic acid sequencing methods are performed using Illumina, Pacific Biosciences, Oxford Nanopore, and / or Roche 454 sequencing platforms.

[0126] In some embodiments, determining the abundance of one or more genes present in a sample includes sequencing at least a portion of the 16S ribosomal RNA (rRNA) of the microorganisms present in the sample (e.g., performing 16S rRNA gene amplicon (16S) sequencing). In some cases, performing 16S sequencing includes amplifying at least a portion of one or more regions of the 16S rRNA genome of the microorganisms present in the sample to generate multiple amplicones. Any nucleic acid amplification method (e.g., PCR) can be used. In some embodiments, one or more regions of the 16S rRNA genome contain at least one hypervariable region (e.g., V4, V3-V4, V1-V2). In some cases, performing 16S sequencing also includes sequencing one or more of the multiple amplicones. Any suitable nucleic acid sequencing method can be used.

[0127] In some implementations, determining the abundance of one or more genes present in a sample includes performing shotgun metagenomic sequencing to sequence the metagenomic contents of the sample. In some cases, shotgun metagenomic sequencing methods include extracting DNA from the sample, fragmenting the extracted DNA into DNA fragments, and sequencing said DNA fragments. Any suitable nucleic acid sequencing method can be used. In some cases, the resulting sequences of the DNA fragments can be analyzed to identify microorganisms present in the sample.

[0128] In some embodiments, determining the abundance of one or more genes present in a sample includes determining the level of one or more gene products (e.g., enzymes) in the sample. The level of one or more gene products can be determined using any method known in the art, including but not limited to enzyme-linked immunosorbent assay (ELISA) and other antibody-based assays, as well as proteomics based on liquid chromatography-mass spectrometry (LC-MS) and other protein-based quantitative assays. In some embodiments, determining the abundance of one or more genes present in a sample includes determining the level of one or more molecules (e.g., as substrates or products) that interact directly or indirectly with one or more gene products (e.g., enzymes) in metabolic pathways. The level of one or more molecules (e.g., substrates, products) can be determined using any method known in the art, including but not limited to high-performance liquid chromatography (HPLC), liquid chromatography-mass spectrometry (LC-MS), gas chromatography-mass spectrometry (GC-MS), and fluorescence-based assays.

[0129] According to some implementation methods, the method includes determining that a therapeutically effective amount of a bacterial protease inhibitor should be administered if the abundance of the bacterial protease is above or below a threshold. In some cases, the threshold may be determined based on the level of bacterial protease in one or more healthy individuals (e.g., individuals not diagnosed with inflammatory bowel disease). In some cases, the threshold may be determined by identifying the optimal distinguishing boundary between a first group of individuals diagnosed with inflammatory bowel disease and a second group of healthy individuals.

[0130] Therapeutic amounts of bacterial protease inhibitors may be administered according to any of the methods described herein.

[0131] III. medicine box This disclosure also covers medicine boxes (e.g., medicine packs). The provided medicine boxes may contain the pharmaceutical compositions or compounds described herein and containers (e.g., vials, ampoules, bottles, syringes and / or dispenser packages, or other suitable containers). In some embodiments, the provided medicine box may optionally also include a second container containing pharmaceutical excipients for diluting or suspending the pharmaceutical compositions or compounds described herein. In some embodiments, the pharmaceutical compositions or compounds described herein provided in the first and second containers are combined to form a unit dosage form.

[0132] In one aspect, this document provides a kit comprising: the compound described herein or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, cocrystal, tautomer, stereoisomer, isotopically labeled compound or a prodrug thereof, or a pharmaceutical composition provided herein; and instructions for use of the compound or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, cocrystal, tautomer, stereoisomer, isotopically labeled compound or a prodrug thereof, or the pharmaceutical composition thereof.

[0133] Therefore, in some embodiments, a kit is provided comprising a first container containing the compound or pharmaceutical composition described herein. In some embodiments, the kit can be used to treat a disease (e.g., metabolic disorder) in a subject in need. In some embodiments, the kit can be used to prevent a disease (e.g., inflammatory bowel disease) in a subject in need. In some embodiments, the kit can be used to reduce the risk of a subject in need developing a disease (e.g., inflammatory bowel disease). In some embodiments, the kit can be used to inhibit the activity of a protease in a subject or cell.

