Compositions and methods for treating inflammatory bowel disease

Abstract

Aspects of the disclosure relate to compositions and methods for treating one or more inflammatory bowel diseases ("IBDs"), 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 exterior 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 of a subject to whom the pharmaceutical dosage form is administered. 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., a bacterial protease) to the large intestine (e.g., colon) and / or small intestine of a subject.

Description

[0001] COMPOSITIONS AND METHODS FOR TREATING INFLAMMATORY BOWEL

[0002] DISEASE

[0003] RELATED APPLICATIONS

[0004] This application claims the benefit under 35 U.S.C. § 119(e) to U.S. Provisional Application No. 63 / 510,884, filed June 28, 2023, entitled “COMPOSITIONS AND METHODS FOR TREATING ULCERATIVE COLITIS” and U.S. Provisional Application No. 63 / 510,885, filed June 28, 2023, entitled “COMPOSITIONS AND METHODS FOR TREATING INFLAMMATORY BOWEL DISEASE,” the entire contents of each of which are incorporated herein by reference.

[0005] BACKGROUND

[0006] An inflammatory bowel disease (“IBD”) is a disease that is characterized by chronic inflammation of the gastrointestinal (“GI”) tract. One type of IBD is ulcerative colitis (“UC”), which causes ulcers on the inner 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 GI tract. IBDs can cause symptoms such as diarrhea, abdominal pain, rectal bleeding, weight loss, anemia, and fatigue, and can be associated with decreased quality of life. In some cases, IBDs can lead to complications requiring hospitalization and / or surgery.

[0007] Millions of individuals around the world are affected by IBDs every year. In 2017, it was found that there were more than 6.8 million cases of IBD globally, with the highest prevalence occurring in the United States. There therefore is a need to continue developing safe, effective treatments for IBDs.

[0008] SUMMARY OF INVENTION

[0009] The present disclosure is related to compositions and methods for treating inflammatory bowel disease (e.g., ulcerative colitis, Crohn’s disease). The subject matter of the present invention involves, in some cases, interrelated products, alternative solutions to a particular problem, and / or a plurality of different uses of one or more systems and / or articles.

[0010] In some embodiments, a composition comprising an inhibitor of a protease is provided. In some embodiments, a composition comprises an inhibitor (e.g., one or more inhibitors) of a bacterial protease. In some embodiments, a composition comprises an inhibitor of a bacterial protease and an excipient. In some embodiments, provided are compositions comprising two or more protease inhibitors (e.g., 2, 3, 4, 5, or 5-10 for example). In some embodiments, provided are compositions comprising two or more bacterial protease inhibitors (e.g., 2, 3, 4, 5, or 5-10 for example).

[0011] In some aspects, a pharmaceutical dosage form is described. In some embodiments, the pharmaceutical dosage form comprises a core comprising an inhibitor of a protease. In certain embodiments, the inhibitor of the protease comprises a gliptin or a pharmaceutically acceptable salt thereof.

[0012] In some aspects, provided are compositions comprising two or more gliptins (e.g., 2, 3, 4, 5, or 5-10 for example). In some aspects, provided are pharmaceutical dosage forms comprising two or more gliptins (e.g., 2, 3, 4, 5, or 5-10 for example).

[0013] In some embodiments, the pharmaceutical dosage form comprises a controlled release coating applied to an exterior surface of the core. In certain embodiments, the controlled release coating is configured to release the inhibitor of the protease in a large intestine and / or small intestine of a subject to whom the pharmaceutical dosage form is administered.

[0014] In some aspects, a method of treating an inflammatory bowel disease is described. In some embodiments, the method comprises delivering a therapeutically effective amount of an inhibitor of a protease to a large intestine and / or small intestine of a subject. In certain embodiments, the inhibitor of the protease comprises a gliptin or a pharmaceutically acceptable salt thereof.

[0015] In some aspects, a method of treating an inflammatory bowel disease is described. In some embodiments, the method comprises determining an abundance of a bacterial protease in a sample obtained from a subject. In some embodiments, the method comprises delivering a therapeutically effective amount of an inhibitor of the bacterial protease to a large intestine and / or small intestine of the subject. In certain embodiments, the inhibitor of the protease comprises a gliptin or a pharmaceutically acceptable salt thereof.

[0016] Other advantages and novel features of the present invention will become apparent from the following detailed description of various non-limiting embodiments of the invention when considered in conjunction with the accompanying figures. In cases where the present specification and a document incorporated by reference include conflicting and / or inconsistent disclosure, the present specification shall control.

[0017] BRIEF DESCRIPTION OF THE DRAWINGS Non-limiting embodiments of the present invention will be described by way of example with reference to the accompanying figures, which are schematic and are not intended to be drawn to scale. In the figures, each identical or nearly identical component illustrated is typically represented by a single numeral. For purposes of clarity, not every component is labeled in every figure, nor is every component of each embodiment of the invention shown where illustration is not necessary to allow those of ordinary skill in the art to understand the invention. In the figures:

[0018] FIG. 1 shows, according to some embodiments, recombinant protease impact on intestinal barrier integrity. FIG. 1 shows a plot of trans-epithelial electrical resistance (“TEER”) (Q) as a function of time (hours) for T84 intestinal cells without dipeptidyl peptidase-4 (“DPP- 4”) (labeled “Cell control”), intestinal cells without DPP-4 and with a protease inhibitor (labeled “Cell control + Protease inhibitor”), intestinal cells with DPP-4 (labeled “DPP-4”), and intestinal cells with DPP-4 and a protease inhibitor (labeled “DPP-4 + Protease inhibitor”). The protease inhibitor was lx Roche cOmplete™ EDTA-Free Protease Inhibitor Cocktail.

[0019] FIG. 2 shows, according to some embodiments, a chart of percent adherence and invasion of intestinal cells for wild-type B. vulgatus with DPP-4 (left) and B. vulgatus with DPP- 4 genetically removed (right).

[0020] FIG. 3 shows, according to some embodiments, a plot of percent inhibition of B. vulgatus DPP-4 for six gliptins: sitagliptin, linagliptin, teneligliptin, trelagliptin, omarigliptin, and vildagliptin.

[0021] FIG. 4 shows, according to some embodiments, chemical structures for sitagliptin, vildagliptin, omarigliptin, and teneligliptin.

[0022] FIG. 5 shows, according to some embodiments, the inhibitory effect of vildagliptin and saxagliptin on different orthologs of DPP-4, two forms encoded in the B. vulgatus genome (BVU3876 and BVU1991), an ortholog from Bacteroides thetaiotaomicron (BT4193) and human DPP-4.

[0023] FIG. 6 shows, according to some embodiments, a plot of disease activity index for sitagliptin administered orally or intrarectal.

[0024] DETAILED DESCRIPTION

[0025] Aspects of the disclosure relate to compositions and methods for treating one or more inflammatory bowel diseases (“IBDs”), 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 exterior 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 whom the pharmaceutical dosage form is administered. 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., a bacterial protease) to the large intestine (e.g., colon) and / or small intestine (e.g., distal ileum) of a subject.

[0026] The term “gliptin” generally refers to a class of compounds that inhibit human dipeptidyl peptidase-4 (“DPP-4” or “DPP-IV”), an enzyme that degrades a wide range of substrates, including glucagon-like peptide- 1 (“GLP-1”) and glucagon-like peptide-2 (“GLP-2”). GLP-1 and GLP-2 are hormones that are secreted by gut endocrine cells and perform a variety of functions. For example, GLP-2 has numerous cytoprotective, reparative, and energy-retentive functions, including, but not limited to, increasing the barrier function of the gut epithelium, regulating gastric motility and gastric acid secretion, stimulating crypt cell proliferation, and inhibiting apoptosis in the enterocyte and crypt compartments. GLP-1 also performs a variety of functions, including but not limited to, promoting insulin secretion and inhibiting gastric emptying, acid secretion, and motility. A number of gliptins, including sitagliptin, saxagliptin, linagliptin, and alogliptin, have been approved by the U.S. Food and Drug Administration (“FDA”) for oral administration for treatment of type 2 diabetes mellitus.

[0027] It has been shown that there are 5 major binding subsites within DPP-4, S2 extensive subsite, SI subsite, S2 subsite, SI’ subsite, and S2’ subsite, which are targets for gliptin drug development (Mathur et al. Molecules, 2023, 28, 5860). Each subsite plays a different role in the inhibitory activity of binding molecules, specifically, occupation of the SI and S2 subsites is mandatory for inhibition, and further interactions with SI’, S2’ and S2 extensive subsite, increase potency. Therefore, in some embodiments, the gliptin of the present disclosure interacts or associates with the SI and S2 subsites of DPP-4. In certain embodiments, the gliptin of the present disclosure interacts or associates with the SI, S2 subsites, and S2 extensive subsites of DPP-4. In certain embodiments, the gliptin of the present disclosure interacts or associates with the SI, S2 subsites, and S2’ subsite of DPP-4. In certain embodiments, the gliptin of the present disclosure interacts or associates with the SI, S2 subsites, and SI’ subsite of DPP-4. In certain embodiments, the gliptin of the present disclosure interacts or associates with the SI, S2 subsites, and the SI’ and S2’ subsites of DPP-4. In certain embodiments, the gliptin of the present disclosure interacts or associates with the SI, S2 subsites, the S2 extensive subsite and the Sl’and S2’ subsites of DPP-4.

[0028] Examples of gliptins include but are not limited to sitagliptin, teneligliptin, omarigliptin, vildagliptin, saxagliptin, alogliptin, lingagliptin, gemigliptin, anagliptin, trelagliptin, evogliptin, gosogliptin, dutogliptin, retagliptin, and prusogliptin, or a derivative or combination thereof.

[0029] Surprisingly, the inventors of the present disclosure have found that administration of compositions comprising one or more gliptins or pharmaceutically acceptable salts thereof that inhibit a protease (e.g., a bacterial protease, such as bacterial DPP-4) may promote treatment and / or prevention of an IBD (e.g., UC, Crohn’s disease). In some cases, overproduction of certain proteases by certain microbial organisms in the gut microbiome may be associated with increased IBD activity. For example, 40% of clinically active UC patients have been found to have an overabundance of certain proteases expressed by certain bacteria in the gut microbiome. A significant percentage of those patients exhibited persistent disease activity despite receiving conventional medical therapy. As described herein, the inventors have recognized and appreciated that administration of one or more protease inhibitors (e.g., gliptins or pharmaceutically acceptable salts thereof) to a subject diagnosed with, or at risk of developing, an IBD (e.g., UC, Crohn’s disease) may advantageously prevent, alleviate, or arrest one or more symptoms of IBD in the subject.

[0030] DEFINITIONS

[0031] The term “inhibition,” “inhibiting,” “inhibit,” or “inhibitor” refer to the ability of a compound to reduce, slow, halt or prevent activity of a particular biological process (e.g., protease activity (e.g., bacterial DPP-4)) in a cell relative to a control. As used herein the term “inhibit” or “inhibition” in the context of enzymes, for example, in the context of bacterial protease (e.g., DPP-4), refers to a reduction in the activity of the enzyme. In some embodiments, the term refers to a reduction of the level of enzyme activity, e.g., (DPP-4) activity, to a level that is statistically significantly lower than an initial level, which may, for example, be a baseline level of enzyme activity. In some embodiments, the term refers to a reduction of the level of enzyme activity, (e.g., DPP-4, bacterial DPP-4) activity, to a level that is 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 an initial level, which may, for example, be a baseline level of enzyme activity. In certain embodiments, the inhibitor is a gliptin.

[0032] The term “small molecule” refers to molecules, whether naturally-occurring or artificially created (e.g., via chemical synthesis) that have a relatively low molecular weight. Typically, a small molecule is an organic compound (e.g.., it contains carbon). The small molecule may contain multiple carbon-carbon bonds, stereocenters, and other functional groups (e.g., amines, hydroxyl, carbonyls, and heterocyclic rings, etc.). In certain embodiments, the molecular weight of a 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 certain embodiments, the molecular weight of a 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 more than about 500 g / mol) are also possible. In certain 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 Code of Federal Regulations (C.F.R.)). The small molecule may also be complexed with one or more metal atoms and / or metal ions. Preferred small molecules are biologically active in that they produce a biological effect (e.g., inhibit a protease) in a microbial organism (e.g., bacteria) of an intestinal microbiome, preferably bacteria of a species of Bacteroides, more preferably a bacteria of B. vulgatus and / or in animals, preferably mammals, more preferably humans. Small molecules include, but are not limited to, radionuclides, imaging agents, and pharmaceutically active ingredients or agents (e.g., bacterial protease inhibitors, gliptins). In certain embodiments, the small molecule is a drug. Preferably, though not necessarily, the drug is one that has already been deemed safe and effective for use in humans or animals by the appropriate governmental agency or regulatory body. For example, drugs approved for human use are listed by the FDA under 21 C.F.R. §§ 330.5, 331 through 361, and 440 through 460, incorporated herein by reference; drugs for veterinary use are listed by the FDA under 21 C.F.R. §§ 500 through 589, incorporated herein by reference. All listed drugs are considered acceptable for use in accordance with the present disclosure.

[0033] Definitions of specific functional groups and chemical terms are described in more detail below. The chemical elements are identified in accordance with the Periodic Table of the Elements, CAS version, Handbook of Chemistry and Physics, 75thEd., inside cover, and specific functional groups are generally defined as described therein. Additionally, general principles of organic chemistry, as well as specific functional moieties and reactivity, are described in Thomas Sorrell, Organic Chemistry, University Science Books, Sausalito, 1999;Michael B. Smith, March’ s Advanced Organic Chemistry, 7thEdition, 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, 3rdEdition, Cambridge University Press, Cambridge, 1987.

