WO2017201322A1

WO2017201322A1 - Treatment of osteoarthritis with gingipain blocking agents

Info

Publication number: WO2017201322A1
Application number: PCT/US2017/033390
Authority: WO
Inventors: Stephen S. Dominy; Casey C. LYNCH; Florian ERMINI; Mai Nguyen
Original assignee: Cortexyme, Inc.
Priority date: 2016-05-19
Filing date: 2017-05-18
Publication date: 2017-11-23

Abstract

The invention provides methods for treating or preventing osteoarthritis. The method includes administering a therapeutically effective amount of one or more gingipain-blocking agents to a patient in need thereof. In certain embodiments, the gingipain blocking agent is a Kgp inhibitor, an RgpA inhibitor, an RgpB inhibitor, a bacteriocidal agent, a bacteriostatic agent, a gingipain-specific antibody, a vaccine, or a combination thereof.

Description

TREATMENT OF OSTEOARTHRITIS WITH

GINGIPAIN BLOCKING AGENTS CROSS-REFERENCES TO RELATED APPLICATIONS

[0001] The present application claims priority to U.S. Provisional Pat. Appl. No.

62/338,930, filed on May 19, 2016, which application is incorporated herein by reference in its entirety. BACKGROUND OF THE INVENTION

[0002] Osteoarthritis is a chronic joint disease that involves degeneration of articular cartilage. A connection between osteoarthritis and an infectious agent has not been established, though various bacterial DNAs have been identified in osteoarthritic joints. See, Gerard, et al. Arthritis Rheum, 2001.44(7): 1689-97; Ehrlich, et al. J Appl Biomater Funct Mater, 2014.12(1): 13-20. Methods for developing treatments or diagnostics based on a specific infectious target in osteoarthritis have not been developed. A Cochrane review of human studies using chronic administration of the broad-spectrum antibiotic doxycycline to slow cartilage degeneration in osteoarthritis patients concluded that symptomatic benefit for patients was minimal to non-existent, and that the disease modifying effect as measured by joint space narrowing was small and did not outweigh the harms of chronic doxycycline administration. See, da Costa, et al. Cochrane Database Syst Rev, 2012.11: p. CD007323. New methods for treating osteoarthritis are needed. The present invention meets this and other needs. BRIEF SUMMARY OF THE INVENTION

[0003] In a first aspect, the invention provides a method of treating or preventing osteoarthritis. The method includes administering a therapeutically effective amount of one or more gingipain-blocking agents to a patient in need thereof. [0004] In some embodiments, the gingipain blocking agent is a compound which inhibits Lysine Gingipain (Kgp) activity or production; a compound which inhibits translocation of Kgp into joint tissue or into systemic circulation; and/or a compound which inhibits the pathological effects of Kgp in a mammal. In some embodiments, the gingipain blocking agent is a compound which inhibits Arginine Gingipain A (RgpA) activity or production; a compound which inhibits translocation of RgpA into joint tissue or into systemic circulation; and/or a compound which inhibits the pathological effects of RgpA in a mammal. In some embodiments, the gingipain blocking agent is a compound which inhibits Arginine Gingipain B (RgpB) activity or production; a compound which inhibits translocation of RgpA into joint tissue or into systemic circulation; and/or a compound which inhibits the pathological effects of RgpB in a mammal. [0005] In some embodiments, the gingipain blocking agent is a an antibacterial agent which is bacteriostatic or bacteriocidal with respect to P. gingivalis. In some embodiments, the gingipain blocking agent is an antibody which binds to a P. gingivalis protein. In some embodiments, the gingipain blocking agent is a vaccine. [0006] In another aspect, the invention provides a method for treating osteoarthritis, wherein the method includes: identifying a subject having P. gingivalis antigens or P.

gingivalis DNA in synovial fluid or tissue, and administering a therapeutically effective amount of a gingipain blocking agent to the subject having the P. gingivalis antigens or the P. gingivalis DNA in synovial fluid or tissue. BRIEF DESCRIPTION OF THE DRAWINGS

[0007] Fig.1 shows the immunohistochemical analysis of arginine gingipain B from P. gingivalis with 18E6 monoclonal antibody in the subchondral bone marrow (SBM) compartment of osteoarthritic (OA) subjects (left panels) and a non-OA subject (right panels). In the OA subjects, multi-nucleated osteoclasts stained for RgpB (marked with white “ *”) and can be seen in contact with eroding subchondral bone (marked with black“ #”). In the non-OA subject, the bone marrow compartment, periosteum, and subchondral bone appear normal. [0008] Fig.2 shows immunohistochemistry of arginine gingipain from P. gingivalis with 18E6 antibody in synovial tissue from an OA subject (left panel) compared to a non-OA subject (right panel). [0009] Fig.3 shows the PCR analysis of 6 joints from an 19 year old beagle dog that was diagnosed with osteoarthritis in three joints (left shoulder, right shoulder, and left stifle). The left shoulder, right shoulder, and left stifle were positive for P. ginigvalis, while three joints that were not diagnosed with osteoarthritis (right stifle, left elbow and right elbow) were negative for P. ginigvalis. [0010] Fig.4 shows that gingipain inhibitors prevent the degradation of human collagen by P. gingivalis (Pg). SDS polyacrylamide gel electrophoresis (SDS-PAGE) was used for analysis of human collagen (lane A); Pg supernatant (lane B); collagen exposed to Pg supernatant in the absence of gingipain inhibitors (lane C); collagen exposed to Pg

supernatant in the presence of Rgp inhibitor (lane D); collagen exposed to Pg supernatant in the presence of Kgp inhibitor (lane E); and collagen exposed to Pg supernatant in the presence of Rgp inhibitor and Kgp inhibitor. DETAILED DESCRIPTION OF THE INVENTION

I. Definitions [0011] As used herein, the terms“Porphyromonas gingivalis” and“P. gingivalis” refer to the gram-negative asaccharolytic bacterium that is recognized as a key causative microbe in the pathogenesis of periodontitis and related conditions.“P. gingivalis infection” refers to the invasion and colonization of P. gingivalis in a bodily tissue such as the gums or the joints. P. gingivalis infection is frequently characterized by subsequent tissue injury and disease. [0012] As used herein, the term“gingipain” refers to cysteine proteases expressed by P. gingivalis having trypsin-like specificity (i.e., Lys-Xaa and Arg-Xaa). Gingipains are recognized as the major virulence factors of the P. gingivalis and contribute to bacterial attachment and colonization, nutrient acquisition, evasion of host defenses, and tissue invasion. The terms“lysine gingipain” and“Kgp” are used interchangeably to refer to the P. gingivalis lysine-specific gingipain known by EC number EC 3.4.22.47. [0013] As used herein the term“gingipain blocking agent” refers to a substance that:

inhibits gingipain activity; inhibits gingipain production; inhibits translocation of gingipains into systemic circulation; and/or inhibits translocation of gingipains into organs or tissues such as joint tissue. Gingipain blocking agents can be used for reducing and/or preventing the pathological effects of gingipains in vivo. Examples of gingipain blocking agents include, but are not limited to, small molecule gingipain inhibitors; antibodies specific for gingipains or P. gingivalis; antibacterial substances that kill P. gingivalis and/or prevent the growth of P. gingivalis; and vaccines that prevent or reduce the extent of P. gingivalis infection. [0014] As used herein, the term“osteoarthritis” refers to a chronic degenerative joint disease that results from breakdown of joint cartilage, synovial tissue, and underlying bone. [0015] As used herein, the term“joint” refers to the point at which two or more bones connect. Joints can be classified in one or more groups according to characteristics including structure (e.g., cartilaginous joints and synovial joints), function (e.g., amphiarthrotic joints and diarthrotic joints), mechanics (e.g., simple joints and compound joints), and anatomy (e.g., hip joints and knee joints). Components of joints can include bone, muscle, cartilage, tendons, ligaments, and other connective tissues in various combinations and amounts.

Osteoarthritis frequently occurs in the hand joints, spine, hips, knees, and great toes. [0016] As used herein, the terms“cartilage” and“articular cartilage” refer to elastic, translucent connective tissue in mammals, including humans and other species. Cartilage is composed predominantly of chondrocytes, type II collagen, small amounts of other collagen types, other noncollagenous proteins, proteoglycans and water. Cartilage is usually surrounded by a layer of perichondrium, containing fibroblasts in a matrix of type I collagen, type II collagen, and other proteoglycans. Cartilage can ossify to form bone tissue, and it can remain in its original form in locations such as the nose, ears, knees, and other joints. [0017] As used herein, the term“collagen” refers to the main extracellular structural protein in the various connective tissues in animal bodies. Depending upon the degree of mineralization, collagen tissues may be rigid (bone), compliant (tendon), or have a gradient from rigid to compliant (cartilage). More than a dozen types of collagen are known, with types I, II, and III being most abundant. Collagen types I, II, and III collagen, form long (300 nm), thin (1.5-nm diameter) fibrils having three polypeptide chains arranged in a triple helix. The triple helix generally consists of two identical chains (α1) and a third chain having the same amino acid sequence (α1) or a third chain that differs slightly in its chemical composition (α2). The amino acid composition of collagen is atypical for proteins, particularly with respect to its high hydroxyproline content. The most common motifs in the amino acid sequence of collagen are glycine-proline-X and glycine-X-hydroxyproline, where X is any amino acid other than glycine, proline or hydroxyproline. [0018] As used herein, the term“chondrocyte” refers to a cartilage cell. [0019] As used herein, the term“synovial sac” refers to a thin tissue that surrounds the joint and that is filled with synovial fluid. Synovial fluid protects the joint, lubricates the joint, and transports nutrients and waste to and from articular cartilage. [0020] As used herein, the terms“treat,”“treatment,” and“treating” refer to any indicia of success in the treatment or amelioration of an injury, pathology, condition, or symptom (e.g., cognitive impairment), including any objective or subjective parameter such as abatement; remission; diminishing of symptoms or making the symptom, injury, pathology or condition more tolerable to the patient; decreasing the frequency or duration of the symptom or condition; or, in some situations, preventing the onset of the symptom. The treatment or amelioration of symptoms can be based on any objective or subjective parameter; including, e.g., the result of a physical examination. [0021] As used herein the terms“effective amount” and“therapeutically effective amount” refer to a dose of a compound such as an Rgp inhibitor or a Kgp inhibitor that produces therapeutic effects for which it is administered. The exact dose will depend on the purpose of the treatment, and will be ascertainable by one skilled in the art using known techniques (see, e.g., Lieberman, Pharmaceutical Dosage Forms (vols.1-3, 1992); Lloyd, The Art, Science and Technology of Pharmaceutical Compounding (1999); Pickar, Dosage Calculations (1999); Goodman & Gilman’s The Pharmacological Basis of Therapeutics, 11^th Edition, 2006, Brunton, Ed., McGraw-Hill; and Remington: The Science and Practice of Pharmacy, 21^st Edition, 2005, Hendrickson, Ed., Lippincott, Williams & Wilkins). [0022] As used herein, the term“subject” refers to animals such as mammals, including, but not limited to, primates (e.g., humans), cows, sheep, goats, horses, dogs, cats, rabbits, rats, mice and the like. [0023] As used herein, the term“alkyl,” by itself or as part of another substituent, refers to a straight or branched, saturated, aliphatic radical having the number of carbon atoms indicated. Alkyl can include any number of carbons, such as C_1-2, C_1-3, C_1-4, C_1-5, C_1-6, C_1-7, C_1-8, C_1-9, C_1-10, C_2-3, C_2-4, C_2-5, C_2-6, C_3-4, C_3-5, C_3-6, C_4-5,

and C_5-6. For example, C_1-6 alkyl includes, but is not limited to, methyl, ethyl, propyl, isopropyl, butyl, isobutyl, sec-butyl, tert-butyl, pentyl, isopentyl, hexyl, etc. Alkyl can also refer to alkyl groups having up to 20 carbons atoms, such as, but not limited to heptyl, octyl, nonyl, decyl, etc. Alkyl groups can be substituted or unsubstituted.“Substituted alkyl” groups can be substituted with one or more groups selected from halo, hydroxy, amino, alkylamino, amido, acyl, nitro, cyano, and alkoxy. [0024] As used herein, the term“alkoxy,” by itself or as part of another substituent, refers to a group having the formula -OR, wherein R is alkyl. The term“lower alkoxy” refers to an alkoxy radical having from one to seven carbons, e.g., methoxy, ethoxy, propoxy, butoxy, pentoxy, hexoxy, or heptoxy radical. [0025] As used herein, the term“cycloalkyl,” by itself or as part of another substituent, refers to a saturated or partially unsaturated, monocyclic, fused bicyclic or bridged polycyclic ring assembly containing from 3 to 12 ring atoms, or the number of atoms indicated.