[0134] In some embodiments, the pillbox described herein also includes instructions for using the pillbox. The pillbox described herein may also include information required by regulatory agencies such as the U.S. Food and Drug Administration (FDA). In some embodiments, the information included in the pillbox is prescribing information. In some embodiments, the pillbox and instructions are provided for treating a disease (e.g., inflammatory bowel disease) in a subject in need. In some embodiments, the pillbox and instructions are provided for preventing a disease (e.g., inflammatory bowel disease) in a subject in need. In some embodiments, the pillbox and instructions are provided for reducing the risk of a subject in need developing a disease (e.g., inflammatory bowel disease). In some embodiments, the pillbox and instructions are provided for inhibiting the activity of proteases in cells. The pillbox described herein may include one or more additional pharmaceutical agents described herein as a separate composition.

[0135] Example 1 In this embodiment, dipeptidyl peptidase-4 (“DPP-4”) from Bacteroides vulgaris was selected as the therapeutic target.

[0136] A pan-genome comparison of S09 family proteases in Bacteroides was performed. Genes from reference genomes of Bacteroides species were compared with the MEROPS database of proteases. Genes belonging to the S09 protease family were counted and compared in each reference genome, and classified by subclass. S09.13 protease was found to be enriched in Bacteroides vulgaris and Bacteroides davidiana.

[0137] Then, a pan-genomic comparison was performed between Bacteroides S09 B / C family proteases and Porphyromonas gingivalis DPP-4, calculating the phylogenetic distances between each sequence belonging to the S09 classification. It was found that the S09.65 protease is specific to both Bacteroides vulgaris and Bacteroides dauricum. Furthermore, the S09.13 protease was found to be closely related to human Porphyromonas gingivalis DPP-4 (i.e., exhibiting the highest sequence similarity).

[0138] Based on pan-genomic comparisons, the DPP-4 sequence from *Bacteroides vulgaris* selected as a therapeutic target is: MTKKNLFTLVLCLFCFGTTTHAQRIPTLEEAVYGGLIKTEGGSNVNWMKDGERYSKIEKNAEGAYEVTAYKAKDNSKEVLIPANMLLNPQTGKPISVRNFVFSEDNSKVLIYTNTRRVWRYDTRGDYWVLNLKDGKLQQLGKSLPEATLMFAKFSPDASRVAYVSRNNIYVESLVDGKINQLTQDGNNEIVNGTFDWVYEEEFNCRDGFRWSPDGQYIAYWQSDTQGTGWFDIINNVDSIYPKIQRFPYPKAGTANSAVKVGYVSADGGNTTWLALPGDARNHYIPRMEFIPGCNELFIQQMNRAQNTNKVWIAKIGENTPVNIFTDQDAAWLETNDNVRWLKGNKYFTWES ERDGWRHLYRVSRDGKEIKPITQGAFDYIQEVGADMDKGFVYFIASPDNFTQRYLYRARLFGNGEVKRLSPVDQSGQHRYIMSPSGKWAVHTFSNSETPPVIDMVSFPAHKSIRLITDNAKAKEQYKALGLQPKEFVKTRSGELELDAWMIKPVNFDPSKKYPVIIDVYGEPANATVQDVWSGGSLWHQYLANLG YIIVSIENRGANAPRGREWRKCIYGEVGTFASEDQARGIQDLARQYSFIDTARIGITGWSGGGSQTLNSMFRYPDVFHTGIAIAFVADQRLYDTVYQERYMNTPQNNPEGYRKGSPISYAAGLKGNLLLIHGTGDDNVHYQNCEMLVNELVRHGKIFSQISYPMRSHGIYEGEGTSLHLRKTMADYWLKNLPAGGK (SEQ ID NO: 1).

[0139] Example 2 In this embodiment, DPP-4 from Bacteroides vulgaris was used as a therapeutic target for validation.