[0034] Compounds described herein can comprise one or more asymmetric centers, and thus can exist in various stereoisomeric forms, e.g., enantiomers and / or diastereomers. For example, the compounds described herein can be in the form of an individual enantiomer, diastereomer or geometric isomer, or can be in the form of a mixture of stereoisomers, including racemic mixtures and mixtures enriched in one or more stereoisomer. Isomers can be isolated from mixtures by methods known to those skilled in the art, including chiral high pressure liquid chromatography (HPLC) and the formation and crystallization of chiral salts; or preferred isomers can be prepared by asymmetric syntheses. See, for example, Jacques et al., Enantiomers, Racemates and Resolutions (Wiley Interscience, New York, 1981); Wilen et al., Tetrahedron 33:2725 (1977); Eliel, E.L. Stereochemistry of Carbon Compounds (McGraw-Hill, NY, 1962); and Wilen, S.H., Tables of Resolving Agents and Optical Resolutions p. 268 (E.L. Eliel, Ed., Univ, of Notre Dame Press, Notre Dame, IN 1972). The present disclosure additionally encompasses compounds as individual isomers substantially free of other isomers, and alternatively, as mixtures of various isomers.

[0035] In a formula, the bond is a single bond, the dashed line — is a single bond or absent, and the bond = or is a single or double bond.

[0036] When a range of values (“range”) is listed, it encompasses each value and sub-range within the range. A range is inclusive of the values at the two ends of the range unless otherwise provided. For example “Ci-6 alkyl” encompasses, Ci, C2, C3, C4, C5, Ce, C1-6, C1-5, CM, C1-3, C1-2, C2-6, C2-5, C2-4, C2-3, C3-6, C3-5, C3 , C4-6, C4-5, and C5-6 alkyl. The term “aliphatic” refers to alkyl, alkenyl, alkynyl, and carbocyclic groups. Likewise, the term “heteroaliphatic” refers to heteroalkyl, heteroalkenyl, heteroalkynyl, and heterocyclic groups.

[0037] The term “alkyl” refers to a radical of a straight-chain or branched saturated hydrocarbon group having from 1 to 20 carbon atoms (“C1-20 alkyl”). Unless otherwise specified, each instance of an alkyl group is independently unsubstituted (an “unsubstituted alkyl”) or substituted (a “substituted alkyl”) with one or more substituents (e.g., halogen, such as F).

[0038] The term “haloalkyl” is a substituted alkyl group, wherein one or more of the hydrogen atoms are independently replaced by a halogen, e.g., fluoro, bromo, chloro, or iodo. “Perhaloalkyl” is a subset of haloalkyl, and refers to an alkyl group wherein all of the hydrogen atoms are independently replaced by a halogen, e.g., fluoro, bromo, chloro, or iodo. In some embodiments, the haloalkyl moiety has 1 to 20 carbon atoms (“C1-20 haloalkyl”). In some embodiments, all of the haloalkyl hydrogen atoms are independently replaced with fluoro to provide a “perfluoroalkyl” group. In some embodiments, all of the haloalkyl hydrogen atoms are independently replaced with chloro to provide a “perchloroalkyl” group.

[0039] The term “heteroalkyl” refers to an alkyl group, which further includes at least one heteroatom (e.g., 1, 2, 3, or 4 heteroatoms) selected from oxygen, nitrogen, or sulfur within (e.g., inserted between adjacent carbon atoms of) and / or placed at one or more terminal position(s) of the parent chain. In certain embodiments, a heteroalkyl group refers to a saturated group having from 1 to 20 carbon atoms and 1 or more heteroatoms within the parent chain (“heteroCi-20 alkyl”).

[0040] The term “alkenyl” refers to a radical of a straight-chain or branched hydrocarbon group having from 1 to 20 carbon atoms and one or more carbon-carbon double bonds (e.g., 1, 2, 3, or 4 double bonds).

[0041] The term “heteroalkenyl” refers to an alkenyl group, which further includes at least one heteroatom (e.g., 1, 2, 3, or 4 heteroatoms) selected from oxygen, nitrogen, or sulfur within (e.g., inserted between adjacent carbon atoms of) and / or placed at one or more terminal position(s) of the parent chain. In certain embodiments, a heteroalkenyl group refers to a group having from 1 to 20 carbon atoms, at least one double bond, and 1 or more heteroatoms within the parent chain (“heteroCi-20 alkenyl”).

[0042] The term “carbocyclyl” or “carbocyclic” refers to a radical of a non-aromatic cyclic hydrocarbon group having from 3 to 14 ring carbon atoms (“C3-14 carbocyclyl”) and zero heteroatoms in the non-aromatic ring system. The term “heterocyclyl” or “heterocyclic” refers to a radical of a 3- to 14-membered non-aromatic ring system having ring carbon atoms and 1 to 4 ring heteroatoms, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur (“3-14 membered heterocyclyl”). In heterocyclyl groups that contain one or more nitrogen atoms, the point of attachment can be a carbon or nitrogen atom, as valency permits. A heterocyclyl group can either be monocyclic (“monocyclic heterocyclyl”) or polycyclic (e.g., a fused, bridged or spiro ring system such as a bicyclic system (“bicyclic heterocyclyl”) or tricyclic system (“tricyclic heterocyclyl”)), and can be saturated or can contain one or more carbon-carbon double or triple bonds. Heterocyclyl polycyclic ring systems can include one or more heteroatoms in one or both rings. “Heterocyclyl” also includes ring systems wherein the heterocyclyl ring, as defined above, is fused with one or more carbocyclyl groups wherein the point of attachment is either on the carbocyclyl or heterocyclyl ring, or ring systems wherein the heterocyclyl ring, as defined above, is fused with one or more aryl or heteroaryl groups, wherein the point of attachment is on the heterocyclyl ring, and in such instances, the number of ring members continue to designate the number of ring members in the heterocyclyl ring system. Unless otherwise specified, each instance of heterocyclyl is independently unsubstituted (an “unsubstituted heterocyclyl”) or substituted (a “substituted heterocyclyl”) with one or more substituents.

[0043] In some embodiments, a heterocyclyl group is a 5-10 membered non-aromatic ring system having ring carbon atoms and 1-4 ring heteroatoms, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur (“5-10 membered heterocyclyl”). In some embodiments, a heterocyclyl group is a 5-6 membered non-aromatic ring system having ring carbon atoms and 1-4 ring heteroatoms, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur (“5-6 membered heterocyclyl”).

[0044] The term “aryl” refers to a radical of a monocyclic or polycyclic (e.g., bicyclic or tricyclic) 4n+2 aromatic ring system (e.g., having 6, 10, or 14 7t electrons shared in a cyclic array) having 6-14 ring carbon atoms and zero heteroatoms provided in the aromatic ring system (“Ce-14 aryl”). In some embodiments, an aryl group has 6 ring carbon atoms (“Ce aryl”; e.g., phenyl).

[0045] “Aralkyl” is a subset of “alkyl” and refers to an alkyl group substituted by an aryl group, wherein the point of attachment is on the alkyl moiety. The term “heteroaryl” refers to a radical of a 5-14 membered monocyclic or polycyclic (e.g., bicyclic, tricyclic) 4n+2 aromatic ring system (e.g., having 6, 10, or 14 7t electrons shared in a cyclic array) having ring carbon atoms and 1-4 ring heteroatoms provided in the aromatic ring system, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur (“5-14 membered heteroaryl”). In heteroaryl groups that contain one or more nitrogen atoms, the point of attachment can be a carbon or nitrogen atom, as valency permits. Heteroaryl polycyclic ring systems can include one or more heteroatoms in one or both rings. In some embodiments, a heteroaryl group is a 5-10 membered aromatic ring system having ring carbon atoms and 1-4 ring heteroatoms provided in the aromatic ring system, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur (“5-10 membered heteroaryl”). In some embodiments, a heteroaryl group is a 5-6 membered aromatic ring system having ring carbon atoms and 1-4 ring heteroatoms provided in the aromatic ring system, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur (“5-6 membered heteroaryl”).

[0046] The term “halo” or “halogen” refers to fluorine (fluoro, -F), chlorine (chloro, -Cl), bromine (bromo, -Br), or iodine (iodo, -I).

[0047] The term “hydroxyl” or “hydroxy” refers to the group -OH. The term “amino” refers to the group -NH2. The term “substituted amino,” by extension, refers to a monosubstituted amino, a disubstituted amino, or a trisubstituted amino. In certain embodiments, the “substituted amino” is a monosubstituted amino or a disubstituted amino group.

[0048] As used herein, the term “salt” refers to any and all salts, and encompasses pharmaceutically acceptable salts. Salts include ionic compounds that result from the neutralization reaction of an acid and a base. A salt is composed of one or more cations (positively charged ions) and one or more anions (negative ions) so that the salt is electrically neutral (without a net charge). Salts of the compounds of the present disclosure include those derived from inorganic and organic acids and bases. Examples of acid addition salts are salts of an amino group formed 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 by using other methods known in the art such as ion exchange. Other salts include adipate, alginate, ascorbate, aspartate, benzenesulfonate, benzoate, bisulfate, borate, butyrate, camphorate, camphorsulfonate, citrate, cyclopentanepropionate, digluconate, dodecylsulfate, ethanesulfonate, formate, fumarate, glucoheptonate, glycerophosphate, gluconate, hemisulfate, heptanoate, hexanoate, hydroiodide, 2-hydroxy-ethanesulfonate, lactobionate, lactate, laurate, lauryl sulfate, malate, maleate, malonate, methanesulfonate, 2-naphthalenesulfonate, nicotinate, nitrate, oleate, oxalate, palmitate, pamoate, pectinate, persulfate, 3-phenylpropionate, phosphate, picrate, pivalate, propionate, stearate, succinate, sulfate, tartrate, thiocyanate, -tolucncsul I'onatc, undecanoate, valerate, hippurate, and the like. Salts derived from appropriate bases include alkali metal, alkaline earth metal, ammonium and N+(Ci - alkyl)4 salts. Representative alkali or alkaline earth metal salts include sodium, lithium, potassium, calcium, magnesium, and the like. Further salts include ammonium, quaternary ammonium, and amine cations formed using counterions such as halide, hydroxide, carboxylate, sulfate, phosphate, nitrate, lower alkyl sulfonate, and aryl sulfonate.

[0049] The term “pharmaceutically acceptable salt” refers to those salts which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of humans and lower animals without undue toxicity, irritation, allergic response, and the like, and are commensurate with a reasonable benefit / risk ratio. Pharmaceutically acceptable salts are well known in the art. For example, Berge et al. describe pharmaceutically acceptable salts in detail in J. Pharmaceutical Sciences, 1977, 66, 1-19, incorporated herein by reference.

[0050] Pharmaceutically acceptable salts of the compounds of the present disclosure include those derived from suitable inorganic and organic acids and bases. Examples of pharmaceutically acceptable, nontoxic acid addition salts are salts of an amino group formed 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 by using other methods known in the art such as ion exchange. Other pharmaceutically acceptable salts include adipate, alginate, ascorbate, aspartate, benzenesulfonate, benzoate, bisulfate, borate, butyrate, camphorate, camphorsulfonate, citrate, cyclopentanepropionate, digluconate, dodecylsulfate, ethanesulfonate, formate, fumarate, glucoheptonate, glycerophosphate, gluconate, hemisulfate, heptanoate, hexanoate, hydroiodide, 2-hydroxy-ethanesulfonate, lactobionate, lactate, laurate, lauryl sulfate, malate, maleate, malonate, methanesulfonate, 2-naphthalenesulfonate, nicotinate, nitrate, oleate, oxalate, palmitate, pamoate, pectinate, persulfate, 3-phenylpropionate, phosphate, picrate, pivalate, propionate, stearate, succinate, sulfate, tartrate, thiocyanate, p-toluenesulfonate, undecanoate, valerate salts, and the like. Salts derived from appropriate bases include alkali metal, alkaline earth metal, ammonium, and N+(CI-4 alkyl)4 salts. Representative alkali or alkaline earth metal salts include sodium, lithium, potassium, calcium, magnesium, and the like. Further pharmaceutically acceptable salts include, when appropriate, nontoxic ammonium, quaternary ammonium, and amine cations formed using counterions such as halide, hydroxide, carboxylate, sulfate, phosphate, nitrate, lower alkyl sulfonate, and aryl sulfonate.

[0051] The term “solvate” refers to forms of the compound, or a salt thereof, that are associated with a solvent, usually by a solvolysis reaction. This physical association may include hydrogen bonding. Conventional solvents include water, methanol, ethanol, acetic acid, DMSO, THF, diethyl ether, and the like. The compounds described herein may be prepared, e.g., in crystalline form, and may be solvated. Suitable solvates include pharmaceutically acceptable solvates and further include both stoichiometric solvates and non-stoichiometric solvates. In certain instances, the solvate will be capable of isolation, for example, when one or more solvent molecules are incorporated in the crystal lattice of a crystalline solid. “Solvate” encompasses both solution-phase and isolatable solvates. Representative solvates include hydrates, ethanolates, and methanolates.

[0052] The term “hydrate” refers to a compound that is associated with water. Typically, the number of the water molecules contained in a hydrate of a compound is in a definite ratio to the number of the compound molecules in the hydrate. Therefore, a hydrate of a compound may be represented, for example, by the general formula R x H2O, wherein R is the compound, and x is a number greater than 0. A given compound may form more than one type of hydrate, including, e.g., monohydrates (x is 1), lower hydrates (x is a number greater than 0 and smaller than 1, e.g., hemihydrates (R O.5 H2O)), and polyhydrates (x is a number greater than 1, e.g., dihydrates (R-2 H2O) and hexahydrates (R-6 H2O)).

[0053] The term “tautomers” or “tautomeric” refers to two or more interconvertible compounds resulting from at least one formal migration of a hydrogen atom and at least one change in valency e.g., a single bond to a double bond, a triple bond to a single bond, or vice versa). The exact ratio of the tautomers depends on several factors, including temperature, solvent, and pH. Tautomerizations (i.e., the reaction providing a tautomeric pair) may catalyzed by acid or base. Exemplary tautomerizations include keto-to-enol, amide-to-imide, lactam-to-lactim, enamine-to- imine, and enamine-to-(a different enamine) tautomerizations.

[0054] It is also to be understood that compounds that have the same molecular formula but differ in the nature or sequence of bonding of their atoms or the arrangement of their atoms in space are termed “isomers”. Isomers that differ in the arrangement of their atoms in space are termed “stereoisomers”.