Cycloalkyl can include any number of carbons, such as C_3-6, C_4-6, C_5-6, C_3-8, C_4-8, C_5-8, C_6-8, C_3-9, C_3-10, C_3-11, and C_3-12. Saturated monocyclic cycloalkyl rings include, for example, cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, and cyclooctyl. Saturated bicyclic and polycyclic cycloalkyl rings include, for example, norbornane, [2.2.2] bicyclooctane, decahydronaphthalene and adamantane. Cycloalkyl groups can also be partially unsaturated, having one or more double or triple bonds in the ring. Representative cycloalkyl groups that are partially unsaturated include, but are not limited to, cyclobutene, cyclopentene, cyclohexene, cyclohexadiene (1,3- and 1,4-isomers), cycloheptene, cycloheptadiene, cyclooctene, cyclooctadiene (1,3-, 1,4- and 1,5-isomers), norbornene, and norbornadiene. When cycloalkyl is a saturated monocyclic C_3-8 cycloalkyl, exemplary groups include, but are not limited to cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl and cyclooctyl. When cycloalkyl is a saturated monocyclic C_3-6 cycloalkyl, exemplary groups include, but are not limited to cyclopropyl, cyclobutyl, cyclopentyl, and cyclohexyl. Cycloalkyl groups can be substituted or unsubstituted.“Substituted cycloalkyl” groups can be substituted with one or more groups selected from halo, hydroxy, amino, alkylamino, amido, acyl, nitro, cyano, and alkoxy. The term“lower cycloalkyl” refers to a cycloalkyl radical having from three to seven carbons including, for example, cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, and cycloheptyl. [0026] As used herein, the term“alkylene” refers to an alkyl group, as defined above, linking at least two other groups (i.e., a divalent alkyl radical). The two moieties linked to the alkylene group can be linked to the same carbon atom or different carbon atoms of the alkylene group. [0027] As used herein, the term“heteroalkyl,” by itself or as part of another substituent, refers to an alkyl group of any suitable length and having from 1 to 3 heteroatoms such as N, O and S. For example, heteroalkyl can include ethers, thioethers and alkyl-amines.

Additional heteroatoms can also be useful, including, but not limited to, B, Al, Si and P. The heteroatoms can be oxidized to form moieties such as, but not limited to, -S(O)- and -S(O)₂-. The heteroatom portion of the heteroalkyl can replace a hydrogen of the alkyl group to form a hydroxy, thio or amino group. Alternatively, the heteroatom portion can be the connecting atom, or be inserted between two carbon atoms. [0028] As used herein, the term“heteroalkylene” refers to a heteroalkyl group, as defined above, linking at least two other groups (i.e., a divalent heteroalkyl radical). The two moieties linked to the heteroalkylene group can be linked to the same atom or different atoms of the heteroalkylene group. [0029] As used herein, the terms“halo” and“halogen,” by themselves or as part of another substituent, refer to a fluorine, chlorine, bromine, or iodine atom. [0030] As used herein, the term“haloalkyl,” by itself or as part of another substituent, refers to an alkyl group where some or all of the hydrogen atoms are replaced with halogen atoms. As for alkyl groups, haloalkyl groups can have any suitable number of carbon atoms, such as C_1-6. For example, haloalkyl includes trifluoromethyl, fluoromethyl, etc. In some instances, the term“perfluoro” can be used to define a compound or radical where all the hydrogens are replaced with fluorine. For example, perfluoromethyl refers to

1,1,1-trifluoromethyl. [0031] As used herein, the term“haloalkoxy,” by itself or as part of another substituent, refers to an alkoxy group where some or all of the hydrogen atoms are replaced with halogen atoms. [0032] As used herein, the term“halocycloalkyl,” by itself or as part of another substituent, refers to a cycloalkyl group where some or all of the hydrogen atoms are replaced with halogen atoms. [0033] As used herein, the term“aryl,” by itself or as part of another substituent, refers to an aromatic ring system having any suitable number of ring atoms and any suitable number of rings. Aryl groups can include any suitable number of ring atoms, such as 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or 16 ring atoms, as well as from 6 to 10, 6 to 12, or 6 to 14 ring members. Aryl groups can be monocyclic, fused to form bicyclic (e.g., benzocyclohexyl) or tricyclic groups, or linked by a bond to form a biaryl group. Representative aryl groups include phenyl, naphthyl and biphenyl. Other aryl groups include benzyl, having a methylene linking group. Some aryl groups have from 6 to 12 ring members, such as phenyl, naphthyl or biphenyl. Other aryl groups have from 6 to 10 ring members, such as phenyl or naphthyl. Some other aryl groups have 6 ring members, such as phenyl. Aryl groups can be substituted or unsubstituted.“Substituted aryl” groups can be substituted with one or more groups selected from halo, hydroxy, amino, alkylamino, amido, acyl, nitro, cyano, and alkoxy. [0034] As used herein, the term“heteroaryl,” by itself or as part of another substituent, refers to a monocyclic or fused bicyclic or tricyclic aromatic ring assembly containing 5 to 16 ring atoms, where from 1 to 5 of the ring atoms are a heteroatom such as N, O or S.

Additional heteroatoms can also be useful, including, but not limited to, B, Al, Si and P. The heteroatoms can be oxidized to form moieties such as, but not limited to, -S(O)- and -S(O)₂-. Heteroaryl groups can include any number of ring atoms, such as 3 to 6, 4 to 6, 5 to 6, 3 to 8, 4 to 8, 5 to 8, 6 to 8, 3 to 9, 3 to 10, 3 to 11, or 3 to 12 ring members. Any suitable number of heteroatoms can be included in the heteroaryl groups, such as 1, 2, 3, 4, or 5, or 1 to 2, 1 to 3, 1 to 4, 1 to 5, 2 to 3, 2 to 4, 2 to 5, 3 to 4, or 3 to 5. Heteroaryl groups can have from 5 to 8 ring members and from 1 to 4 heteroatoms, or from 5 to 8 ring members and from 1 to 3 heteroatoms, or from 5 to 6 ring members and from 1 to 4 heteroatoms, or from 5 to 6 ring members and from 1 to 3 heteroatoms. The heteroaryl group can include groups such as pyrrole, pyridine, imidazole, pyrazole, triazole, tetrazole, pyrazine, pyrimidine, pyridazine, triazine (1,2,3-, 1,2,4- and 1,3,5-isomers), thiophene, furan, thiazole, isothiazole, oxazole, and isoxazole. The heteroaryl groups can also be fused to aromatic ring systems, such as a phenyl ring, to form members including, but not limited to, benzopyrroles such as indole and isoindole, benzopyridines such as quinoline and isoquinoline, benzopyrazine (quinoxaline), benzopyrimidine (quinazoline), benzopyridazines such as phthalazine and cinnoline, benzothiophene, and benzofuran. Other heteroaryl groups include heteroaryl rings linked by a bond, such as bipyridine. Heteroaryl groups can be substituted or unsubstituted.