[0140] Figure 1The graph shows the change in transepithelial electrical resistance (“TEER”) of T84 intestinal cells over time (hours). Intestinal cells containing DPP-4 from *Bacteroides vulgaris* (labeled “DPP-4”) had significantly lower TEER values ​​than intestinal cells without DPP-4 from *Bacteroides vulgaris* (labeled “cell control”), indicating disruption of epithelial barrier integrity. Further investigation revealed that adding a protease inhibitor (1x Roche cOmplete, a mixture of EDTA-free protease inhibitors) to intestinal cells containing DPP-4 from *Bacteroides vulgaris* significantly increased the TEER value, bringing it closer to that of intestinal cells without DPP-4 from *Bacteroides vulgaris*. Therefore… Figure 1 The results indicate that DPP-4 from Bacteroides vulgaris reduces intestinal barrier integrity, and the addition of protease inhibitors mitigates the effects of DPP-4.

[0141] Figure 2 The image shows the percentage of intestinal cell adhesion and invasion in wild-type Bacteroides containing DPP-4 (left) and Bacteroides with DPP-4 removed (right). Removal of DPP-4 was found to prevent Bacteroides from adhering to and invading intestinal cells.

[0142] Example 3 In this embodiment, it was demonstrated that certain gliptin drugs differentially inhibit DPP-4 from Bacteroides vulgaris.

[0143] The effects of six gliptin compounds—sitagliptin, linagliptin, ticagliptin, trogliptin, ocagliptin, and vildagliptin—on the in vitro DPP-4 activity of Bacteroides vulgaris were evaluated. Figure 3 The graph shows the percentage of inhibition as a function of gliptin concentration (µM). Sitagliptin, octagliptin, ticagliptin, and vildagliptin were found to inhibit Bacteroides vulgaris DPP-4 activity in the micromolar concentration range. The IC50 of sitagliptin was 3.17 µM. In contrast, trelgliptin and linagliptin were not found to inhibit Bacteroides vulgaris DPP-4 activity. The structures of sitagliptin, octagliptin, ticagliptin, and vildagliptin are shown in [image / description missing]. Figure 4 The inhibitory effects of two gliptin compounds, saxagliptin and vildagliptin, were further tested in vitro using different orthologs of DPP-4 (two forms encoded in the genome of Bacteroides vulgaris (BVU3876 and BVU1991), an ortholog from Bacteroides polymorpha (BT4193), and human DPP-4). The table demonstrating the IC50 values ​​of vildagliptin and saxagliptin against each ortholog is shown in [the table]. Figure 5In the previous examples, the Bacteroides commonis DPP-4 (BVU 3876) tested showed IC50 values ​​of 5.65 µM for vildagliptin and 3.5 µM for saxagliptin.

[0144] Example 4 It has been demonstrated that rectal administration of the DPP-4 inhibitor sitagliptin showed improved protection against colitis compared with oral administration of sitagliptin.

[0145] Figure 6 This study investigated the disease activity index in 10-week-old male C57BL / 6 mice after administration of 3% sodium dextran sulfate in drinking water and 30 mg / kg sitagliptin daily for 6 days via oral tube feeding or rectal administration. Rectal administration of sitagliptin on day 7 produced a significant improvement in disease activity compared to the oral sitagliptin treatment group and the rectal control group.

[0146] While several embodiments of the invention have been described and illustrated herein, those skilled in the art will readily envision a variety of other means and / or structures for performing the functions and / or obtaining one or more of the results and / or advantages described herein, and such variations and / or modifications are each considered to be within the scope of the invention. More generally, those skilled in the art will readily understand that all parameters, dimensions, materials, and configurations described herein are intended to be exemplary, and actual parameters, dimensions, materials, and / or configurations will depend on one or more specific applications for which the teachings of the invention are applied. Those skilled in the art will recognize or be able to determine many equivalent embodiments of the specific embodiments of the invention described herein using only conventional experimentation. Therefore, it should be understood that the foregoing embodiments are presented by way of example only, and that the invention may be practiced in ways different from the specific descriptions and claims within the scope of the appended claims and their equivalents. The invention relates to each individual feature, system, article, material, and / or method described herein. Furthermore, any combination of two or more such features, systems, articles, materials, and / or methods is included within the scope of the invention if such features, systems, articles, materials, and / or methods are not inconsistent with each other.