[0055] Stereoisomers that are not mirror images of one another are termed “diastereomers” and those that are non-superimposable mirror images of each other are termed “enantiomers”. When a compound has an asymmetric center, for example, it is bonded to four different groups, a pair of enantiomers is possible. An enantiomer can be characterized by the absolute configuration of its asymmetric center and is described by the R- and S-sequencing rules of Cahn and Prelog, or by the manner in which the molecule rotates the plane of polarized light and designated as dextrorotatory or levorotatory (z.e., as (+) or (-)-isomers respectively). A chiral compound can exist as either individual enantiomer or as a mixture thereof. A mixture containing equal proportions of the enantiomers is called a “racemic mixture”.

[0056] The term “crystalline” or “crystalline form” refers to a solid form substantially exhibiting three-dimensional order. In certain embodiments, a crystalline form of a solid is a solid form that is substantially not amorphous. In certain embodiments, the X-ray powder diffraction (XRPD) pattern of a crystalline form includes one or more sharply defined peaks.

[0057] The term “amorphous” or “amorphous form” refers to a form of a solid (“solid form”), the form substantially lacking three-dimensional order. In certain embodiments, an amorphous form of a solid is a solid form that is substantially not crystalline. In certain embodiments, the X- ray powder diffraction (XRPD) pattern of an amorphous form includes a wide scattering band with a peak at 29 of, e.g., between 20 and 70°, inclusive, using Cu rz radiation. In certain embodiments, the XRPD pattern of an amorphous form further includes one or more peaks attributed to crystalline structures. In certain embodiments, the maximum intensity of any one of the one or more peaks attributed to crystalline structures observed at a 29 of between 20 and 70°, inclusive, is not more than 300-fold, not more than 100-fold, not more than 30-fold, not more than 10-fold, or not more than 3-fold of the maximum intensity of the wide scattering band. In certain embodiments, the XRPD pattern of an amorphous form includes no peaks attributed to crystalline structures.

[0058] The term “co-crystal” refers to a crystalline structure comprising at least two different components e.g., a compound disclosed herein and an acid), wherein each of the components is independently an atom, ion, or molecule. In certain embodiments, none of the components is a solvent. In certain embodiments, at least one of the components is a solvent. A co-crystal of a compound disclosed herein and an acid is different from a salt formed from a compound disclosed herein and the acid. In the salt, a compound disclosed herein is complexed with the acid in a way that proton transfer (e.g., a complete proton transfer) from the acid to a compound disclosed herein easily occurs at room temperature. In the co-crystal, however, a compound disclosed herein is complexed with the acid in a way that proton transfer from the acid to a compound disclosed herein does not easily occur at room temperature. In certain embodiments, in the co-crystal, there is no proton transfer from the acid to a compound disclosed herein. In certain embodiments, in the co-crystal, there is partial proton transfer from the acid to a compound disclosed herein. Co-crystals may be useful to improve the properties (e.g., solubility, stability, and ease of formulation) of a compound disclosed herein.

[0059] The term “polymorph” refers to a crystalline form of a compound (or a salt, hydrate, or solvate thereof). All polymorphs have the same elemental composition. Different crystalline forms usually have different X-ray diffraction patterns, infrared spectra, melting points, density, hardness, crystal shape, optical and electrical properties, stability, and solubility. Recrystallization solvent, rate of crystallization, storage temperature, and other factors may cause one crystal form to dominate. Various polymorphs of a compound can be prepared by crystallization under different conditions.

[0060] The term “prodrugs” refers to compounds that have cleavable groups and become by solvolysis or under physiological conditions the compounds described herein, which are pharmaceutically active in vivo. Such examples include, but are not limited to, choline ester derivatives and the like, N-alkylmorpholine esters and the like. Other derivatives of the compounds described herein have activity in both their acid and acid derivative forms, but in the acid sensitive form often offer advantages of solubility, tissue compatibility, or delayed release in the mammalian organism (see, Bundgaard, H., Design of Prodrugs, pp. 7-9, 21-24, Elsevier, Amsterdam 1985). Prodrugs include acid derivatives well known to practitioners of the art, such as, for example, esters prepared by reaction of the parent acid with a suitable alcohol, or amides prepared by reaction of the parent acid compound with a substituted or unsubstituted amine, or acid anhydrides, or mixed anhydrides. Simple aliphatic or aromatic esters, amides, and anhydrides derived from acidic groups pendant on the compounds described herein are particular prodrugs.

[0061] The terms “composition” and “formulation” are used interchangeably.

[0062] Accordingly, provided are compositions comprising an inhibitor of a protease. In some embodiments, a composition comprises an inhibitor of a bacterial protease. In some embodiments, a composition comprises an inhibitor of a bacterial protease and an excipient. In some embodiments, a composition comprises two or more protease inhibitors (e.g., 2, 3, 4, 5, or 5-10). In some embodiments, a composition comprises two or more bacterial protease inhibitors (e.g., 2, 3, 4, 5, or 5-10). In some embodiments, an excipient comprises an agent that facilitates targeted delivery of a protease inhibitor to an intestinal location. In some embodiments, a composition comprises an inhibitor of a bacterial protease and an agent that facilitates targeted delivery of the protease inhibitor to a small intestine. In some embodiments, a composition comprises an inhibitor of a bacterial protease and an agent that facilitates targeted delivery of the protease inhibitor to a caecum and / or colon.

[0063] In some embodiments, provided are compositions comprising a gliptin or a pharmaceutically acceptable salt thereof. In some embodiments, provided are compositions comprising two or more gliptins (e.g., 2, 3, 4, 5, or 5-10). In some embodiments, provided are pharmaceutical dosage forms comprising a gliptin or a pharmaceutically acceptable salt thereof. In some embodiments, provided are pharmaceutical dosage forms comprising two or more gliptins (e.g., 2, 3, 4, 5, or 5-10).

[0064] In some embodiments the gliptin is selected from sitagliptin, teneligliptin, omarigliptin, vildagliptin, saxagliptin, alogliptin, lingagliptin, gemigliptin, anagliptin, trelagliptin, evogliptin, gosogliptin, dutogliptin, retagliptin, and prusogliptin, or a derivative thereof. In some embodiments the gliptin is sitagliptin. In some embodiments the gliptin is vildagliptin. In some embodiments the gliptin is omargliptin. In some embodiments the gliptin is tenegliptin.

[0065] In some embodiments, the gliptin may have the formula (I): or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled compound, or prodrug thereof, wherein:

[0066] X is NRi or CRi; dashed line is absent or a double bond;

[0067] Y is absent or -CH2-;

[0068] R is optionally substituted alkyl, optionally substituted heteroalkyl, optionally substituted alkenyl, optionally substituted heteroalkenyl, halo, optionally substituted acyl, or carbonyl; n is 0-5,

[0069] Ri isalkyl, optionally substituted alkyl, optionally substituted heteroalkyl, optionally substituted alkenyl, or optionally substituted heteroalkenyl, aryl, optionally substituted aryl, optionally substituted cycloalkyl, optionally amine substituted alkyl, optionally hydroxyl substituted alkyl, optionally halogen substituted alkyl, optionally amine substituted aryl, optionally hydroxyl substituted aryl, optionally halogen substituted aryl, optionally amine substituted cycloalkyl, optionally hydroxyl substituted cycloalkyl, optionally halogen substituted cycloalkyl.

[0070] In certain embodiments, the gliptin comprises a central scaffold comprising a pyrimidine substituted with two carbonyl groups. In certain embodiments, the gliptin comprises a central

[0071] O

[0072] I / (R2)n l scaffold of formula (II):0 N N(RS)P(II), or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled compound, or prodrug thereof, wherein: n is 2 or 3; p is 1 or 2; each instance of R2is independently hydrogen, optionally substituted alkyl, optionally substituted heteroalkyf each instance of R3 is optionally substituted alkyl, or optionally substituted alkenyl, optionally wherein two instances of R3 form an optionally substituted heterocyclyl with the nitrogen atom to which they are attached; and each instance of R4 is optionally substituted alkyl.

[0073] The inventors have further recognized and appreciated that, in cases of oral administration of a protease inhibitor (e.g., a bacterial protease inhibitor), it may be desirable for an oral dosage form to comprise a controlled release coating to facilitate targeted delivery of the protease inhibitor to a particular location within the GI tract (e.g., the colon, and / or the small intestine). In some cases, targeted delivery of the protease inhibitor to a particular location within the GI tract may enhance treatment efficacy, reduce systemic drug exposure and associated toxicity, and / or improve drug bioavailability. I. Compositions and Pharmaceutical Dosage Forms

[0074] In some embodiments, provided are compositions comprising one or more protease inhibitor (e.g., 2, 3, 4, 5, or 5-10 gliptins or compounds described herein), or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled compound, or prodrug thereof. In some embodiments, provided is a pharmaceutical composition comprising one or more protease inhibitor (e.g., 2, 3, 4, 5, or 5-10 gliptins or compounds described herein), or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled compound, or prodrug thereof, and a pharmaceutically acceptable carrier. In some embodiments, the pharmaceutical composition described herein, further comprises an additional pharmaceutical agent. Pharmaceutical compositions described herein can be prepared by any method known in the art of pharmaceutics.

[0075] The present 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 certain embodiments, the pharmaceutical compositions described herein comprise a protease inhibitor (e.g., one or more protease inhibitor described herein), or a pharmaceutically acceptable salt thereof, and a pharmaceutically acceptable excipient.

[0076] The inventors have recognized and appreciated that, in cases of oral administration of a protease inhibitor (e.g., a human or bacterial protease inhibitor), it may be desirable for an oral dosage form to comprise a controlled release coating to facilitate targeted delivery of the protease inhibitor to a particular location within the gut of a subject (e.g., the colon, the small intestine). In some cases, targeted delivery of the protease inhibitor to a particular location within the gut may enhance treatment efficacy, reduce systemic drug exposure and associated toxicity, and / or improve drug bioavailability. In some embodiments, the pharmaceutical compositions described herein comprise a core comprising a protease inhibitor (e.g., active ingredient) in an effective amount and a controlled release coating applied to an exterior surface of the core, wherein the controlled release coating is configured to release the inhibitor of the protease in the gut of a subject to whom the pharmaceutical dosage form is administered.

[0077] Pharmaceutical compositions can be prepared, packaged, and / or sold in bulk, as a single unit dose, and / or as a plurality of single unit doses. A “unit dose” is a discrete amount of the pharmaceutical composition comprising a predetermined amount of the active ingredient (e.g., protease inhibitor). The amount of the active ingredient is generally equal to the dosage of the active ingredient which would be administered to a subject and / or a convenient fraction of such a dosage, such as one-half or one-third of such a dosage.

[0078] In some embodiments, a composition comprises a protease inhibitor (e.g., one or more protease inhibitor described herein) or a pharmaceutically acceptable salt thereof, and a targeted delivery facilitating agent. In some embodiments, the targeted delivery facilitating agent comprises one or more materials that dissolve under certain conditions. In some embodiments, a targeted delivery facilitating agent comprises one or more materials that dissolve under certain pH conditions. In some embodiments, the targeted delivery facilitating agent comprises one or more materials that are susceptible to degradation by a microbial organism.

[0079] In some embodiments, a targeted delivery facilitating agent comprises one or more materials that dissolve under certain pH conditions and / or one or more materials that are susceptible to degradation by a microbial organism.

[0080] According to some embodiments, provided is a pharmaceutical dosage form that comprises a core comprising an inhibitor of a protease (e.g., one or more protease inhibitors). In some embodiments, the core comprises an effective amount of a protease inhibitor (e.g., one or more protease inhibitor) 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 prophylactic ally effective amount. In some embodiments, a therapeutically effective amount of the protease inhibitor is an amount sufficient to alleviate (e.g., delay or reduce the onset, progression, and / or severity of) one or more symptoms of an inflammatory bowel disease in a subject. In some embodiments, a therapeutically effective amount of the protease inhibitor is an amount sufficient to reduce the risk of a subject developing an inflammatory bowel disease. In certain embodiments, a 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 certain embodiments, a 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 certain embodiments, a therapeutically effective amount of the protease inhibitor is an amount sufficient to modulate (e.g., reduce) bacterial protease activity in the large intestine (e.g., colon) and / or small intestine (e.g., distal ileum) of a subject.

[0081] In some embodiments, a therapeutically effective amount of the protease inhibitor is an amount sufficient to provide desired side effects in a subject.

[0082] A protease generally refers to an enzyme that catalyzes proteolysis (e.g., cleavage of one or more peptide bonds to break proteins into smaller polypeptides or single amino acids). In some embodiments, the protease is a bacterial protease. In some embodiments, the protease is a protease expressed by a microbial organism of an intestinal microbiome. In some embodiments, the protease is a protease expressed by a microbial organism of an intestinal microbiome present in a human. In some embodiments, the protease is a protease expressed by a microbial organism of an intestinal microbiome present in a human who has at least one symptom of an IBD. In some embodiments, the protease is a protease expressed by a microbial organism of an intestinal microbiome present in a human who does not have diabetes. In some embodiments, the protease is a protease expressed by a microbial organism of an intestinal microbiome present in a human who does not have an inflammatory condition or disease other than IBD. In some embodiments, the protease is a serine protease, a cysteine protease, or a metalloprotease. In certain embodiments, the protease is a serine protease. In certain instances, the serine protease is an S09 type protease (e.g., an S09.13 protease) under the MEROPS classification system. In some embodiments, the protease is configured to cleave GLP-1 and / or GLP-2. In certain 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 instances, 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 a microbial organism of an intestinal microbiome. In some embodiments, the protease is DPP-4 expressed by a microbial organism of an intestinal microbiome present in a human. In some embodiments, the protease is DPP-4 expressed by a microbial organism of an intestinal microbiome present in a human who has at least one symptom of an IBD. In some embodiments, the protease is DPP-4 expressed by a microbial organism of an intestinal microbiome present in a human who does not have diabetes. In some embodiments, the protease is DPP-4 expressed by a microbial organism of an intestinal microbiome present in a human who does not have an inflammatory conditions or disease other than IBD.