“Substituted heteroaryl” groups can be substituted with one or more groups selected from halo, hydroxy, amino, alkylamino, amido, acyl, nitro, cyano, and alkoxy. [0035] The heteroaryl groups can be linked via any position on the ring. For example, pyrrole includes 1-, 2- and 3-pyrrole, pyridine includes 2-, 3- and 4-pyridine, imidazole includes 1-, 2-, 4- and 5-imidazole, pyrazole includes 1-, 3-, 4- and 5-pyrazole, triazole includes 1-, 4- and 5-triazole, tetrazole includes 1- and 5-tetrazole, pyrimidine includes 2-, 4-, 5- and 6- pyrimidine, pyridazine includes 3- and 4-pyridazine, 1,2,3-triazine includes 4- and 5-triazine, 1,2,4-triazine includes 3-, 5- and 6-triazine, 1,3,5-triazine includes 2-triazine, thiophene includes 2- and 3-thiophene, furan includes 2- and 3-furan, thiazole includes 2-, 4- and 5-thiazole, isothiazole includes 3-, 4- and 5-isothiazole, oxazole includes 2-, 4- and 5- oxazole, isoxazole includes 3-, 4- and 5-isoxazole, indole includes 1-, 2- and 3-indole, isoindole includes 1- and 2-isoindole, quinoline includes 2-, 3- and 4-quinoline, isoquinoline includes 1-, 3- and 4-isoquinoline, quinazoline includes 2- and 4-quinoazoline, cinnoline includes 3- and 4-cinnoline, benzothiophene includes 2- and 3-benzothiophene, and benzofuran includes 2- and 3-benzofuran. [0036] Some heteroaryl groups include those having from 5 to 10 ring members and from 1 to 3 ring atoms including N, O or S, such as pyrrole, pyridine, imidazole, pyrazole, triazole, pyrazine, pyrimidine, pyridazine, triazine (1,2,3-, 1,2,4- and 1,3,5-isomers), thiophene, furan, thiazole, isothiazole, oxazole, isoxazole, indole, isoindole, quinoline, isoquinoline, quinoxaline, quinazoline, phthalazine, cinnoline, benzothiophene, and benzofuran. Other heteroaryl groups include those having from 5 to 8 ring members and from 1 to 3

heteroatoms, such as pyrrole, pyridine, imidazole, pyrazole, triazole, pyrazine, pyrimidine, pyridazine, triazine (1,2,3-, 1,2,4- and 1,3,5-isomers), thiophene, furan, thiazole, isothiazole, oxazole, and isoxazole. Some other heteroaryl groups include those having from 9 to 12 ring members and from 1 to 3 heteroatoms, such as indole, isoindole, quinoline, isoquinoline, quinoxaline, quinazoline, phthalazine, cinnoline, benzothiophene, benzofuran and bipyridine. Still other heteroaryl groups include those having from 5 to 6 ring members and from 1 to 2 ring atoms including N, O or S, such as pyrrole, pyridine, imidazole, pyrazole, pyrazine, pyrimidine, pyridazine, thiophene, furan, thiazole, isothiazole, oxazole, and isoxazole. [0037] Some heteroaryl groups include from 5 to 10 ring members and only nitrogen heteroatoms, such as pyrrole, pyridine, imidazole, pyrazole, triazole, pyrazine, pyrimidine, pyridazine, triazine (1,2,3-, 1,2,4- and 1,3,5-isomers), indole, isoindole, quinoline, isoquinoline, quinoxaline, quinazoline, phthalazine, and cinnoline. Other heteroaryl groups include from 5 to 10 ring members and only oxygen heteroatoms, such as furan and benzofuran. Some other heteroaryl groups include from 5 to 10 ring members and only sulfur heteroatoms, such as thiophene and benzothiophene. Still other heteroaryl groups include from 5 to 10 ring members and at least two heteroatoms, such as imidazole, pyrazole, triazole, pyrazine, pyrimidine, pyridazine, triazine (1,2,3-, 1,2,4- and 1,3,5-isomers), thiazole, isothiazole, oxazole, isoxazole, quinoxaline, quinazoline, phthalazine, and cinnoline. [0038] As used herein the term“heterocyclyl,” by itself or as part of another substituent, refers to a saturated ring system having from 3 to 12 ring members and from 1 to 4 heteroatoms of N, O and S. Additional heteroatoms can also be useful, including, but not limited to, B, Al, Si and P. The heteroatoms can be oxidized to form moieties such as, but not limited to, -S(O)- and -S(O)₂-. Heterocyclyl groups can include any number of ring atoms, such as, 3 to 6, 4 to 6, 5 to 6, 3 to 8, 4 to 8, 5 to 8, 6 to 8, 3 to 9, 3 to 10, 3 to 11, or 3 to 12 ring members. Any suitable number of heteroatoms can be included in the heterocyclyl groups, such as 1, 2, 3, or 4, or 1 to 2, 1 to 3, 1 to 4, 2 to 3, 2 to 4, or 3 to 4. The heterocyclyl group can include groups such as aziridine, azetidine, pyrrolidine, piperidine, azepane, azocane, quinuclidine, pyrazolidine, imidazolidine, piperazine (1,2-, 1,3- and 1,4- isomers), oxirane, oxetane, tetrahydrofuran, oxane (tetrahydropyran), oxepane, thiirane, thietane, thiolane (tetrahydrothiophene), thiane (tetrahydrothiopyran), oxazolidine, isoxazolidine, thiazolidine, isothiazolidine, dioxolane, dithiolane, morpholine,

thiomorpholine, dioxane, or dithiane. The heterocyclyl groups can also be fused to aromatic or non-aromatic ring systems to form members including, but not limited to, indoline.

Heterocyclyl groups can be unsubstituted or substituted.“Substituted heterocyclyl” groups can be substituted with one or more groups selected from halo, hydroxy, amino, oxo (=O), alkylamino, amido, acyl, nitro, cyano, and alkoxy. [0039] The heterocyclyl groups can be linked via any position on the ring. For example, aziridine can be 1- or 2-aziridine, azetidine can be 1- or 2- azetidine, pyrrolidine can be 1-, 2- or 3-pyrrolidine, piperidine can be 1-, 2-, 3- or 4-piperidine, pyrazolidine can be 1-, 2-, 3-, or 4-pyrazolidine, imidazolidine can be 1-, 2-, 3- or 4-imidazolidine, piperazine can be 1-, 2-, 3- or 4-piperazine, tetrahydrofuran can be 1- or 2-tetrahydrofuran, oxazolidine can be 2-, 3-, 4- or 5-oxazolidine, isoxazolidine can be 2-, 3-, 4- or 5-isoxazolidine, thiazolidine can be 2-, 3-, 4- or 5-thiazolidine, isothiazolidine can be 2-, 3-, 4- or 5- isothiazolidine, and morpholine can be 2-, 3- or 4-morpholine. [0040] When heterocyclyl includes 3 to 8 ring members and 1 to 3 heteroatoms, representative members include, but are not limited to, pyrrolidine, piperidine,