[0147] Unless explicitly indicated otherwise, the indefinite articles “a” and “an” used herein in the specification and claims shall be understood as “at least one”.

[0148] As used herein in the specification and claims, the phrase “and / or” should be understood to mean “any one or both” of elements so combined (i.e., elements that coexist in some cases and exist separately in others). Unless expressly indicated otherwise, other elements may be optionally present, whether or not they are related to the explicitly identified elements. Thus, as a non-limiting example, when used in conjunction with open-ended language such as “comprising,” a reference to “A and / or B” may refer to A without B (optionally including elements other than B) in one embodiment; to B without A (optionally including elements other than A) in another embodiment; to both A and B (optionally including other elements) in yet another embodiment; and so on.

[0149] As used herein in the specification and claims, “or” should be understood to have the same meaning as “and / or” as defined above. For example, when separating items in a list, “or” or “and / or” should be interpreted as inclusive, that is, including multiple elements or at least one element in a list of elements, but also including more than one element, as well as optional other items not listed. Only terms that explicitly indicate the opposite meaning, such as “only one of…” or “exact one of…”, or when used in the claims, “consisting of…” refers to including multiple elements or exactly one element in a list of elements. In general, the term “or” as used herein, when preceded by an exclusive term, should be interpreted only to indicate an exclusive choice (i.e., “one or the other, not two”), such as “any one,” “one of…,” “only one of…,” or “exact one of…”. When used in the claims, “consisting substantially of…” should have its usual meaning in the field of patent law.

[0150] As used herein in the specification and claims, the phrase “at least one” when referring to a list of one or more elements should be understood to mean at least one element selected from any one or more elements in the list of elements, but does not necessarily include at least one of each element specifically listed in the list of elements, and does not exclude any combination of elements in the list of elements. This definition also allows for the optional presence of elements other than those expressly identified in the list of elements referred to by the phrase “at least one”, whether related to or unrelated to the expressly identified elements. Thus, as a non-limiting example, “at least one of A and B” (or equivalently, “at least one of A or B”, or equivalently, “at least one of A and / or B”) in one embodiment may refer to at least one A, optionally including more than one A, but without B (and optionally including elements other than B); in another embodiment may refer to at least one B, optionally including more than one B, but without A (and optionally including elements other than A); in yet another embodiment may refer to at least one A, optionally including more than one A, and at least one B, optionally including more than one B (and optionally including other elements); and so on.

[0151] Some implementations can be implemented as methods, and various instances of said methods have been described. Actions performed as part of said method can be ordered in any suitable manner. Therefore, implementations in which actions are performed in a different order than shown can be constructed, and these implementations may include different (e.g., more or fewer) actions, and / or may involve performing some actions simultaneously, even if said actions are shown as being performed sequentially in the implementations specifically described above.

[0152] The use of sequential terms such as "first," "second," and "third" in the claims to modify claim elements does not imply any priority, order, or sequence of one claim element relative to another claim element, or the chronological order of the execution of method actions. Rather, it serves only as a marker to distinguish one claim element with a specific name from another element with the same name (but using sequential terms).

[0153] In the claims and in the above description, all transitional phrases such as “comprising,” “including,” “carrying,” “having,” “containing,” “involving,” “holding,” etc., should be understood as open-ended, meaning including but not limited to. As set forth in Section 2111.03 of the U.S. Patent Examination Procedure Manual, only the transitional phrases “consisting of…” and “consisting substantially of…” should be closed or semi-closed transitional phrases, respectively.

Claims

1. A composition comprising an inhibitor of bacterial protease and a carrier.

2. The composition of claim 1, wherein the carrier comprises a polymer that is not absorbed in the gastrointestinal tract.