[0083] In some embodiments, the protease is expressed by a microbial organism in the intestinal microbiome. In certain embodiments, the microbial organism is a bacterium. In certain cases, the bacterium is a pathogenic bacterium that disrupts intestinal epithelial permeability and / or is otherwise associated with an IBD. In some instances, the bacterium is a species of Bacteroides bacteria. Non-limiting examples of suitable species of Bacteroides bacteria include B. vulgatus, B. dorei, B. fragilis, B. massiliensis, B. ovatus, B. theta, B. uniforms, B. stercoris, B. cellulosilyticus, B. xylanisolvens, and B. caccae. In some cases, the bacterium is B. vulgatus and / or B. dorei. In certain instances, the bacterium is B. vulgatus. In some instances, the genera of the bacteria may be from the genera Phocaeicola, which was reclassified from the genera Bacteroides. Non-limiting examples of suitable species of the Phocaeicola genera include P. vulgatus and P. dorei. In some instances, the protease comprises a DPP-4 expressed by B. vulgatus and / or B. dorei.

[0084] An inhibitor of a protease generally refers to a compound that reduces or inhibits activity of the protease. In some embodiments, a protease inhibitor reduces or inhibits activity of a bacterial protease. In some embodiments, a protease inhibitor reduces or inhibits activity of a bacterial protease of a microbial organism present in an intestinal microbiome. In some embodiments, a protease inhibitor reduces or inhibits activity of a bacterial protease of a microbial organism present in an intestinal microbiome present in a human. In some embodiments, a protease inhibitor reduces or inhibits activity of a bacterial protease of a microbial organism present in an intestinal microbiome present in a human who has at least one symptom of IBD. In some embodiments, a protease inhibitor reduces or inhibits activity of a bacterial protease of a microbial organism present in an intestinal microbiome in a human who does not have diabetes. In some embodiments, a protease inhibitor reduces or inhibits activity of a bacterial protease of a microbial organism present in an intestinal microbiome in a human who does not have an inflammatory condition or disease other than IBD. In some embodiments, the protease inhibitor comprises a gliptin or a pharmaceutically acceptable salt thereof. Examples of gliptins include but are not limited to sitagliptin, teneligliptin, omarigliptin, vildagliptin, saxagliptin, aloliptin, lingagliptin, gemigliptin, anagliptin, trelagliptin, evogliptin, gosogliptin, dutogliptin, neogliptin, retagliptin, cofrogliptin, fotagliptin, and prusogliptin, or a derivative or combination thereof.

[0085] In some embodiments, a protease inhibitor comprises a gliptin that reduces or inhibits activity of a bacterial protease. In some embodiments, a protease inhibitor comprises a gliptin that reduces or inhibits activity of a bacterial protease of a microbial organism present in an intestinal microbiome. In some embodiments, a protease inhibitor comprises a gliptin that reduces or inhibits activity of a bacterial protease of a microbial organism present in an intestinal microbiome present in a human. In some embodiments, a protease inhibitor comprises a gliptin that reduces or inhibits activity of a bacterial protease of a microbial organism present in an intestinal microbiome present in a human who has at least one symptom of IBD. In some embodiments, a protease inhibitor comprises a gliptin that reduces or inhibits activity of a bacterial protease of a microbial organism present in an intestinal microbiome in a human who does not have diabetes. In some embodiments, a protease inhibitor comprises a gliptin that reduces or inhibits activity of a bacterial protease of a microbial organism present in an intestinal microbiome in a human who does not have an inflammatory condition or disease other than IBD.

[0086] In some embodiments, a composition comprises a therapeutically effective amount of a protease inhibitor or a pharmaceutically acceptable salt thereof. In some embodiments, a composition comprises a therapeutically effective amount of more than one (e.g., 2, 3, 4, 5, or 5- 10) protease inhibitors or pharmaceutically acceptable salts thereof. In some embodiments, a pharmaceutical dosage form comprises a core that comprises a therapeutically effective amount of a protease inhibitor or a pharmaceutically acceptable salt thereof. In some embodiments, a pharmaceutical dosage form comprises a core that comprises a therapeutically effective amount of more than one (e.g., 2, 3, 4, 5, or 5-10) protease inhibitors or pharmaceutically acceptable salts thereof. In certain embodiments, a therapeutically effective amount of the protease inhibitor is an amount sufficient to alleviate (e.g., delay or reduce the onset, progression, and / or severity of) one or more symptoms of an IBD (e.g., UC, Crohn’s disease) in a subject. In certain embodiments, a therapeutically effective amount of a protease inhibitor is an amount sufficient to reduce the risk of a subject developing an IBD (e.g., UC, Crohn’s disease). In certain embodiments, a therapeutically effective amount of a 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 a subject. In some embodiments, the effective amount is an amount effective for inhibiting the activity of a 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 embodiments, the therapeutically effective amount of a protease inhibitor is in a range from 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 embodiments, a therapeutically effective amount of a 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. Dose ranges as described herein provide guidance for the administration of provided pharmaceutical compositions to an adult. The amount to be administered to, for example, a child or an adolescent can be determined by a medical practitioner or person skilled in the art and can be lower or the same as that administered to an adult.

[0087] In some embodiments, a composition comprises one or more pharmaceutically acceptable excipients. In some embodiments, a core of a pharmaceutical dosage form comprises one or more pharmaceutically acceptable excipients. In some cases, the one or more pharmaceutically acceptable excipients comprise one or more pharmaceutically acceptable carriers, buffers, salts, inert diluents or filling agents, binders, stabilizers, emulsifiers, disintegrants, diluents, lubricants, additives, preservatives, taste maskers, colorants, adjuvants, dispersing and / or granulating agents, surface active agents 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 derivatives thereof, starches, dextran), sugar alcohols (e.g., xylitol, sorbitol, mannitol), gelatin, polymers (e.g., polyvinylpyrrolidone, polyethylene glycol, polyacrylates), colloidal silicon dioxide, calcium carbonate, calcium phosphate, calcium hydroxide, magnesium stearate, sodium lauryl sulfate, and sodium acetate. Excipients such as cocoa butter and suppository waxes, coloring agents, coating agents, sweetening, flavoring, and perfuming agents may also be present in the composition. Relative amounts of the active ingredient, the pharmaceutically acceptable excipient, and / or any additional ingredients in a pharmaceutical composition described herein will vary, depending upon the identity, size, and / or condition of the subject treated and further depending upon the route by which the composition is to be administered. The composition may comprise between 0.1% and 100% (w / w) active ingredient.

[0088] In some embodiments, a composition comprises an inhibitor of a protease and a carrier. In some embodiments, a composition comprises an inhibitor of a protease and a carrier that is not absorbed by intestinal cells. In some embodiments, a composition comprises an inhibitor of a protease and a carrier that is minimally absorbed by intestinal cells. For example, in some aspects, a composition comprises an inhibitor of a protease and an amount of a carrier, about 99% of which amount of carrier is not absorbed into the blood. In some aspects, a composition comprises an inhibitor of a protease and an amount of a carrier, 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 which amount of carrier is not absorbed into the blood.

[0089] In some embodiments, a composition comprises an inhibitor of a protease and a carrier that is not absorbed through an intestinal wall of a subject. In some embodiments, a composition comprises an inhibitor of a protease and a carrier about 51% to about 99% of which carrier is not absorbed through an intestinal wall of a subject. In some embodiments, a composition comprises an inhibitor of a protease and a carrier about 1%, about 5%, about 10%, about 15%, about 20%, about 25%, about 30%, about 35%, about 40%, about 45%, or about 49% of which carrier is absorbed into the blood of a subject. In some embodiments, a composition comprises an inhibitor of a protease and a carrier that targets the protease inhibitor to an intestinal microbiome. In some embodiments, a composition comprises an inhibitor of a protease and a carrier that specifically targets the protease inhibitor to an intestinal microbiome present in a subject and does not target the protease inhibitor to the blood of the subject. In some embodiments, a carrier that specifically targets the protease inhibitor to an intestinal microbiome present in a subject and does not target the protease inhibitor to the blood of the subject comprises a polymer. In some embodiments, a carrier that specifically targets the protease inhibitor to an intestinal microbiome and does not target the protease inhibitor to the blood comprises a polymer comprising polyvinylpyrrolidone. In some embodiments, a carrier that specifically targets the protease inhibitor to an intestinal microbiome and does not target the protease inhibitor to the blood comprises a polymer hydrogel, e.g., a polyvinylpyrrolidone (PVP) hydrogel. In some embodiments, a carrier that specifically targets the protease inhibitor to an intestinal microbiome and does not target the protease inhibitor to the blood comprises a polymer, e.g., a PVP hydrogel loaded with the protease inhibitor.. The term “loaded with,” as used herein, refers to an interaction between two molecules, e.g., a polymer and a protease inhibitor. The interaction can be an interaction based on hydrophilic interaction, e.g., a charge interaction, or a hydrophobic interaction. In some embodiments, a composition comprising a polymer, e.g., a PVP hydrogel loaded with a protease inhibitor, targets the protease inhibitor to a location in an intestine. In some embodiments, a composition comprising a polymer, e.g., a PVP hydrogel loaded with a protease inhibitor targets the protease inhibitor to an intestinal location with alkaline pH. For example, a composition comprising a polymer, e.g., a PVP hydrogel loaded with a protease inhibitor may target the protease inhibitor to a distal ileum and / or colon where an alkaline pH decreases hydrogen bonds within the polymer, e.g., PVP hydrogel and hydrogen bonds between the polymer, e.g., PVP hydrogel and the protease inhibitor effectuating the release of the protease inhibitor in the distal ileum and / or colon. In some embodiments, a carrier comprising a polymer, e.g., a PVP polymer is associated with a protease inhibitor through a linker. In some embodiments, a carrier comprising a polymer, e.g., a PVP polymer is associated with a protease inhibitor through a non-digestable linker. In some embodiments, a protease inhibitor is dispersed in a polymer, e.g., a PVP polymer. In some embodiments, a protease inhibitor is present in a core, e.g., of a tablet and a polymer, e.g., a PVP polymer surrounds the tablet core.

[0090] In some embodiments, a composition comprises a pH-sensitive material and / or a microbe- sensitive material described herein. In some embodiments, a composition comprises a pH-sensitive material and / or a microbe-sensitive material, and / or a carrier. In some embodiments, a composition comprises a pH-sensitive material and / or a microbe- sensitive material, and / or a carrier comprising a polymer. In some embodiments, a composition comprises a pH-sensitive material and / or a microbe- sensitive material, and / or a carrier comprising a PVP polymer. In some embodiments, a composition comprises a pH-sensitive material and / or a microbe- sensitive material, and / or a carrier comprising a PVP polymer that is loaded with a protease inhibitor. In some embodiments, a core comprises a pH-sensitive material and / or a microbe- sensitive material described herein. In some embodiments, a composition comprises one or more nanoparticles (e.g., lipid nanoparticles, polymeric nanoparticles). In some embodiments, a core comprises one or more nanoparticles (e.g., lipid nanoparticles, polymeric nanoparticles).

[0091] In some embodiments, a composition comprises a tablet, gelcap, capsule, lozenge, sachet, or other suitable solid form. In some embodiments, a core comprises a tablet, gelcap, capsule, lozenge, sachet, or other suitable solid form. In some embodiments, a composition comprises a capsule (e.g., a hard-shelled capsule) containing a powdered form of one or more protease inhibitors. In some embodiments, a pharmaceutical dosage form comprises a capsule (e.g., a hard-shelled capsule) containing a powdered form of one or more protease inhibitors.

[0092] In some embodiments, a composition comprises a capsule (e.g., a soft-shelled capsule) containing a liquid form of one or more protease inhibitors (e.g., a solution or suspension of the protease inhibitor(s)). In some embodiments, a pharmaceutical dosage form comprises a capsule (e.g., a soft-shelled capsule) containing a liquid form of one or more protease inhibitors (e.g., a solution or suspension of the protease inhibitor(s)).

[0093] In some embodiments, a composition comprises a controlled release coating. In some embodiments, a pharmaceutical dosage form comprises a controlled release coating applied to an exterior surface of a core. In some cases, the controlled release coating provides targeted delivery of a core to a desired location within the GI tract, such as one or more portions of the large intestine (e.g., the colon) and / or the small intestine (e.g., distal ileum) of a subject to whom the pharmaceutical dosage form is administered. In certain embodiments, a controlled release coating is configured to release a composition in the large intestine (e.g., colon) of a subject. In certain embodiments, a controlled release coating is configured to release a core in a large intestine (e.g., colon) of a subject. In some instances, a controlled release coating is configured to release a composition in a small intestine of a subject. In some instances, a controlled release coating is configured to release a composition in a distal ileum of a subject. In some instances, a controlled release coating is configured to release a core in a small intestine of the subject.

[0094] In some embodiments, a controlled release coating comprises a single layer. In some embodiments, a controlled release coating consists of a single layer. In some embodiments, a controlled release coating comprises a plurality of layers. The plurality of layers may comprise two, three, four, five, or more layers. In some cases, two or more layers of the plurality of layers comprise the same material. In some cases, two or more layers of the plurality of layers comprise different materials.