tetrahydrofuran, oxane, tetrahydrothiophene, thiane, pyrazolidine, imidazolidine, piperazine, oxazolidine, isoxazolidine, thiazolidine, isothiazolidine, morpholine, thiomorpholine, dioxane and dithiane. Heterocyclyl can also form a ring having 5 to 6 ring members and 1 to 2 heteroatoms, with representative members including, but not limited to, pyrrolidine, piperidine, tetrahydrofuran, tetrahydrothiophene, pyrazolidine, imidazolidine, piperazine, oxazolidine, isoxazolidine, thiazolidine, isothiazolidine, and morpholine. [0041] As used herein, the term“thiol-reactive group” refers to a functional group capable of forming a reversible or irreversible covalent bond with a thiol group (i.e., a group having the structure“-SH”) such as the thiol group present in the α-sidechain of cysteine. Non- limiting examples of thiol reactive groups include thiazol-2-yl-carbonyl; benzothiazol-2-yl- carbonyl; oxazol-2-yl-carbonyl; benzooxazol-2-yl-carbonyl; pyridin-2-yl-carbonyl;

pyrimidin-4-yl-carbonyl; pyrimidin-2-yl-carbonyl; isoxazol-5-yl-carbonyl; isoxazol-3-yl- carbonyl; 1,2,4-oxadiazol-3-yl-carbonyl; 1,2,4-oxadiazol-5-yl-carbonyl; maleimidyl;

pyridinyldisulfanyl (including pyridin-2-yldisulfanyl); cyano; ethynyl; fluoromethyl- carbonyl; acyloxymethyl-carbonyl; aryloxymethyl-carbonyl; alkylsulfonyl-vinyl; and arylsulfonyl-vinyl. Other thiol-reactive groups are known to those of skill in the art including, for example, those described by Hermanson (Bioconjugate Techniques, 3^rd Ed. 2013, Academic Press, San Diego). [0042] A“masked thiol-reactive group” refers to a non-reactive precursor moiety that can be converted into a functional group capable of forming a reversible or irreversible covalent bond with a thiol group. [0043] As used herein, the term“amine protecting group” refers to a chemical moiety that renders an amino group unreactive, but is also removable so as to restore the amino group. Examples of amine protecting groups include, but are not limited to, benzyloxycarbonyl, 9-fluorenylmethyloxycarbonyl (Fmoc), tert-butyloxycarbonyl (Boc), allyloxycarbonyl (Alloc), acetamido, phthalimido, and the like. Other amine protecting groups are known to those of skill in the art including, for example, those described by Green and Wuts

(Protective Groups in Organic Synthesis, 4^th Ed.2007, Wiley-Interscience, New York). [0044] As used herein, the term“carbonyl,” by itself or as part of another substituent, refers to–C(O)-, i.e., a carbon atom double-bonded to oxygen and bound to two other groups in the moiety having the carbonyl. [0045] As used herein, the term“amino” refers to a moiety–NR₃, wherein each R group is H or alkyl. An amino moiety can be ionized to form the corresponding ammonium cation. [0046] As used herein, the term“hydroxy” refers to the moiety–OH. [0047] As used herein, the term“cyano” refers to a carbon atom triple-bonded to a nitrogen atom (i.e., the moiety–C≡N). [0048] As used herein, the term“carboxy” refers to the moiety–C(O)OH. A carboxy moiety can be ionized to form the corresponding carboxylate anion. [0049] As used herein, the term“amido” refers to a moiety–NRC(O)R or–C(O)NR₂, wherein each R group is H or alkyl. [0050] As used herein, the term“nitro” refers to the moiety–NO₂. [0051] As used herein, the term“oxo” refers to an oxygen atom that is double-bonded to a compound (i.e., O=). [0052] As used herein, the term“pharmaceutically acceptable excipient” refers to a substance that aids the administration of an active agent to a subject. By“pharmaceutically acceptable,” it is meant that the excipient is compatible with the other ingredients of the formulation and is not deleterious to the recipient thereof. Pharmaceutical excipients useful in the present invention include, but are not limited to, binders, fillers, disintegrants, lubricants, glidants, coatings, sweeteners, flavors and colors. [0053] As used herein, the term“salt” refers to acid or base salts of the compounds of the invention. Illustrative examples of pharmaceutically acceptable salts are mineral acid (hydrochloric acid, hydrobromic acid, phosphoric acid, and the like) salts, organic acid (acetic acid, propionic acid, glutamic acid, citric acid and the like) salts, quaternary ammonium (methyl iodide, ethyl iodide, and the like) salts. It is understood that the pharmaceutically acceptable salts are non-toxic. [0054] Pharmaceutically acceptable salts of the acidic compounds of the present invention are salts formed with bases, namely cationic salts such as alkali and alkaline earth metal salts, such as sodium, lithium, potassium, calcium, magnesium, as well as ammonium salts, such as ammonium, trimethyl-ammonium, diethylammonium, and tris-(hydroxymethyl)-methyl- ammonium salts. [0055] Similarly acid addition salts, such as of mineral acids, organic carboxylic and organic sulfonic acids, e.g., hydrochloric acid, methanesulfonic acid, maleic acid, are also possible provided a basic group, such as pyridyl, constitutes part of the structure. [0056] The neutral forms of the compounds can be regenerated by contacting the salt with a base or acid and isolating the parent compound in the conventional manner. The parent form of the compound differs from the various salt forms in certain physical properties, such as solubility in polar solvents, but otherwise the salts are equivalent to the parent form of the compound for the purposes of the present invention. [0057] The terms“about” and“around,” as used herein to modify a numerical value, indicate a close range surrounding that explicit value. If“X” were the value,“about X” or “around X” would indicate a value from 0.9X to 1.1X, and more preferably, a value from 0.95X to 1.05X. Any reference to“about X” or“around X” specifically indicates at least the values X, 0.95X, 0.96X, 0.97X, 0.98X, 0.99X, 1.01X, 1.02X, 1.03X, 1.04X, and 1.05X. Thus,“about X” and“around X” are intended to teach and provide written description support for a claim limitation of, e.g.,“0.98X.” II. P. gingivalis and gingipain activity in osteoarthritic subjects [0058] In a first aspect, the invention provides a method of treating or preventing osteoarthritis. The method includes administering a therapeutically effective amount of one or more gingipain-blocking agents to a patient in need thereof. [0059] P. gingivalis is an anaerobic gram-negative rod. Extracellular proteases produced by P. gingivalis, including Arginine Gingipain A (RgpA), Arginine Gingipain B (RgpB), and Lysine Gingipain (Kgp), can degrade a broad range of proteins in connective tissue and plasma (e.g., collagen, immunoglobulins, and proteinase inhibitors, etc.). Gingipains can enter systemic circulation and/or synoviocytes and chondrocytes, and they can also cause disruption to the kallikrein - kinin cascade, blood coagulation, and host defense systems. Patients with gingipains in their joints and circulatory system may be subject to gingipain- induced death of synovial cells and/or chondrocytes, contributing to osteoarthritis. [0060] A correlation between the periodontal pathogen Porphyromonas gingivalis and rheumatoid arthritis has previously been noted. P. gingivalis DNA has been identified in synovial tissue from rheumatoid arthritis subjects, particularly in persons positive for HLA- DR4. See, Koziel, et al. Curr Rheumatol Rep, 2014.16(3): 408; Totaro, et al. Arthritis Res Ther, 2013.15(3): R66. P. gingivalis may contribute to joint damage in rheumatoid arthritis through multiple mechanisms, including apoptosis of chondrocytes, degradation of collagen, and citrullination of proteins. See, Rohner, et al. Calcif Tissue Int, 2010.87(4): 333-40;