3. The composition of claim 1 or 2, wherein the carrier comprises polyvinylpyrrolidone.

4. The composition of any one of claims 1-3, wherein the inhibitor of the bacterial protease is loaded into the carrier.

5. The composition according to any one of claims 1-4, wherein the inhibitor of the bacterial protease is a gliptin or a pharmaceutically acceptable salt thereof.

6. The composition of any one of claims 1-5, wherein the composition further comprises an inhibitor that promotes the targeted delivery of the bacterial protease and the carrier to the intestinal site.

7. The composition of any one of claims 1-6, wherein the agent comprises a first material dissolved at a pH between about 6.0 and about 7.

6.

8. The composition of claim 7, wherein the first material is dissolved at pH 7.

5.

9. The composition of any one of claims 1-8, wherein the agent comprises a second material that is readily degraded by microorganisms.

10. The composition of claim 9, wherein the second material is readily degraded by microorganisms present in the large intestine of the subject.

11. The composition of claim 10, wherein the second material is readily degraded by microorganisms present in the colon of the subject.

12. The composition of any one of claims 7-11, wherein the first material dissolves at a pH between about pH 6.0 and about pH 7.6, and the second material is readily degraded by microorganisms present in the large intestine of the subject.

13. The composition of any one of claims 6-12, wherein the agent comprises one or more layers.

14. The composition of claim 13, wherein the first material of the agent is present in the first layer.

15. The composition of claim 13 or 14, wherein the second material of the agent is present in the second layer.

16. The composition of any one of claims 1-15, wherein the bacterial protease cleaves GLP-1.

17. The composition of any one of claims 1-15, wherein the bacterial protease cleaves GLP-2.

18. The composition of any one of claims 1-17, wherein the bacterial protease is a serine protease.

19. The composition of any one of claims 1-18, wherein the bacterial protease is dipeptidyl peptidase-4 (DPP-4).

20. The composition of claim 19, wherein the bacterial protease comprises DPP-4 expressed by Bacteroides commonis and / or Bacteroides dysplasia.

21. The composition of any one of claims 5-20, wherein the gliptin includes sitagliptin, ticagliptin, ocagliptin, vildagliptin, saxagliptin, alogliptin, linagliptin, giglitazone, alagliptin, treagliptin, iverogliptin, gogliptin, dugliptin, repagliptin, and pulugliptin or derivatives or combinations thereof.

22. A pharmaceutical dosage form comprising: The core contains inhibitors of bacterial proteases; and A controlled-release coating applied to the outer surface of the core, wherein the controlled-release coating is configured to release the inhibitor of the bacterial protease in the large and / or small intestine of a subject who has been administered the drug formulation.

23. The pharmaceutical dosage form of claim 22, wherein the bacterial protease cleaves GLP-1.

24. The pharmaceutical dosage form of claim 22, wherein the bacterial protease cleaves GLP-2.

25. The pharmaceutical dosage form according to any one of claims 22-24, wherein the bacterial protease is a serine protease.

26. The pharmaceutical dosage form according to any one of claims 22-25, wherein the bacterial protease is dipeptidyl peptidase-4 (DPP-4).

27. The pharmaceutical dosage form of any one of claims 22-26, wherein the inhibitor of the bacterial protease is a gliptin or a pharmaceutically acceptable salt thereof.

28. The pharmaceutical dosage form of any one of claims 22-27, wherein the bacterial protease comprises DPP-4 expressed by Bacteroides vulgaris and / or Bacteroides dysporidis.

29. The pharmaceutical dosage form of claim 27 or 28, wherein the gliptin class comprises sitagliptin, ticagliptin, octagliptin, vildagliptin, saxagliptin, alogliptin, linagliptin, giglitazone, alagliptin, treagliptin, evogliptin, gogliptin, dugliptin, repagliptin, and pulugliptin or derivatives or combinations thereof.

30. The pharmaceutical dosage form of any one of claims 22-29, wherein the controlled-release coating is configured to release the inhibitor of the protease in the large intestine.

31. The pharmaceutical dosage form of claim 30, wherein the controlled-release coating is configured to release the inhibitor of the protease in the colon.