[0095] In some embodiments, one or more layers of a controlled release coating comprise one or more pH-sensitive materials. A pH-sensitive material generally refers to a material configured to dissolve above or below a threshold pH value. In healthy individuals, pH values are generally low (e.g., 0.95 to 3.5) in the stomach, increase from the proximal small intestine (e.g., 5.5 to 7.0) to the distal ileum (e.g., 6.5 to 7.5), fall in the caecum (e.g., 5.5 to 7.0), and then increase in the colon (e.g., 6.0 to 7.5). In individuals with IBD, gastric pH values and / or colonic pH values may be higher or lower than those in healthy individuals particularly in the stomach, distal ileum, caecum, and right colon, where pH may be higher in IBD patients than healthy individuals (see e.g., Press et al., Aliment. Pharmacol. Ther. 1998, 12: 672-78). In some embodiments, a pH-sensitive material is configured to resist dissolution at the relatively low pH values of the stomach and to dissolve at the relatively high pH values of the colon and / or small intestine. In certain embodiments, a pH-sensitive material is configured to dissolve at a pH of 5.5 or higher, 6.0 or higher, 6.5 higher, 7.0 or higher, or 7.5 or higher. In some embodiments, a pH-sensitive material is configured to dissolve at a pH of 5.5, at a pH of about 5.6, at a pH of about 5.7, at a pH of about 5.8, at a pH of about 5.9, at a pH of about 6.0, at a pH of about 6.1, at a pH of about 6.2, at a pH of about 6.3, at a pH of about 6.4, at a pH of about 6.5, at a pH of about 6.6, at a pH of about 6.7, at a pH of about 6.8, at a pH of about 6.9, at a pH of about 7.0, at a pH of about 7.1, at a pH of about 7.2, at a pH of about 7.3, at a pH of about 7.4, or at a pH of about 7.5. In some embodiments, a pH of 7.5 or higher includes a pH of about 7.6, a pH of about

[0096] 7.7, a pH of about 7.8, a pH of about 7.9, a pH of about 8.0, a pH of about 8.1, a pH of about

[0097] 8.2, a pH of about 8.3, a pH of about 8.4, a pH of about 8.5, a pH of about 8.6, a pH of about

[0098] 8.7, a pH of about 8.8, a pH of about 8.9, or a pH of about 9.0. In some embodiments, a pH- sensitive material is configured to dissolve at a pH higher than 7.1. In some embodiments, a pH- sensitive material is configured to dissolve at a pH higher than 7.2. In some embodiments, a pH- sensitive material is configured to dissolve at a pH higher than 7.3. In some embodiments, a pH- sensitive material is configured to dissolve at a pH higher than 7.4. In some embodiments, a pH- sensitive material is configured to dissolve at a pH higher than 7.5. In some embodiments, a pH- sensitive material is configured to dissolve at a pH of about 7.1. In some embodiments, a pH- sensitive material is configured to dissolve at a pH of about 7.2. In some embodiments, a pH- sensitive material is configured to dissolve at a pH of about 7.3. In some embodiments, a pH- sensitive material is configured to dissolve at a pH of about 7.4. In some embodiments, a pH- sensitive material is configured to dissolve at a pH of about 7.5.

[0099] In some embodiments, a pH-sensitive material is configured to dissolve at a pH of about 7.2 to about 7.5. In some embodiments, a pH-sensitive material is configured to dissolve at a pH of about 7.3 to about 7.5. In some embodiments, a pH-sensitive material is configured to dissolve at a pH of about 7.4 to about 7.5. In some embodiments, a pH-sensitive material is configured to dissolve at a pH of about 7.2 to about 7.4. In some embodiments, a pH-sensitive material is configured to dissolve at a pH of about 7.2 to about 7.3.

[0100] In some embodiments, a composition comprises more than one pH-sensitive material. In some embodiments, a composition comprises a first pH-sensitive material that is configured to dissolve at a first pH and a second pH-sensitive material that is configured to dissolve at a second pH. In some embodiments, a composition further comprises a third pH-sensitive material that dissolves at a third pH. In some embodiments, a composition further comprises a fourth pH- sensitive material that dissolves at a fourth pH. In some embodiments, a composition further comprises a fifth pH-sensitive material that dissolves at a fifth pH. For example, a composition may target a protease inhibitor to a caecum or right colon location, wherein the composition comprises a first material that is configured to dissolve at about pH 7.5, which is first reached when the intestinal content reaches the distal ileum, and a second material that is configured to dissolve at about pH 5.5, which is reached when the intestinal content reaches the caecum.

[0101] In some embodiments, a composition comprises a material that is configured to dissolve at a pH above 7.5, e.g., pH 7.6, which may be a pH in a distal ileum of a subject having IBD. In some embodiments, a composition comprises a first material that is configured to dissolve at a pH above 7.5, e.g., pH 7.6, which may be a pH in a distal ileum of a subject having IBD and a second material that is configured to dissolve at a pH above 7.5, e.g., pH 7.6 which may be a pH in a colon of a subject having IBD. In some embodiments, a composition comprises an agent that increase a pH in an intestinal location. In some embodiments, a composition comprises a pH-sensitive material configured to dissolve at a pH of 7.5 or higher. In some embodiments, a composition comprises a pH-sensitive material configured to dissolve at a pH of about 7.6, a pH of about 7.7, a pH of about 7.8, a pH of about 7.9, a pH of about 8.0, a pH of about 8.1, a pH of about 8.2, a pH of about 8.3, a pH of about 8.4, a pH of about 8.5, a pH of about 8.6, a pH of about 8.7, a pH of about 8.8, a pH of about 8.9, or a pH of about 9.0. In some embodiments, a composition comprises an agent that increases a pH in an intestinal location and the composition further comprises a pH-sensitive material configured to dissolve at a pH of about 7.6, a pH of about 7.7, a pH of about 7.8, a pH of about 7.9, a pH of about 8.0, a pH of about 8.1, a pH of about 8.2, a pH of about 8.3, a pH of about 8.4, a pH of about 8.5, a pH of about 8.6, a pH of about 8.7, a pH of about 8.8, a pH of about 8.9, or a pH of about 9.0.

[0102] In some embodiments, a composition comprises multiple layers. In some embodiments, a composition comprises a core comprising a polymer, e.g., a PVP polymer loaded with a protease inhibitor. In some embodiments, the composition further comprises added to the outside surface of the core a first layer comprising a pH-sensitive material configured to dissolve at a pH of about 7.6, a pH of about 7.7, a pH of about 7.8, a pH of about 7.9, a pH of about 8.0, a pH of about 8.1, a pH of about 8.2, a pH of about 8.3, a pH of about 8.4, a pH of about 8.5, a pH of about 8.6, a pH of about 8.7, a pH of about 8.8, a pH of about 8.9, or a pH of about 9.0. In some embodiments, the composition further comprises added to the outside surface of the first layer, a second layer comprising an agent that increases a pH in an intestinal location. In some embodiments, the second layer is configured to dissolve at a pH present in a distal ileum. In some embodiments, the second layer is configured to dissolve at a pH present in a caecum. In some embodiments, the second layer is configured to dissolve at a pH present in a colon. In some embodiments, when the second layer dissolves in a distal ileum or caecum or colon, the agent contained in the second layer increases the pH in the distal ileum, caecum or colon to a pH of about 7.6, a pH of about 7.7, a pH of about 7.8, a pH of about 7.9, a pH of about 8.0, a pH of about 8.1, a pH of about 8.2, a pH of about 8.3, a pH of about 8.4, a pH of about 8.5, a pH of about 8.6, a pH of about 8.7, a pH of about 8.8, a pH of about 8.9, or a pH of about 9.0. In some embodiments, the first layer comprising the pH-sensitive material that dissolves at a pH of about

[0103] 7.6, a pH of about 7.7, a pH of about 7.8, a pH of about 7.9, a pH of about 8.0, a pH of about 8.1, a pH of about 8.2, a pH of about 8.3, a pH of about 8.4, a pH of about 8.5, a pH of about

[0104] 8.6, a pH of about 8.7, a pH of about 8.8, a pH of about 8.9, or a pH of about 9.0. dissolves thereby releasing the core comprising the PVP polymer loaded with the protease inhibitor in the distal ileum, caecum, or colon, respectively.

[0105] In some embodiments, the one or more pH-sensitive materials comprise a pH-sensitive polymer. In certain cases, a pH-sensitive polymer comprises one or more of the following monomers: methacrylic acid, methyl methacrylate, methyl acrylate, ethyl acrylate, acrylic acid, dimethylaminoethyl methacrylate, butyl methacrylate, and N-isopropylacrylamide. Nonlimiting examples of suitable pH-sensitive polymers include copolymers of methacrylic acid and methyl methacrylate, copolymers of methacrylic acid and ethyl acrylate, copolymers of methyl acrylate, methyl methacrylate, and methacrylic acid, an aminoalkyl methacrylate copolymer, cellulose acetate phthalate (“CAP”), hydroxypropyl methylcellulose phthalate (“HPMCP”), hydroxypropyl methylcellulose acetate succinate (“HPMC-AS”), poly(N-isopropylacrylamide) (“PNI-PAM”), EUDRAGIT® S, EUDRAGIT® FS, EUDRAGIT® L, and Kollicoat® MAE 100P.

[0106] In some embodiments, a composition comprises one or more microbe-sensitive materials. In some cases, one or more layers of the controlled release coating comprise a microbe- sensitive material. In some cases, a microbe-sensitive material is susceptible to degradation by one or more microbial organisms residing in a portion of the GI tract (e.g., the colon). Non-limiting examples of suitable microbe- sensitive materials include amylose, lactulose, amylopectin, pectin, guar gum, locust bean gum, inulin, chitosan, arabinoxylans, agave fructans, alginate, chondroitin sulfate, dextran, and cyclodextrin.

[0107] In some embodiments, a composition comprises a pH-sensitive material and / or a microbe- sensitive material. In some embodiments, a composition comprises more than one pH- sensitive material and / or more than one microbe-sensitive material. In certain embodiments, a controlled release coating comprises a layer comprising a pH-sensitive material and a microbesensitive material. In certain embodiments, a controlled release coating comprises a layer comprising a pH-sensitive material and / or a layer comprising a microbe- sensitive material. In certain embodiments, the controlled release coating comprises one or more layers comprising a pH-sensitive material and one or more layers comprising a microbe-sensitive material. In certain embodiments, the controlled release coating comprises one or more layers comprising a first pH-sensitive material and one or more layers comprising a second pH-sensitive material. In some instances, the controlled release coating comprises one, two, three, four, five, or more pH- sensitive materials. In certain embodiments, the controlled release coating comprises one or more layers comprising a first microbe-sensitive material and one or more layers comprising a second microbe-sensitive material. In some instances, the controlled release coating comprises one, two, three, four, five, or more microbe-sensitive materials.

[0108] In some embodiments, a composition comprises a controlled release coating. In some embodiments, a composition comprises more than one controlled release coating. In some embodiments, a composition comprises one layer of a controlled release coating. In some embodiments, a composition comprises more than one layer of a controlled release coating. In some embodiments, a composition comprises one layer of a controlled release coating that comprises a pH-sensitive material. In some embodiments, a composition comprises one layer of a controlled release coating that comprises a microbe-sensitive material. In some embodiments, a composition comprises one layer of a controlled release coating that comprises a pH-sensitive material and one layer that comprises a microbe-sensitive material.

[0109] In some embodiments, a composition comprises more than one layer of a controlled release coating that comprises a pH-sensitive material. In some embodiments, a composition comprises more than one layer of a controlled release coating that comprises a microbe- sensitive material. In some embodiments, a composition comprises more than one layer of a controlled release coating that comprises a pH-sensitive material and more than one layer of a controlled release coating that comprises a microbe-sensitive material. In some embodiments, a composition comprises one, two, three four, five or more layers of controlled release coating that comprise a pH-sensitive material. In some embodiments, a composition comprises one, two, three four, five or more layers of controlled release coating that comprise a microbe-sensitive material. In some embodiments, a composition comprises one, two, three four, five or more layers of controlled release coating that comprise a pH-sensitive material and / or one, two, three four, five or more layers of controlled release coating that comprise a pH-sensitive material. In some embodiments, a composition comprises one, two, three four, five or more layers of controlled release coating that comprise a pH-sensitive material and / or one, two, three four, five or more layers of controlled release coating that comprise a pH- sensitive material and / or a carrier as described herein. In some embodiments, a carrier comprising a polymer is contained within one, two, three four, five or more layers of controlled release coating that comprise a pH-sensitive material and / or one, two, three four, five or more layers of controlled release coating that comprise a pH-sensitive material. In some embodiments, a carrier comprising a PVP polymer is contained within one, two, three four, five or more layers of controlled release coating that comprise a pH-sensitive material and / or one, two, three four, five or more layers of controlled release coating that comprise a pH-sensitive material. In some embodiments, a carrier comprising a 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 controlled release coating that comprise a pH-sensitive material and / or one, two, three four, five or more layers of controlled release coating that comprise a pH-sensitive material.

[0110] In some embodiments, a composition comprises a layer of controlled release coating that comprises a pH-sensitive material that is configured to dissolve at a pH of a distal ileum and a layer of a controlled release coating that comprises a microbe- sensitive material that is susceptible to degradation by one or more microbial organisms residing in a caecum and / or colon.

[0111] In some embodiments, a composition comprises a layer of controlled release coating that comprises a pH-sensitive material that is configured to dissolve at a pH of a proximal small intestine and a layer of a controlled release coating that comprises a microbe- sensitive material that is susceptible to degradation by one or more microbial organisms residing in a small intestine. In some embodiments, a composition comprises a layer of controlled release coating that comprises a pH-sensitive material that is configured to dissolve at a pH of a proximal small intestine and a layer of a controlled release coating that comprises a microbe- sensitive material that is susceptible to degradation by one or more microbial organisms residing in an ileum.

[0112] In some embodiments, a composition comprises a first layer of controlled release coating that comprises a microbe- sensitive material that is susceptible to degradation by one or more microbial organisms residing in a small intestine and a second layer of a controlled release coating that comprises a pH-sensitive material that is configured to dissolve in an ileum. In some embodiments, a composition comprises a first layer of controlled release coating that comprises a microbe-sensitive material that is susceptible to degradation by one or more microbial organisms residing in a small intestine and a second layer of a controlled release coating that comprises a pH-sensitive material that is configured to dissolve in an ileum, and a third layer of controlled release coating that comprises a microbe-sensitive material that is susceptible to degradation by one or more microbial organisms residing in a colon. In some embodiments, a composition further comprises a carrier comprising a polymer, e.g., a PVP polymer associated with a protease inhibitor, e.g. a bacterial protease inhibitor.