Houle, et al. FEMS Microbiol Lett, 2003.221(2): 181-5; Wegner, et al. Arthritis Rheum, 2010.62(9): 2662-72; Maresz, et al. PLoS Pathog, 2013.9(9): e1003627. [0061] In a small study of six subjects with osteoarthritis of the knee, Ehrlich et al. found bacterial DNA from the periodontal pathogens T. denticola in four of six patients’ synovial fluid aspirates and E. faecalis in three of six patients’ synovial fluid aspirates. In the same study, periodontal pathogens were detected in 12 of 25 knee aspirates from failed

arthroplasties of the knee, leading the authors to speculate a bacteremic source of infection where periodontal pathogens enter the bloodstream from oral lesions and then“settle out”, especially in the knee, which possesses a unique ramifying end capillary system compared to other joints. Similarly, in a study by Moen et al., oral bacterial DNAs were found in the synovial fluid from nine of nine osteoarthritis patients, but P. gingivalis DNA was not detected. See, Ehrlich, et al.2014, supra; Moen, et al. Clin Exp Rheumatol, 2006.24(6): 656-63. [0062] It has now been discovered that P. gingivalis can infiltrate human and dog joints, contributing to the development of osteoarthritis. As shown in Fig.1, immunohistochemistry of subchondral bone marrow (SBM) compartment in OA subjects (Fig.1, left panels) shows multi-nucleated osteoclast filled with RgpB in contact with eroding subchondral bone. In the non-OA subject (Fig.1, right panels), the bone marrow compartment, periosteum, and subchondral bone appear normal. Pathology in the subchondral bone marrow compartment in OA has been noted to be integral to the OA disease process. See, Pippenger, et al. J Cell Mol Med 2015.19(6): 1390-1399; Geurts, et al. J Orthop Res 2016.34(2): 262-269; Barr, et al. Arthritis Res Ther 2015.17: 228. As shown in Fig.2, synovial tissue from OA joint also contains arginine gingipain B from P. gingivalis. As shown in Fig.3, P. gingivalis DNA was identified in 3/3 osteoarthritic joints and 0/3 normal joints from an aged beagle dog. It is believed that P. gingivalis and gingipains can infiltrate joint tissues via a number of routes, giving rise to these new observations. Gingipains can be secreted, transported to outer membrane surfaces of P. gingivalis, or released in outer membrane vesicles by the bacterium. P. gingivalis has previously been identified in periodontal tissues, coronary arteries, aorta, and recently, the liver. Release of P. gingivalis and/or gingipains from any of these niches into the systemic circulation could result in translocation of P. gingivalis and/or gingipains to the joints. See, Travis, et al. Adv Exp Med Biol, 2000.477: 455-65; Byrne, et al. Oral Microbiol Immunol, 2009.24(6): 469-77; Mahendra, et al. J Maxillofac Oral Surg, 2009. 8(2): 108-13; Stelzel, et al. J Periodontol, 2002.73(8): 868-70; Ishikawa, et al. Biochim Biophys Acta, 2013.1832(12): 2035-2043. [0063] P. gingivalis and/or gingipains may also enter joints by degrading the endothelial cells protecting the blood/joint barrier, or by a traumatic event to the joint, such as a meniscus injury, which permanently or transiently reduces the integrity of the joint tissues. Such a disruption in traumatic joint injury for example, may contribute to the infiltration of P.

gingivalis and/or gingipains in infected individuals and subsequent development of chronic osteoarthritis. People who are at a high risk of joint injury and osteoarthritis, including people with obesity or athletes in contact sports like football, could be preventatively treated with gingipain inhibitors to reduce the risk of injury-related osteoarthritis. [0064] P. gingivalis and gingipains may also reach the joint through other mechanisms including active transport, passive transport or macrophage delivery. Osteoarthritis resulting from any of these mechanisms can be limited to a single joint or present in multiple joints. Once in the joint, P. gingivalis can kill chondrocytes, induce MMPs which act as

collagenases, and secrete gingipains which can also act as collagenases. See, Rohner, 2010, supra; Herath, et al. BMC Microbiol, 2013.13: 73; Houle, 2003, supra. Additionally P. gingivalis has been shown to invade osteoblasts, induce osteoclasts and cause bone pathology. See, Zhang, et al. Microbes Infect 2010.12(11): 838-845l; Zhang, et al. BMC Oral Health 2014.14: 89. [0065] Similar to humans, P. gingivalis infection and periodontal disease is one of the most common infectious diseases affecting adult dogs and cats. Using adult beagle dogs, researchers demonstrated the existence of Rgp in plaque samples taken from beagle dogs given a specific soft diet to increase plaque formation on tooth surfaces. (See, e.g.,: Davis and Head, Front Pharmacol, 2014.5: 47; Reichart, et al., Journal of Periodontal Research, 1984. 19(1): 67-75; Kataoka, S., et al., FASEB J, 201428(8): 3564-78.) Dogs and cats with P. gingivalis infection and gingipains in their joints and circulatory system may experience periodontal disease and osteoarthritis due to gingipain-induced cell death, which could be treated or prevented according to the methods of the invention. [0066] Aged dogs spontaneously develop many features of osteoarthritis, including a common inflammatory knee arthritis associated with degeneration of the anterior cruciate ligament (ACL). A study by Muir et al. of dogs with inflammatory knee arthritis and ACL degeneration detected DNA from a range of bacterial species in 37% of knee joints from affected dogs. Muir et al. hypothesized that bacteria may be an important causative factor in the pathogenesis of inflammatory arthritis in dogs. In the Muir et al. study, DNA from P. gingivalis was not detected in the dog joints. See, Muir, et al. Microb Pathog, 2007.42: 47- 55. However, similar to humans, Porphyromonas gingivalis is a common oral pathogen affecting adult dogs, and could potentially translocate from the oral cavity to joint tissues as a result of bacteremia. See, Berglundh, et al. J Clin Periodontol, 1991.18: 616-23;

Albuquerque, et al. Vet J, 2012.191: 299-305. [0067] Using adult beagle dogs, researchers have demonstrated the existence of Arg- gingipain, a secreted cysteine protease virulence factor of Porphyromonas gingivalis, in oral plaque samples taken from beagle dogs given a specific soft diet to increase plaque formation on tooth surfaces. Arginine-gingipain has been identified as the main collagenase factor of P. gingivalis, and could lead to collagen breakdown in infected joint tissues of dogs.