32. The pharmaceutical dosage form of any one of claims 22-31, wherein the controlled-release coating is configured to release the inhibitor of the protease in the small intestine.

33. The pharmaceutical dosage form according to any one of claims 22-32, wherein the controlled-release coating comprises one or more pH-sensitive materials.

34. The pharmaceutical dosage form according to any one of claims 22-33, wherein the controlled-release coating comprises one or more microbial-sensitive materials.

35. The pharmaceutical dosage form of any one of claims 22-34, wherein the core comprises an amount of the inhibitor of the bacterial protease sufficient to alleviate one or more symptoms of inflammatory bowel disease.

36. The pharmaceutical dosage form of claim 35, wherein the inflammatory bowel disease includes ulcerative colitis.

37. The pharmaceutical dosage form of any one of claims 35, wherein the inflammatory bowel disease includes Crohn's disease.

38. The pharmaceutical dosage form of any one of claims 22-37, wherein the core comprises the inhibitor of the bacterial protease in an amount sufficient to promote wound healing in the large intestine and / or small intestine of the subject.

39. The pharmaceutical dosage form according to any one of claims 22-38, wherein the core is in the form of a tablet, a capsule, or a sac tablet.

40. A method for treating inflammatory bowel disease, the method comprising: A therapeutically effective amount of the bacterial protease inhibitor is delivered to the subject’s large and / or small intestine.

41. The method of claim 40, wherein the inflammatory bowel disease includes ulcerative colitis.

42. The method of claim 40, wherein the inflammatory bowel disease includes Crohn's disease.

43. The method of any one of claims 40-42, wherein the bacterial protease cleaves GLP-1.

44. The method of any one of claims 40-42, wherein the bacterial protease cleaves GLP-2.

45. The method of any one of claims 40-44, wherein the bacterial protease is a serine protease.

46. ​​The method of any one of claims 40-45, wherein the bacterial protease is dipeptidyl peptidase-4 (DPP-4).

47. The method of claim 46, wherein the bacterial protease comprises DPP-4 expressed by Bacteroides commonis and / or Bacteroides multifiliis.

48. The method of any one of claims 40-47, wherein the inhibitor of the bacterial protease comprises a gliptin or a pharmaceutically acceptable salt thereof.

49. The method of claim 48, wherein the gliptin class comprises sitagliptin, ticagliptin, ocagliptin, vildagliptin, saxagliptin, alogliptin, linagliptin, giglitazone, alagliptin, treagliptin, evogliptin, gogliptin, dugliptin, repagliptin, and pulugliptin or derivatives or combinations thereof.

50. The method of any one of claims 40-49, wherein delivering the therapeutically effective amount of the inhibitor of the bacterial protease comprises administering a composition comprising the inhibitor of the bacterial protease.

51. The method of claim 50, wherein delivering the therapeutically effective amount of the inhibitor of the bacterial protease comprises oral administration of the composition comprising the inhibitor of the bacterial protease.

52. The method of claim 50, wherein delivering the therapeutically effective amount of the inhibitor of the bacterial protease comprises rectal administration of the composition comprising the inhibitor of the bacterial protease.

53. The method of any one of claims 40-52, wherein the composition comprises a carrier.

54. The method of claim 53, wherein the carrier comprises a polymer.

55. The method of claim 54, wherein the polymer is not absorbed in the gastrointestinal tract.

56. The method of claim 54 or 55, wherein the polymer comprises polyvinylpyrrolidone.

57. The method of any one of claims 53-56, wherein a therapeutically effective amount of the inhibitor of the bacterial protease is loaded into the carrier.

58. The method of any one of claims 53-57, wherein the composition further comprises a first agent that promotes the targeted delivery of the inhibitor and carrier of the bacterial protease to the intestinal site.

59. The method of claim 58, wherein the first agent comprises a first material dissolved at a pH between about 6.5 and about 7.

6.

60. The method of claim 59, wherein the first material is dissolved at a pH of about 7.

5.

61. The method of any one of claims 58-60, wherein the composition further comprises a second agent comprising a second material readily degradable by microorganisms.