[0113] In some embodiments, a composition comprises first layer of controlled release coating that comprises a pH-sensitive material configured to dissolve in an ileum and a second layer of controlled release coating that comprises a microbe-sensitive material that is susceptible to degradation by one or more microbial organisms residing in a colon.

[0114] In some embodiments, a composition comprises first layer of controlled release coating that comprises a pH-sensitive material configured to dissolve in a proximal small intestine and a second layer of controlled release coating that comprises a second pH configured to dissolve in a distal ileum of a subject.

[0115] In some embodiments, a composition comprises one or more hydrophilic layers and one or more lipophilic layers. In some embodiments, a composition comprises one or more layers formed from an aqueous solution and one or more layers formed from an organic solution. In some embodiments, a composition comprises one or more hydrophilic layers and does not comprise a lipophilic layer. In some embodiments, a composition comprises one or more layers formed from an aqueous solution and does not comprise a layer formed from an organic solution.

[0116] In some cases, a controlled release coating comprises one or more hydrophilic layers and one or more lipophilic layers. In some cases, a controlled release coating comprises one or more layers formed from an aqueous solution and one or more layers formed from an organic solution. In some embodiments, a controlled release coating comprises one or more hydrophilic layers and one or more lipophilic layers. In some embodiments, a controlled release coating comprises one or more layers formed from an aqueous solution and one or more layers formed from an organic solution. In some embodiments, a controlled release coating comprises one or more hydrophilic layers and does not comprise a lipophilic layer. In some embodiments, a controlled release coating comprises one or more layers formed from an aqueous solution and does not comprise a layer formed from an organic solution.

[0117] In certain embodiments, the controlled release coating comprises a rupturable film. In certain embodiments, the controlled release coating comprises a hydrogel plug configured to swell upon exposure to moisture and rupture the coating. In some instances, the hydrogel plug may be covered by a cap comprising a pH-sensitive material and / or a microbe-sensitive material.

[0118] In some embodiments, a composition comprises a protease inhibitor described herein and a carrier. In some embodiments, a composition comprises a protease inhibitor described herein and a liquid or gel carrier. Non-limiting examples of suitable liquid or gel carriers include water, saline solutions, alcohol solutions, dextrose solutions, glycerol solutions, and oils, including but not limited to petroleum oil (e.g., mineral oil), vegetable oil (e.g., peanut oil, soybean oil, sesame oil), animal oil, and oil of synthetic origin.

[0119] In some embodiments, a composition is formulated as a solution, emulsion, or suspension. In some embodiments, a composition is formulated as a solution, emulsion, or suspension for oral administration. In some embodiments, a composition is formulated as a solution, emulsion, or suspension for intrarectal administration. In some embodiments, a composition is formulated as an aqueous solution, an alcoholic solution, an emulsion, a gel, a cream, and / or an ointment. In some embodiments, a composition is formulated as an aqueous solution, an alcoholic solution, an emulsion, a gel, a cream, and / or an ointment for rectal administration. In some embodiments, a composition is formulated as an aqueous solution, an alcoholic solution, an emulsion, a gel, a cream, and / or an ointment for oral administration.

[0120] In some embodiments, a composition is formulated as a solution for intravenous administration. In some embodiments, a composition is formulated as an aqueous solution for intravenous administration. In some embodiments, a composition is formulated as a solution for intraperitoneal, intramuscular, subcutaneous, intravenous, or intrathecal administration. In some embodiments, a composition is formulated as a solution for intraperitoneal, intramuscular, subcutaneous, intravenous, or intrathecal injection. In some embodiments, a composition is formulated as an intraperitoneal, intramuscular, subcutaneous, intravenous, or intrathecal infusion.

[0121] In some aspects, a pharmaceutical dosage form comprises a protease inhibitor described herein (e.g., a gliptin or a pharmaceutically acceptable salt thereof) and a liquid or gel carrier. In certain embodiments, the pharmaceutical dosage form is formulated as a solution, emulsion, or suspension for oral administration. In certain embodiments, the pharmaceutical dosage form is formulated as an aqueous solution, an alcoholic solution, an emulsion, a gel, a cream, and / or an ointment for rectal administration. In certain embodiments, rectal administration is achieved through the use of an enema, a suppository, a tube, or an aerosol with an attachment that is inserted into the anus. In certain 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, saline solutions, alcohol solutions, dextrose solutions, glycerol solutions, and oils, including but not limited to petroleum oil (e.g., mineral oil), vegetable oil (e.g., peanut oil, soybean oil, sesame oil), animal oil, and oil of synthetic origin.

[0122] II. Methods of Use

[0123] Some aspects relate to a method of treating an IBD. The IBD may be UC and / or Crohn’s disease. In some embodiments, the method comprises 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.

[0124] The protease inhibitor may be any protease inhibitor described herein. In some embodiments, provided are methods comprising delivering an inhibitor of a protease to a subject in need thereof. In some embodiments, provided are methods comprising delivering two or more (e.g., 2, 3, 4, 5, or 5-10) protease inhibitors to a subject in need thereof. In some embodiments, provided are methods comprising administering an inhibitor of a protease to a subject in need thereof. In some embodiments, provided are methods comprising administering two or more (e.g., 2, 3, 4, 5, or 5-10) protease inhibitors to a subject in need thereof. In some embodiments, provided are methods comprising delivering an inhibitor of a bacterial protease to a subject in need thereof. In some embodiments, provided are methods comprising delivering two or more (e.g., 2, 3, 4, 5, or 5-10) bacterial protease inhibitors to a subject in need thereof. In some embodiments, provided are methods comprising administering an inhibitor of a bacterial protease to a subject in need thereof. In some embodiments, provided are methods comprising administering two or more (e.g., 2, 3, 4, 5, or 5-10) bacterial protease inhibitors to a subject in need thereof. In some embodiments, the protease is a serine protease, a cysteine protease, or a metalloprotease. In certain embodiments, the protease is a serine protease (e.g., an S09 protease). In some embodiments, the protease is configured to cleave GLP-1 and / or GLP-2. In certain embodiments, the protease is configured to preferentially cleave GLP-2. In some instances, the protease is dipeptidyl peptidase-4 (“DPP-4”).

[0125] In some embodiments, the protease is expressed by a microbial organism (e.g., a bacterium) in the intestinal microbiome. In some instances, the bacterium is a species of Bacteroides bacteria. Non-limiting examples of suitable species of Bacteroides bacteria include B. vulgatus, B. dorei, B. fragilis, B. massiliensis, B. ovatus, B. theta, B. uniforms, B. stercoris, B. cellulosilyticus, B. xylanisolvens, and B. caccae. In some cases, the bacterium is B. vulgatus and / or B. dorei. In certain instances, the bacterium is B. vulgatus. In some instances, the genera of the bacteria may be from the genera Phocaeicola, which was reclassified from the genera Bacteroides. Non-limiting examples of suitable species of the Phocaeicola genera include P. vulgatus and P. dorei. In some instances, a protease comprises a DPP-4 expressed by B. vulgatus and / or B. dorei.

[0126] In some embodiments, a protease inhibitor comprises a gliptin or a pharmaceutically acceptable salt thereof. Non-limiting examples of suitable gliptins include sitagliptin, teneligliptin, omarigliptin, vildagliptin, saxagliptin, alogliptin, lingagliptin, gemigliptin, anagliptin, trelagliptin, evogliptin, gosogliptin, dutogliptin, neogliptin, retagliptin, cofrogliptin, fotagliptin, and prusogliptin, or a derivative or combination thereof (see, e.g., K. Wang, Science 2023, 381, 501; A. Wang, BMC Pharmacology 2012, 12(2), p. 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 gliptin is a gliptin that inhibits a bacterial protease. In some embodiments, a suitable gliptin is a gliptin that inhibits a bacterial protease of a microbiome present in a subject having IBD. In some embodiments, a suitable gliptin is a gliptin that inhibits a bacterial protease of a microbiome present in a subject that does not have diabetes. In some embodiments, a suitable gliptin is a gliptin that inhibits a bacterial protease of a microbiome present in a subject that does not have an inflammatory disease or disorder other than IBD. In some embodiments, a protease inhibitor comprises a prodrug of a gliptin or a pharmaceutically acceptable salt thereof. In some embodiments, the subject is a mammalian subject. In certain embodiments, the subject is a human subject. In certain embodiments, 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, cows, pigs, horses, mice, rats, and rabbits. The subject may be male or female. In some cases, the subject is an adult (e.g., 18 years old or older). In some cases, the subject is a child (e.g., 17 years old or younger).

[0127] In some embodiments, the subject has been diagnosed with an IBD (e.g., UC, Crohn’s disease). In some embodiments, the subject exhibits one or more symptoms of an IBD (e.g., UC, Crohn’s disease). In some embodiments, the subject is at risk of developing an 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 an inflammatory disease or condition other than IBD. In some embodiments, the subject is not at risk of developing an inflammatory disease or condition other than IBD.

[0128] In some embodiments, the subject has not received another IBD treatment. In some embodiments, the subject has received another IBD treatment. In some embodiments, the subject is concomitantly receiving another IBD treatment. In some embodiments, the subject is refractory to another IBD treatment. In some embodiments, the other IBD treatment comprises an aminosalicylate, a corticosteroid, an immunosuppressant, a biologic agent, an anti-tumor necrosis factor agent, or a combination or two or more thereof.

[0129] In some embodiments, a therapeutically effective amount of the protease inhibitor is an amount sufficient to alleviate (e.g., delay or reduce the onset, progression, and / or severity of) one or more symptoms of an IBD (e.g., UC, Crohn’s disease) in a subject. In certain embodiments, a therapeutically effective amount of the protease inhibitor is an amount sufficient to reduce the risk of a subject developing an IBD (e.g., UC, Crohn’s disease). In certain embodiments, a 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 of a subject.

[0130] In some embodiments, a method comprises 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 comprises administering a composition comprising a protease inhibitor and / or a carrier via oral, rectal, enteral, parenteral (e.g., intravenous, intramuscular, subcutaneous, intrathecal), nasal, urogenital, topical, and / or intraperitoneal administration. In some embodiments, the method comprises administering a composition comprising a protease inhibitor and / or a carrier via oral, rectal, or enteral administration. In some embodiments, “enteral” administration comprises administration to an enteral location other than the oral cavity. In some embodiments, enteral administration comprises administration via an enteral catheter. In some embodiments, enteral administration comprises administration via an enteral catheter to a small intestine. In some embodiments, enteral administration comprises administration via an enteral catheter to a large intestine (e.g., colon). In some embodiments, enteral administration comprises intrarectal administration.

[0131] In some embodiments, 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 comprises administering a pharmaceutical composition comprising the protease inhibitor via oral, rectal, enteral, parenteral (e.g., intravenous, intramuscular, subcutaneous, intrathecal), nasal, urogenital, topical, and / or intraperitoneal administration. In certain embodiments, a pharmaceutical composition is formulated for delivery of the protease inhibitor to the gut of a subject. In certain embodiments, a pharmaceutical composition is formulated for delivery of the protease inhibitor to the large intestine of a subject. In certain embodiments, a pharmaceutical composition is formulated for delivery of the protease inhibitor to the colon of a subject. In certain embodiments, a pharmaceutical composition is formulated for delivery of the protease inhibitor to the small intestine of a subject.

[0132] In some embodiments, a composition has a solid form. In some embodiments, a pharmaceutical composition has a solid form. In certain embodiments, solid forms comprise tablets, gelcaps, capsules, lozenges, pills, powders, granules, sachets, or other suitable solid forms. In some instances, the solid form comprises 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 (a) fillers or extenders such as starches, lactose, sucrose, glucose, mannitol, and silicic acid, (b) binders such as, for example, carboxymethylcellulose, alginates, gelatin, polyvinylpyrrolidone, sucrose, and acacia, (c) humectants such as glycerol, (d) disintegrating agents such as agar, calcium carbonate, potato or tapioca starch, alginic acid, certain silicates, and sodium carbonate, (e) solution retarding agents such as paraffin, (f) absorption accelerators such as quaternary ammonium compounds, (g) wetting agents such as, for example, cetyl alcohol and glycerol monostearate, (h) absorbents such as kaolin and bentonite clay, and (i) lubricants such as talc, calcium stearate, magnesium stearate, solid polyethylene glycols, sodium lauryl sulfate, and mixtures thereof. In the case of capsules, tablets, and pills, the dosage form may include a buffering agent. In some instances, the solid form comprises a controlled release coating, as described herein. In some embodiments, the solid form is formulated for oral administration. In some instances, the solid form is formulated as a suppository (e.g., for rectal administration).

[0133] In some instances, the solid form comprises a controlled release coating, as described herein. In some embodiments, the solid form is formulated for oral administration. In some instances, the solid form is formulated as a suppository (e.g., for rectal administration).

[0134] In some embodiments, a composition has a liquid or gel form. In some embodiment, a liquid or gel form comprises a solution, emulsion, or suspension configured for oral, rectal, enteral, parenteral (e.g., intravenous, intramuscular, subcutaneous, intrathecal), nasal, urogenital, topical, and / or intraperitoneal administration. In some embodiments, the pharmaceutical composition has a liquid or gel form. In some instances, the liquid or gel form comprises a solution, emulsion, or suspension configured for oral, rectal, enteral, parenteral (e.g., intravenous, intramuscular, subcutaneous, intrathecal), nasal, urogenital, topical, and / or intraperitoneal administration. In certain embodiments, the liquid or gel form is formulated as a solution, emulsion, or suspension for oral administration. In certain embodiments, the liquid or gel form is formulated as an enema for rectal administration. In certain embodiments, the liquid or gel form is formulated as an injection for intraperitoneal, intramuscular, subcutaneous, intravenous, or intrathecal administration.

[0135] In some embodiments, the liquid or gel form comprises a liquid or gel carrier. Nonlimiting examples of suitable liquid or gel carriers include water, saline solutions, dextrose solutions, glycerol solutions, and oils, including but not limited to petroleum oil (e.g., mineral oil), vegetable oil (e.g., peanut oil, soybean oil, sesame oil), animal oil, and oil of synthetic origin.