Additionally, P. gingivalis has been demonstrated to infect chondrocytes in vitro causing chondrocyte apoptosis, indicating a pathway for cartilage loss in osteoarthritis of both dogs and humans. See, Kataoka, et al., FASEB J, 2014.28: 3564-3578; Houle, 2003, supra;

Rohner, 2010, supra; Pischon, et al. Ann Rheum Dis, 2009.68: 1902-7. III. Gingipain blocking agents A. Gingipain inhibitors [0068] In some embodiments, the gingipain blocking agent is a compound which inhibits gingipain activity or production; a compound which inhibits translocation of gingipains into joint tissue or into systemic circulation; and/or a compound which inhibits the pathological effects of gingipains in a mammal. In certain embodiments, the gingipain inhibitor administered according to the method of the invention exhibits a gingipain Ki value and/or a gingipain IC₅₀ value well below 1 µM. [0069] The term“IC₅₀” indicates how much of a compound is needed to inhibit a given biological process (or component of a process, e.g., an enzyme, cell, cell receptor, or microorganism) by one half (50%). The IC₅₀ of a compound can be determined by constructing a dose-response curve and examining the effect of different concentrations of the compound on reversing the activity of the enzyme. From the dose-response curve, IC₅₀ values can be calculated for a given compound by determining the concentration needed to inhibit half of the maximum biological response of the enzyme. [0070] In general, the gingipain IC₅₀ value for compounds administered in the methods of the invention ranges from about 0.001 nM to about 500 nM. The gingipain IC50 value can range, for example, from about 1 nM to about 20 nM, or from about 20 nM to about 40 nM, or from about 40 nM to about 60 nM, or from about 60 nM to about 80 nM, or from about 80 nM to about 100 nM, or from about 100 nM to about 150 nM, or from about 150 nM to about 200 nM, or from about 200 nM to about 250 nM, or from about 250 nM to about 300 nM, or from about 300 nM to about 350 nM, or from about 350 nM to about 400 nM, or from about 400 nM to about 450 nM, or from about 450 nM to about 500 nM. The gingipain IC50 value can range from about 0.001 nM to about 0.025 nM, or from about 0.025 nM to about 0.050 nM, or from about 0.050 nM to about 0.075 nM, or from about 0.075 nM to about 0.100 nM, or from about 0.100 nM to about 0.250 nM, or from about 0.250 nM to about 0.500 nM, or from about 0.500 nM to about 0.750 nM, or from about 0.750 nM to about 1 nM. [0071] In some embodiments, a Kgp inhibitor according to the invention has a Kgp IC₅₀ of 50 nM or less. In some embodiments, the Kgp inhibitor has a Kgp IC₅₀ of 15 nM or less. [0072] In certain embodiments, gingipain inhibitors administered according to the methods of the invention are selective for gingipains or a particular gingipain. As used herein, a “selective” gingipain inhibitor is a compound that does not substantially affect the activity of proteases other than Kgp, RgpA, and RgpB when administered at a therapeutically effective dose for treating a disease or condition associated with P. gingivalis infection. Typically, a protease that is not substantially affected by a particular compound exhibits at least 90% of its normal enzymatic activity in the presence of the compound under physiological conditions. Selective Kgp inhibitors include those compounds that do not affect the activity of proteases other than Kgp when administered at a therapeutically effective dose for treating osteoarthritis. Selective RgpA inhibitors include those compounds that do not affect the activity of proteases other than RgpA when administered at a therapeutically effective dose for treating osteoarthritis. Selective RgpB inhibitors include those compounds that do not affect the activity of proteases other than RgpB when administered at a therapeutically effective dose for treating osteoarthritis. Preferably, selective gingipain inhibitors do not adversely affect the coagulation cascade or lysosomal activity when administered at therapeutically effective levels. [0073] In some embodiments, the gingipain inhibitor is at least 30 times more selective for gingipains than for trypsin or cathepsins. For some compounds, the gingipain IC₅₀ is 10 nM or less, and the trypsin IC₅₀ and/or the cathepsin IC₅₀ are 30 nM or more. In some embodiments, the gingipain IC₅₀ is 1 nM or less, and the trypsin IC₅₀ and/or the cathepsin IC₅₀ are 115 μM or more. In some embodiments, the gingipain IC₅₀ is 50 nM or less and the trypsin IC₅₀ is 100 nM or more. In some embodiments, the gingipain IC₅₀ is 15 nM or less and the trypsin IC₅₀ trypsin is 1 µM or more. In some embodiments, the gingipain IC₅₀ is 50 pM or less, and the trypsin IC₅₀ and/or the cathepsins are 10 nM or more. [0074] In some embodiments, the gingipain blocking agent is a compound which inhibits Lysine Gingipain (Kgp) activity or production; a compound which inhibits translocation of Kgp into joint tissue or into systemic circulation; and/or a compound which inhibits the pathological effects of Kgp in a mammal. In some such embodiments, the compound has IC₅₀ of Lysine Gingipain (Kgp) of less than or equal to 10 nanomolar (nM). [0075] In some embodiments, the gingipain blocking agent is a compound which inhibits Arginine Gingipain A (RgpA) activity or production; a compound which inhibits

translocation of RgpA into joint tissue or into systemic circulation; and/or a compound which inhibits the pathological effects of RgpA in a mammal. In some such embodiments, the compound has an IC₅₀ of Arginine Gingipain A (RgpA) of less than or equal to 10 nanomolar (nM). [0076] In some embodiments, the gingipain blocking agent is a compound which inhibits Arginine Gingipain B (RgpB) activity or production; a compound which inhibits

translocation of RgpA into joint tissue or into systemic circulation; and/or a compound which inhibits the pathological effects of RgpB in a mammal. In some such embodiments, the compound has an IC₅₀ of Arginine Gingipain B (RgpB) of less than or equal to 10 nanomolar (nM). [0077] In some embodiments, the gingipain blocking agent is a compound or combination of compounds that inhibits Kgp and RgpA/B activity. [0078] In some embodiments, the gingipain blocking agent is a Kgp inhibitor according to Formula I:

or a pharmaceutically acceptable salt thereof, wherein

Z is a thiol-reactive group or a masked thiol-reactive group;

A is selected from -CH₂- and -O-;

B and D are independently selected from hydrogen, halogen, C_1-4 haloalkyl, and C_1-4 haloalkoxy;