62. The method of claim 61, wherein the second material is readily degraded by microorganisms present in the large intestine of the subject.

63. The method of any one of claims 59-62, wherein the first material dissolves at a pH between about pH 6.5 and about pH 7.6, and the second material is readily degraded by microorganisms present in the large intestine of the subject.

64. The method of claim 58, wherein the first agent comprises a first material dissolved at a pH between about 5.5 and about 7.

1.

65. The method of claim 64, wherein the first material is dissolved at a pH of about 6.

0.

66. The method of claim 64 or 65, wherein the composition further comprises a second agent comprising a second material readily degradable by microorganisms.

67. The method of claim 66, wherein the second material is readily degraded by microorganisms present in the small intestine of the subject.

68. The method of any one of claims 64-67, wherein the first material dissolves at a pH between about pH 5.5 and about pH 7.1, and the second material is readily degraded by microorganisms present in the small intestine of the subject.

69. The method of any one of claims 53-68, wherein delivering the therapeutically effective amount of the inhibitor of the bacterial protease comprises oral administration of a pharmaceutical composition comprising the inhibitor of the bacterial protease.

70. The method of any one of claims 53-68, wherein delivering the therapeutically effective amount of the inhibitor of the bacterial protease comprises rectal administration of a pharmaceutical composition comprising the inhibitor of the bacterial protease.

71. The method of claim 69 or 70, wherein the pharmaceutical composition comprises: The core of the inhibitor comprises the therapeutically effective amount of the bacterial protease; and A controlled-release coating applied to the outer surface of the core, wherein the controlled-release coating is configured to release the inhibitor of the bacterial protease in the large intestine and / or small intestine of the subject.

72. The method of claim 71, wherein the controlled-release coating comprises one or more pH-sensitive materials.

73. The method of claim 71 or 72, wherein the controlled-release coating comprises one or more microbial-sensitive materials.

74. The method of any one of claims 71-73, wherein the core is in the form of a tablet, a capsule, or a sac.

75. The method of any one of claims 70-73, wherein delivering the therapeutically effective amount of the inhibitor of the bacterial protease comprises oral administration of a pharmaceutical composition comprising the inhibitor of the bacterial protease.

76. The method of any one of claims 70-73, wherein delivering the therapeutically effective amount of the inhibitor of the bacterial protease comprises rectal administration of a pharmaceutical composition comprising the inhibitor of the bacterial protease.

77. The method of any one of claims 40-76, wherein the subject is a human subject.

78. The method of any one of claims 69-77, wherein the oral administration of the pharmaceutical composition comprising the inhibitor of the bacterial protease comprises delivering the therapeutically effective amount of the inhibitor of the bacterial protease to the large intestine of the subject.

79. The method of claim 78, wherein delivering the therapeutically effective amount of the inhibitor of the bacterial protease to the large intestine of the subject comprises delivering the therapeutically effective amount of the inhibitor of the bacterial protease to the colon of the subject.

80. The method of any one of claims 69-76, wherein the oral administration of the pharmaceutical composition comprising the inhibitor of the bacterial protease comprises delivering the therapeutically effective amount of the inhibitor of the bacterial protease into the small intestine of the subject.

81. The method of any one of claims 40-80, wherein the therapeutically effective amount is an amount sufficient to alleviate one or more symptoms of inflammatory bowel disease.

82. The method of claim 81, wherein the inflammatory bowel disease includes ulcerative colitis.

83. The method of claim 81, wherein inflammatory bowel disease includes Crohn's disease.

84. A method for treating inflammatory bowel disease, the method comprising: The abundance of bacterial proteases in samples obtained from subjects was determined; as well as A therapeutically effective amount of the bacterial protease inhibitor is delivered to the subject’s large and / or small intestine, wherein the inhibitor comprises a gliptin or a pharmaceutically acceptable salt thereof.