[0136] In some embodiments, a composition is formulated as a spray. In some embodiments, a pharmaceutical composition is formulated as a spray (e.g., for nasal administration).

[0137] In some embodiments, a composition is administered chronically. In some embodiments, a pharmaceutical composition is administered chronically. In certain embodiments, the pharmaceutical composition is administered over 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 certain embodiments, the pharmaceutical composition is administered 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, a pharmaceutical composition is administered to a subject daily, weekly, monthly, or at shorter or longer time intervals. In some embodiments, the 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, a pharmaceutical composition is administered to a subject every other day, every third day, every fourth day, every fifth day, every sixth day, every seventh day, every eighth day, every nineth day, every tenth day, every eleventh day, every twelfth day, every thirteenth day, biweekly, or every 3 weeks. In some embodiments, administration at longer intervals includes 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 embodiments, a pharmaceutical composition is administered to a subject until one or more symptoms of an IBD (e.g., UC, Crohn’s disease) are alleviated. The pharmaceutical dosage forms described herein can be administered concurrently with, prior to, or subsequent to one or more additional pharmaceutical agents, which may be useful as, e.g., combination therapies. Pharmaceutical agents include therapeutically active agents. Pharmaceutical agents also include prophylactically active agents. Pharmaceutical agents include small organic molecules such as drug compounds (e.g., compounds approved for human or veterinary use by the U.S. Food and Drug Administration as provided in the Code of Federal Regulations (CFR)), peptides, proteins, carbohydrates, monosaccharides, oligosaccharides, polysaccharides, nucleoproteins, mucoproteins, lipoproteins, synthetic polypeptides or proteins, small molecules linked to proteins, glycoproteins, steroids, nucleic acids, DNAs, RNAs, nucleotides, nucleosides, oligonucleotides, antisense oligonucleotides, lipids, hormones, vitamins, and cells. In certain embodiments, the additional pharmaceutical agent is a pharmaceutical agent useful for treating and / or preventing a disease (e.g., an inflammatory bowel disorder). Examples of additional pharmaceutical agents include, but are not limited to, aminosalicylates (e.g., sulfasalazine or 5- aminosalicylates or portions thereof including mesalamine, olasalazine and balsalzide), glucocorticoids (e.g., prednisolone, ileal acting budesonide, budenoside MMX, and beclomethasone dipropionate), immunomodulators (e.g., azathioprine, 6-mercaptopurine, cyclosporine, or methotrexate), anti-TNF antibodies (e.g., infliximab, adalimumab, certolizumab pegol, or golimumab), anti-integrin antibodies (e.g., natalizumab or vedolizumab), antiinterleukin antibodies (ustekinumab, risankizumab, or mirikizumab), Janus Kinase (JAK) inhibitors (e.g., tofacitinib, filgotinib, or upadacitinib), or Sphingosine- 1 -phosphate (Sip) modulators (e.g., ozanimod or etrasimod).

[0138] Each additional pharmaceutical agent may be administered at a dose and / or on a time schedule determined for that pharmaceutical agent. The additional pharmaceutical agents may also be administered together with each other and / or with the compound or composition described herein in a single dose or composition or administered separately in different doses or compositions. The particular combination to employ in a regimen will take into account compatibility of the compound described herein with the additional pharmaceutical agent(s) and / or the desired therapeutic and / or prophylactic effect to be achieved. In general, it is expected that the additional pharmaceutical agent(s) in combination be utilized at levels that do not exceed the levels at which they are utilized individually. In some embodiments, the levels utilized in combination will be lower than those utilized individually.

[0139] Some aspects relate to a method of treating an IBD (e.g., UC, Crohn’s disease) comprising determining an abundance of a bacterial protease in a sample obtained from a subject and delivering a therapeutically effective amount of an inhibitor of the bacterial protease to the large intestine (e.g., colon) and / or small intestine of the subject. In some embodiments, a method of treating an IBD comprises administering to a subject determined to have an abundance of bacterial protease in the intestine a therapeutically effective amount of an inhibitor of a bacterial protease to a large intestine, (e.g., colon) and / or a small intestine of the subject. The bacterial protease may be any bacterial protease described herein. The inhibitor of the bacterial protease may be any protease inhibitor (e.g., a gliptin or a pharmaceutically acceptable salt thereof) described herein. The subject may be any subject described herein.

[0140] In some embodiments, determining an abundance of a bacterial protease in a sample obtained from a subject comprises obtaining the sample from the subject. In certain embodiments, the sample represents characteristics of the subject’s GI tract. In some instances, the sample is a fecal sample. In some instances, the sample is a gastrointestinal sample taken from the GI tract (e.g., the lower GI tract, the upper GI tract). The gastrointestinal sample may be obtained during any suitable procedure, including but not limited to colonoscopy, endoscopy, swabbing, or brushing a part of the GI tract. In some instances, the sample is a serum sample.

[0141] In some embodiments, determining the abundance of the bacterial protease comprises determining an abundance of one or more genes present in the sample from the subject. In some embodiments, determining the abundance of one or more genes present in the sample comprises extracting DNA and / or RNA from at least a portion of the sample. Any nucleic acid extraction method known in the art may be used. In some embodiments, determining the abundance of one or more genes present in the sample further comprises amplifying at least a portion of the DNA and / or RNA to produce a plurality of amplicons. Any nucleic acid amplification method known in the art may 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 the sample comprises 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 the sample further comprises sequencing one or more amplicons. Any suitable nucleic acid sequencing method may be used. In certain embodiments, the nucleic acid sequencing method is a long-read sequencing method. In certain embodiments, the nucleic acid sequencing method is a short-read sequencing method. In some embodiments, the nucleic acid sequencing method is a next-generation sequencing method. In some embodiments, the nucleic acid sequencing method is performed using an Illumina, Pacific Biosciences, Oxford Nanopore, and / or Roche 454 sequencing platform.

[0142] In some embodiments, determining the abundance of one or more genes present in a sample comprises sequencing at least a portion of 16S ribosomal RNA (rRNA) of microbes present in the sample (e.g., performing 16S rRNA gene amplicon (16S) sequencing). In some cases, performing 16S sequencing comprises amplifying at least a portion of one or more regions of the 16S rRNA genome of microbes present in the sample to produce a plurality of amplicons. Any nucleic acid amplification method (e.g., PCR) may be used. In some embodiments, the one or more regions of the 16S rRNA genome comprise at least one hypervariable region (e.g., V4, V3-V4, V1-V2). In some cases, performing 16S sequencing further comprises sequencing one or more amplicons of the plurality of amplicons. Any suitable nucleic acid sequencing method may be used.

[0143] In some embodiments, determining the abundance of one or more genes present in a sample comprises performing shotgun metagenomic sequencing to sequence the metagenomic content of the sample. In some cases, shotgun metagenomic sequencing methods comprise extracting DNA from a sample, fragmenting the extracted DNA into DNA fragments, and sequencing the DNA fragments. Any suitable nucleic acid sequencing method may be used. In some cases, the resulting sequences of the DNA fragments may be analyzed to identify microbes present in the sample.

[0144] In some embodiments, determining the abundance of one or more genes present in a sample comprises determining the level of one or more gene products (e.g., enzymes) in a sample. The level of the one or more gene products may be determined according to any method known in the art, including but not limited to an enzyme-linked immunosorbent assay (ELISA) and other antibody-based assays, and liquid chromatography-mass spectrometry (LC- MS)-based proteomics and other protein-based quantification assays. In some embodiments, determining the abundance of one or more genes present in a sample comprises determining the level of one or more molecules that directly or indirectly interact with one or more gene products (e.g., enzymes) in a metabolic pathway (e.g., as a substrate or a product). The level of the one or more molecules (e.g., substrates, products) may be determined according to 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. According to some embodiments, a method comprises determining, if the abundance of the bacterial protease is higher or lower than a threshold value, that a therapeutically effective amount of an inhibitor of the bacterial protease should be administered. In some cases, the threshold value may be determined based on the level of the bacterial protease in one or more healthy individuals (e.g., individuals who have not been diagnosed with an inflammatory bowel disease). In some cases, the threshold value may be determined by identifying an optimal discriminatory boundary between a first population of individuals diagnosed with an inflammatory bowel disease and a second population of healthy individuals.

[0145] Administering the therapeutically effective amount of the inhibitor of the bacterial protease may be performed according to any method described herein.

[0146] III. Kits

[0147] Also encompassed by the disclosure are kits (e.g., pharmaceutical packs). The kits provided may comprise a pharmaceutical composition or compound described herein and a container (e.g., a vial, ampule, bottle, syringe, and / or dispenser package, or other suitable container). In some embodiments, provided kits may optionally further include a second container comprising a pharmaceutical excipient for dilution or suspension of a pharmaceutical composition or compound described herein. In some embodiments, the pharmaceutical composition or compound described herein provided in the first container and the second container are combined to form one unit dosage form.

[0148] In one aspect, provided herein is a kit comprising: a compound described herein, or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled compound, or prodrug thereof, or a pharmaceutical composition provided herein; and instructions for using the compound, or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled compound, or prodrug thereof, or the pharmaceutical composition.

[0149] Thus, in certain embodiments, provided are kits including a first container comprising a compound or pharmaceutical composition described herein. In certain embodiments, the kits are useful for treating a disease (e.g., metabolic disorder) in a subject in need thereof. In certain embodiments, the kits are useful for preventing a disease (e.g., an inflammatory bowel disease) in a subject in need thereof. In certain embodiments, the kits are useful for reducing the risk of developing a disease (e.g., inflammatory bowel disease) in a subject in need thereof. In certain embodiments, the kits are useful for inhibiting the activity of a protease in a subject or cell.

[0150] In certain embodiments, a kit described herein further includes instructions for using the kit. A kit described herein may also include information as required by a regulatory agency such as the U.S. Food and Drug Administration (FDA). In certain embodiments, the information included in the kits is prescribing information. In certain embodiments, the kits and instructions provide for treating a disease (e.g., inflammatory bowel disease) in a subject in need thereof. In certain embodiments, the kits and instructions provide for preventing a disease (e.g., inflammatory bowel disease) in a subject in need thereof. In certain embodiments, the kits and instructions provide for reducing the risk of developing a disease (e.g., inflammatory bowel disease) in a subject in need thereof. In certain embodiments, the kits and instructions provide for inhibiting the activity of a protease in a cell. A kit described herein may include one or more additional pharmaceutical agents described herein as a separate composition.

[0151] EXAMPLE 1

[0152] In this Example, dipeptidyl peptidase-4 (“DPP-4”) from B. vulgatus was selected as a therapeutic target.

[0153] A pangenomic comparison of S09 family proteases among Bacteroides was performed. Genes from reference genomes of Bacteroides species were aligned to the MEROPS database of proteases. Genes falling under the S09 family of proteases were counted and compared among each reference genome and split by sub-class. It was found the S09.13 proteases were enriched within B. vulgatus and B. dorei organisms.

[0154] A pangenomic comparison of Bacteroides S09 B / C family proteases and Porphyromonas gingivalis DPP-4 was then performed, with the phylogenetic distance between each sequence falling under the S09 classification being calculated. The S09.65 protease was found to be unique to B. vulgatus and B. dorei. It was also found that the S09.13 proteases were closely related (i.e., had the highest sequence similarity) to human and P. gingivalis DPP-4.

[0155] Based on the pangenomic comparisons, the sequence of the DPP-4 from B. vulgatus selected as a therapeutic target is: MTKKNLFTLVLCLFCFGTTTHAQRIPTLEEAVYGGLIKTEGGSNVNWMKDGERYSKIEK NAEGAYEVTAYKAKDNSKEVLIPANMLLNPQTGKPISVRNFVFSEDNSKVLIYTNTRRV WRYDTRGDYWVLNLKDGKLQQLGKSLPEATLMFAKFSPDASRVAYVSRNNIYVESLV DGKINQLTQDGNNEIVNGTFDWVYEEEFNCRDGFRWSPDGQYIAYWQSDTQGTGWFD IINNVDSIYPKIQRFPYPKAGTANSAVKVGYVSADGGNTTWLALPGDARNHYIPRMEFIP GCNELFIQQMNRAQNTNKVWIAKIGENTPVNIFTDQDAAWLETNDNVRWLKGNKYFT WESERDGWRHLYRVSRDGKEIKPITQGAFDYIQEVGADMDKGFVYFIASPDNFTQRYL YRARLFGNGEVKRLSPVDQSGQHRYIMSPSGKWAVHTFSNSETPPVIDMVSFPAHKSIR LITDNAKAKEQYKALGLQPKEFVKTRSGELELDAWMIKPVNFDPSKKYPVIIDVYGEPA NATVQDVWSGGSLWHQYLANLGYIIVSIENRGANAPRGREWRKCIYGEVGTFASEDQA RGIQDLARQYSFIDTARIGITGWSGGGSQTLNSMFRYPDVFHTGIAIAFVADQRLYDTVY QERYMNTPQNNPEGYRKGSPISYAAGLKGNLLLIHGTGDDNVHYQNCEMLVNELVRH GKIFSQISYPMRSHGIYEGEGTSLHLRKTMADYWLKNLPAGGK (SEQ ID NO: 1).

[0156] EXAMPLE 2

[0157] In this Example, DPP-4 from B. vulgatus was validated as a therapeutic target.

[0158] FIG. 1 shows a plot of trans-epithelial electrical resistance (“TEER”) as a function of time (hours) for T84 intestinal cells. It was found that intestinal cells with DPP-4 from B. vulgatus (labeled “DPP-4”) had significantly lower TEER values than intestinal cells without DPP-4 from B. vulgatus (labeled “Cell control”), indicating a disruption of epithelial barrier integrity. It was further found that adding a protease inhibitor (lx Roche cOmplete EDTA-Free Protease Inhibitor Cocktail) to intestinal cells with DPP-4 from B. vulgatus significantly increased TEER values, resulting in TEER values that were relatively close to those of the intestinal cells without DPP-4 from B. vulgatus. FIG. 1 thus demonstrates that DPP-4 from B. vulgatus reduces intestinal barrier integrity and that addition of a protease inhibitor mitigates the effects of DPP-4.