85. The method of claim 84, wherein the inflammatory bowel disease includes ulcerative colitis.

86. The method of claim 84, wherein the inflammatory bowel disease includes Crohn's disease.

87. The method of any one of claims 84-86, wherein the sample is a fecal sample.

88. The method of any one of claims 84-87, wherein the bacterial protease cleaves GLP-1.

89. The method of any one of claims 84-87, wherein the bacterial protease cleaves GLP-2.

90. The method of any one of claims 84-89, wherein the bacterial protease is a bacterial serine protease.

91. The method of any one of claims 84-90, wherein the bacterial protease is bacterial dipeptidyl peptidase-4 (DPP-4).

92. The method of claim 91, wherein the bacterial DPP-4 comprises DPP-4 expressed by Bacteroides commonis and / or Bacteroides multifiliis.

93. The method of any one of claims 84-92, wherein the gliptin includes sitagliptin, ticagliptin, octagliptin, saxagliptin, and / or vildagliptin.

94. The method of any one of claims 84-93, wherein delivering the therapeutically effective amount of the inhibitor of the bacterial protease to the large intestine and / or small intestine of the subject comprises delivering the therapeutically effective amount of the inhibitor of the bacterial protease to the large intestine of the subject.

95. The method of claim 94, wherein delivering the therapeutically effective amount of the inhibitor of the bacterial protease to the large intestine of the subject comprises delivering the therapeutically effective amount of the inhibitor of the bacterial protease to the colon of the subject.

96. The method of any one of claims 84-93, wherein delivering the therapeutically effective amount of the inhibitor of the bacterial protease to the large intestine and / or small intestine of the subject comprises delivering the therapeutically effective amount of the inhibitor of the bacterial protease to the small intestine of the subject.

97. The method of any one of claims 84-96, wherein the therapeutically effective amount is an amount sufficient to alleviate one or more symptoms of ulcerative colitis.

98. The method of any one of claims 84-96, wherein the therapeutically effective amount is an amount sufficient to alleviate one or more symptoms of Crohn's disease.

99. A method for treating inflammatory bowel disease in a subject identified as having a high level of bacterial proteases in the intestine, the method comprising delivering a therapeutically effective amount of an inhibitor of the bacterial proteases to the large and / or small intestine of the subject, wherein the inhibitor comprises a gliptin or a pharmaceutically acceptable salt thereof.

100. The method of claim 99, wherein the inflammatory bowel disease includes ulcerative colitis.

101. The method of claim 99, wherein the inflammatory bowel disease includes Crohn's disease.

102. The method of any one of claims 99-101, wherein the bacterial protease cleaves GLP-1.

103. The method of any one of claims 99-101, wherein the bacterial protease cleaves GLP-2.

104. The method of any one of claims 99-103, wherein the bacterial protease is a bacterial serine protease.

105. The method of any one of claims 99-104, wherein the bacterial protease is bacterial dipeptidyl peptidase-4 (DPP-4).

106. The method of claim 105, wherein the bacterial DPP-4 comprises DPP-4 expressed by Bacteroides commonis and / or Bacteroides multifiliis.

107. The method of any one of claims 99-106, wherein the gliptin includes sitagliptin, ticagliptin, octagliptin, saxagliptin, and / or vildagliptin.

108. The method of any one of claims 99-107, wherein delivering the therapeutically effective amount of the inhibitor of the bacterial protease to the large intestine and / or small intestine of the subject comprises delivering the therapeutically effective amount of the inhibitor of the bacterial protease to the large intestine of the subject.

109. The method of claim 108, wherein delivering the therapeutically effective amount of the inhibitor of the bacterial protease to the large intestine of the subject comprises delivering the therapeutically effective amount of the inhibitor of the bacterial protease to the colon of the subject.

110. The method of any one of claims 99-107, wherein delivering the therapeutically effective amount of the inhibitor of the bacterial protease to the large intestine and / or small intestine of the subject comprises delivering the therapeutically effective amount of the inhibitor of the bacterial protease to the small intestine of the subject.

111. The method of any one of claims 99-110, wherein the therapeutically effective amount is an amount sufficient to alleviate one or more symptoms of ulcerative colitis.

112. The method of any one of claims 99-110, wherein the therapeutically effective amount is an amount sufficient to alleviate one or more symptoms of Crohn's disease.

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