[0159] FIG. 2 shows percent adherence and invasion of intestinal cells for wild-type B. vulgatus with DPP-4 (left) and B. vulgatus with DPP-4 genetically removed (right). It was found that removing DPP-4 prevented B. vulgatus from adhering to and invading intestinal cells.

[0160] EXAMPLE 3

[0161] In this Example, it was demonstrated that certain gliptins differentially inhibited DPP-4 from B. vulgatus. The effect of six gliptin compounds - sitagliptin, linagliptin, teneligliptin, trelagliptin, omarigliptin, and vildagliptin - on B. vulgatus DPP-4 activity in vitro was evaluated. FIG. 3 shows a plot of percent inhibition as a function of gliptin concentration (pM). It was found that sitagliptin, omarigliptin, teneligliptin, and vildagliptin inhibited B. vulgatus DPP-4 activity in the micromolar range. The IC50 for sitagliptin was 3.17 pM. In contrast, trelagliptin and linagliptin were not found to inhibit B. vulgatus DPP-4 activity. The structures of sitagliptin, omariglitpin, teneligliptin, and vildagliptin are shown in FIG. 4. The inhibitory effect of two gliptin compounds, saxagliptin and vildagliptin, were further tested in vitro using different orthologs of DPP-4, two forms encoded in the B. vulgatus genome (BVU3876 and BVU1991), an ortholog from Bacteroides thetaiotaomicron (BT4193) and the human DPP-4. A table demonstrating the IC50 values for vildagliptin and saxagliptin on each ortholog are shown in FIG. 5. The B. vulgatus DPP-4 examined in the previous examples, BVU3876, demonstrated IC50’s of 5.65 pM and 3.5 pM for vildagliptin and saxagliptin respectively.

[0162] EXAMPLE 4

[0163] In this Example, it was demonstrated that rectal administration of the DPP-4 inhibitor, sitagliptin, shows improved protection from colitis in comparison to orally administered sitagliptin.

[0164] FIG. 6 shows the disease activity index of 10-week old male C57BL / 6 mice after 6 days of administering 3% Dextran Sodium Sulfate in drinking water and administration of daily 30 mg / kg sitagliptin by oral gavage or intrarectal dosing. Intrarectal administration of sitagliptin resulted in a significant improvement in disease activity at day 7 in comparison to oral sitagliptin treatment and intrarectal control groups.

[0165] While several embodiments of the present invention have been described and illustrated herein, those of ordinary skill in the art will readily envision a variety of other means and / or structures for performing the functions and / or obtaining the results and / or one or more of the advantages described herein, and each of such variations and / or modifications is deemed to be within the scope of the present invention. More generally, those skilled in the art will readily appreciate that all parameters, dimensions, materials, and configurations described herein are meant to be exemplary and that the actual parameters, dimensions, materials, and / or configurations will depend upon the specific application or applications for which the teachings of the present invention is / are used. Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, many equivalents to the specific embodiments of the invention described herein. It is, therefore, to be understood that the foregoing embodiments are presented by way of example only and that, within the scope of the appended claims and equivalents thereto, the invention may be practiced otherwise than as specifically described and claimed. The present invention is directed to each individual feature, system, article, material, and / or method described herein. In addition, any combination of two or more such features, systems, articles, materials, and / or methods, if such features, systems, articles, materials, and / or methods are not mutually inconsistent, is included within the scope of the present invention.

[0166] The indefinite articles “a” and “an,” as used herein in the specification and in the claims, unless clearly indicated to the contrary, should be understood to mean “at least one.”

[0167] The phrase “and / or,” as used herein in the specification and in the claims, should be understood to mean “either or both” of the elements so conjoined, i.e., elements that are conjunctively present in some cases and disjunctively present in other cases. Other elements may optionally be present other than the elements specifically identified by the “and / or” clause, whether related or unrelated to those elements specifically identified unless clearly indicated to the contrary. Thus, as a non-limiting example, a reference to “A and / or B,” when used in conjunction with open-ended language such as “comprising” can refer, in one embodiment, to A without B (optionally including elements other than B); in another embodiment, to B without A (optionally including elements other than A); in yet another embodiment, to both A and B (optionally including other elements); etc.

[0168] As used herein in the specification and in the 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” shall be interpreted as being inclusive, i.e., the inclusion of at least one, but also including more than one, of a number or list of elements, and, optionally, additional unlisted items. Only terms clearly indicated to the contrary, such as “only one of’ or “exactly one of,” or, when used in the claims, “consisting of,” will refer to the inclusion of exactly one element of a number or list of elements. In general, the term “or” as used herein shall only be interpreted as indicating exclusive alternatives (i.e. “one or the other but not both”) when preceded by terms of exclusivity, such as “either,” “one of,” “only one of,” or “exactly one of.” “Consisting essentially of,” when used in the claims, shall have its ordinary meaning as used in the field of patent law.

[0169] As used herein in the specification and in the claims, the phrase “at least one,” in reference to a list of one or more elements, should be understood to mean at least one element selected from any one or more of the elements in the list of elements, but not necessarily including at least one of each and every element specifically listed within the list of elements and not excluding any combinations of elements in the list of elements. This definition also allows that elements may optionally be present other than the elements specifically identified within the list of elements to which the phrase “at least one” refers, whether related or unrelated to those elements specifically identified. 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”) can refer, in one embodiment, to at least one, optionally including more than one, A, with no B present (and optionally including elements other than B); in another embodiment, to at least one, optionally including more than one, B, with no A present (and optionally including elements other than A); in yet another embodiment, to at least one, optionally including more than one, A, and at least one, optionally including more than one, B (and optionally including other elements); etc.

[0170] Some embodiments may be embodied as a method, of which various examples have been described. The acts performed as part of the methods may be ordered in any suitable way. Accordingly, embodiments may be constructed in which acts are performed in an order different than illustrated, which may include different (e.g., more or less) acts than those that are described, and / or that may involve performing some acts simultaneously, even though the acts are shown as being performed sequentially in the embodiments specifically described above.

[0171] Use of ordinal terms such as “first,” “second,” “third,” etc., in the claims to modify a claim element does not by itself connote any priority, precedence, or order of one claim element over another or the temporal order in which acts of a method are performed, but are used merely as labels to distinguish one claim element having a certain name from another element having a same name (but for use of the ordinal term) to distinguish the claim elements.

[0172] In the claims, as well as in the specification above, all transitional phrases such as “comprising,” “including,” “carrying,” “having,” “containing,” “involving,” “holding,” and the like are to be understood to be open-ended, i.e., to mean including but not limited to. Only the transitional phrases “consisting of’ and “consisting essentially of’ shall be closed or semi-closed transitional phrases, respectively, as set forth in the United States Patent Office Manual of Patent Examining Procedures, Section 2111.03.

Claims

CLAIMSWhat is claimed is:

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

2. The composition of claim 1, wherein the carrier comprises a polymer that is not absorbed in a 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 of any one of claims 1-4, wherein the inhibitor of the bacterial protease is a gliptin or a pharmaceutical salt thereof.

6. The composition of any one of claim 1-5, further comprising an agent that facilitates a targeted delivery of the inhibitor of the bacterial protease and carrier to an intestinal location.

7. The composition of any one of claims 1-6, wherein the agent comprises a first material that dissolves at a pH between about 6.0 and about pH 7.6.

8. The composition of claim 7, wherein the first material dissolves at a pH 7.5.

9. The composition of any one of claims 1-8, wherein the agent comprises a second material that is susceptible to degradation by a microbial organism.

10. The composition of claim 9 wherein the second material is susceptible to degradation by a microbial organism present in a large intestine of a subject.

11. The composition of claim 10 wherein the second material is susceptible to degradation by a microbial organism present in a colon of a 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 susceptible to degradation by a microbial organism present in a large intestine of a 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 a first layer.

15. The composition of claim 13 or 14, wherein the second material of the agent is present in a 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 a dipeptidyl peptidase-4 (DPP-4).

20. The composition of claim 19, wherein the bacterial protease comprises a DPP-4 expressed by B. vulgatus and / or B. dorei.

21. The composition of any one of claims 5-20, wherein the gliptin comprises sitagliptin, teneligliptin, omarigliptin, vildagliptin, saxagliptin, alogliptin, lingagliptin, gemigliptin, anagliptin, trelagliptin, evogliptin, gosogliptin, dutogliptin, retagliptin, and prusogliptin, or a derivative or combination thereof.

22. A pharmaceutical dosage form, comprising: a core comprising an inhibitor of a bacterial protease; anda controlled release coating applied to an exterior surface of the core, wherein the controlled release coating is configured to release the inhibitor of the bacterial protease in a large intestine and / or small intestine of a subject to whom the pharmaceutical dosage form is administered.

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 of any one of claims 22-24, wherein the bacterial protease is a serine protease.

26. The pharmaceutical dosage form of any one of claims 22-25, wherein the bacterial protease is a 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 a DPP-4 expressed by B. vulgatus and / or B. dorei.

29. The pharmaceutical dosage form of claim 27 or 28, wherein the gliptin comprises sitagliptin, teneligliptin, omarigliptin, vildagliptin, saxagliptin, alogliptin, lingagliptin, gemigliptin, anagliptin, trelagliptin, evogliptin, gosogliptin, dutogliptin, retagliptin, and prusogliptin, or a derivative or combination 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 a 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 of any one of claims 22-32, wherein the controlled release coating comprises one or more pH-sensitive materials.

34. The pharmaceutical dosage form of any one of claims 22-33, wherein the controlled release coating comprises one or more microbe- 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 an inflammatory bowel disease.

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

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

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

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

40. A method of treating an inflammatory bowel disease, comprising: delivering a therapeutically effective amount of an inhibitor of a bacterial protease to a large intestine and / or small intestine of a subject41. The method of claim 40, wherein the inflammatory bowel disease comprises ulcerative colitis.

42. The method of claim 40, wherein the inflammatory bowel disease comprises 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 a dipeptidyl peptidase-4 (DPP-4).

47. The method of claim 46, wherein the bacterial protease comprises a DPP-4 expressed by B. vulgatus and / or B. dorei.

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 thereof49. The method of 48, wherein the gliptin comprises sitagliptin, teneligliptin, omarigliptin, vildagliptin, saxagliptin, alogliptin, lingagliptin, gemigliptin, anagliptin, trelagliptin, evogliptin, gosogliptin, dutogliptin, retagliptin, and prusogliptin, or a derivative or combination 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 claim 50, wherein delivering the therapeutically effective amount of the inhibitor of the bacterial protease comprises orally administering the composition comprising the inhibitor of the bacterial protease.

52. The method of claim 50, wherein delivering the therapeutically effective amount of theinhibitor of the bacterial protease comprises rectally administering 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 the therapeutically effective amount of the inhibitor of the bacterial protease is loaded into the carrier.

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

59. The method of claim 58, wherein the first agent comprises a first material that dissolves at a pH between about 6.5 and about 7.6.

60. The method of claim 59, wherein the first material dissolves 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 that is susceptible to degradation by a microbial organism.

62. The method of claim 61, wherein the second material is susceptible to degradation by a microbial organism present in a large intestine of a 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 susceptible to degradation by a microbial organism present in a large intestine of a subject.

64. The method of claim 58, wherein the first agent comprises a first material that dissolves at a pH between about 5.5 and about 7.1.

65. The method of claim 64, wherein the first material dissolves 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 that is susceptible to degradation by a microbial organism.

67. The method of claim 66, wherein the second material is susceptible to degradation by a microbial organism present in a small intestine of a subject.

68. The 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 susceptible to degradation by a microbial organism present in a small intestine of a 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 orally administering 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 rectally administering a pharmaceutical composition comprising the inhibitor of the bacterial protease.

71. The method of claim 69 or 70, wherein the pharmaceutical composition comprises: a core comprising the therapeutically effective amount of the inhibitor of the bacterial protease; and a controlled release coating applied to an exterior 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 microbe- sensitive materials.

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

75. The method of any one of claims 70-73, wherein delivering the therapeutically effective amount of the inhibitor of the bacterial protease comprises orally administering 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 rectally administering 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 orally administering a pharmaceutical composition comprising the inhibitor of the bacterial protease comprises delivering the therapeutically effective amount of the inhibitor of the bacterial protease to a 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 a colon of the subject.

80. The method of any one of claims 69-76, wherein the orally administering a pharmaceutical composition comprising the inhibitor of the bacterial protease comprises delivering the therapeutically effective amount of the inhibitor of the bacterial protease to a 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 an inflammatory bowel disease.

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

83. The method of claim 81, wherein inflammatory bowel disease comprises Crohn’s disease.

84. A method of treating an inflammatory bowel disease, comprising: determining an abundance of a bacterial protease in a sample obtained from a subject; and delivering a therapeutically effective amount of an inhibitor of the bacterial protease to a large intestine and / or small intestine of the subject, wherein the inhibitor comprises a gliptin or a pharmaceutically acceptable salt thereof.

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

86. The method of claim 84, wherein the inflammatory bowel disease comprises 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 a bacterialdipeptidyl peptidase-4 (DPP-4).

92. The method of claim 91, wherein the bacterial DPP-4 comprises a DPP-4 expressed by B. vulgatus and / or B. dorei.

93. The method of any one of claims 84-92, wherein the gliptin comprises sitagliptin, teneligliptin, omarigliptin, 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 a 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 of treating an inflammatory bowel disease in a subject determined to have an abundance of a bacterial protease in an intestine, the method comprising delivering a therapeutically effective amount of an inhibitor of the bacterial protease to a large intestineand / 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 comprises ulcerative colitis.

101. The method of claim 99, wherein the inflammatory bowel disease comprises 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 a bacterial dipeptidyl peptidase-4 (DPP-4).

106. The method of claim 105, wherein the bacterial DPP-4 comprises a DPP-4 expressed by B. vulgatus and / or B. dorei.

107. The method of any one of claims 99-106, wherein the gliptin comprises sitagliptin, teneligliptin, omarigliptin, 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 thetherapeutically effective amount of the inhibitor of the bacterial protease to a 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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