R¹ is selected from hydrogen and an amine protecting group; R² is hydrogen; and

R³ is selected from C_3-8 cycloalkyl, C_6-10 aryl, 5-to-12 membered heteroaryl, C_1-8 alkyl, 5-to-12 membered saturated heterocyclyl, -L-R⁵, and -OR⁶, wherein

L is selected from -O-, -NR-, C_1-4 alkylene, and 2- to 4-membered heteroalkylene, wherein R is selected from hydrogen and C_1-8 alkyl,

R⁵ is selected from C_6-10 aryl, 5-to-12 membered heteroaryl, C_3-8 cycloalkyl, and 5-to-12 membered saturated heterocyclyl, and

-OR⁶ and the carbonyl to which it is bonded form an amine protecting group, and wherein R³ is optionally substituted with one or more substituents selected from halo, -CN, -NO₂, -N₃, -OH, R^a, R^b, -OR^a, -OR^b, -(CH₂)_kC(O)R^c,-NR^d(CH₂)_uC(O)R^c, -O(CH₂)_uC(O)R^c, -(CH₂)_kCONR^dR^d, -(CH₂)_kNR^dC(O)R^c, -NR^d(CH₂)_uCONR^dR^d,

-NR^d(CH₂)_uNR^dC(O)R^c, -O(CH₂)_uCONR^dR^d, -O(CH₂)_uNR^dC(O)R^c, -(CH₂)_kS(O)₂NR^dR^d, -(CH₂)_kNR^dS(O)₂R^c, -(CH₂)_kS(O)₂R^c, -(CH₂)_kS(O)R^c, -(CH₂)_kSR^d, -NR^d(CH₂)_uS(O)₂NR^dR^d, -NR^d(CH₂)_uNR^dS(O)₂R^c, -NR^d(CH₂)_uS(O)₂R^c, -NR^d(CH₂)_uS(O)R^c, -NR^d(CH₂)_uSR^d,

-O(CH₂)_uS(O)₂NR^dR^d, -O(CH₂)_uNR^dS(O)₂R^c, -O(CH₂)_uS(O)₂R^c, -O(CH₂)_uS(O)R^c, and -O(CH₂)_uSR^c, wherein:

each R^a is independently selected from C_1-4 alkyl and C_1-4 haloalkyl, each R^b is independently selected from C_3-6 cycloalkyl, C_3-6 halocycloalkyl, C_6-10 aryl, 5-to-12 membered heteroaryl, and 5-to-12 membered saturated heterocyclyl,

each R^c is independently selected from -OH, C_1-8 alkyl, C_1-8 haloalkyl, C_3-8 cycloalkyl, C_3-8 halocycloalkyl, C_6-10 aryl, (C_6-10 aryl)-(C_1-8 alkyl), 5-to-12 membered heteroaryl, and 5-to-12 membered saturated heterocyclyl,

each R^d is independently selected from hydrogen and C_1-8 alkyl, each subscript k is independently selected from 0, 1, 2, 3, 4, 5, and 6, and each subscript u is independently selected from 1, 2, 3, 4, 5, and 6; and R⁴ is selected from hydrogen, halogen, C_1-4 alkyl, C_1-4 alkoxy, C_1-4 haloalkyl, and C_1-4 haloalkoxy. [0079] In some embodiments, when Z is benzothiazol-2-yl-carbonyl, A is -CH₂-, and B, D, and R¹ are hydrogen in the compound of Formula I, then R³ is other than benzyloxy, substituted benzyloxy, or 1-(3-phenyl-propanoyl)piperidin-3-yl. [0080] In some embodiments, when Z is phenoxymethyl-carbonyl or substituted phenoxymethyl-carbonyl, A is -CH₂-, and B and D are hydrogen in the compound of Formula I, then R³ is other than (2-phenyl)ethyl or substituted (2-phenyl)ethyl. [0081] In some embodiments, the Kgp inhibitor of Formula I has a structure according to Formula Ia:

[0082] In some embodiments, the Kgp inhibitor of Formula I has a structure according to Formula Ib:

or a pharmaceutically acceptable salt thereof, wherein

B and D are independently selected from hydrogen, halogen, halomethyl, and halomethoxy. [0083] In some embodiments, the method includes administering a Kgp inhibitor of Formula I, Formula Ia, or Formula Ib, or a pharmaceutically acceptable salt thereof, wherein Z is selected from halogen-substituted aryloxymethyl-carbonyl; benzothiazol-2-yl-carbonyl; thiazol-2-yl-carbonyl; oxazol-2-yl-carbonyl; benzooxazol-2-yl-carbonyl; pyridin-2-yl- carbonyl; pyrimidin-4-yl-carbonyl; pyrimidin-2-yl-carbonyl; isoxazol-5-yl-carbonyl;

isoxazol-3-yl-carbonyl; 1,2,4-oxadiazol-3-yl-carbonyl; 1,2,4-oxadiazol-5-yl-carbonyl; cyano; ethynyl; fluoromethyl-carbonyl; acyloxymethyl-carbonyl; aryloxymethyl-carbonyl;

alkylsulfonyl-vinyl; and arylsulfonyl-vinyl; each of which is optionally substituted with one or more substituents selected from C_1-4 alkyl, C_1-4 alkoxy, C_1-4 haloalkyl, C_1-4 haloalkoxy, halogen, and–N₃. [0084] In some embodiments, the method includes administering a Kgp inhibitor of Formula I, Formula Ia, or Formula Ib, or a pharmaceutically acceptable salt thereof, wherein Z is selected from benzothiazol-2-yl-carbonyl; thiazol-2-yl-carbonyl; oxazol-2-yl-carbonyl; benzooxazol-2-yl-carbonyl; pyridin-2-yl-carbonyl; pyrimidin-4-yl-carbonyl; pyrimidin-2-yl- carbonyl; isoxazol-5-yl-carbonyl; isoxazol-3-yl-carbonyl; 1,2,4-oxadiazol-3-yl-carbonyl; 1,2,4-oxadiazol-5-yl-carbonyl; cyano; ethynyl; fluoromethyl-carbonyl; acyloxymethyl- carbonyl; aryloxymethyl-carbonyl; alkylsulfonyl-vinyl; and arylsulfonyl-vinyl; each of which is optionally substituted with one or more substituents selected from C_1-4 alkyl, C_1-4 alkoxy, C_1-4 haloalkyl, C_1-4 haloalkoxy, halogen, and–N₃. [0085] In some embodiments, Z is selected from halogen-substituted aryloxymethyl- carbonyl, benzothiazol-2-yl-carbonyl, pyridin-2-yl-carbonyl, and thiazol-2-yl-carbonyl. [0086] In some embodiments, the method includes administering a Kgp inhibitor of Formula I or Formula Ia as described above, or a pharmaceutically acceptable salt thereof, wherein Z is selected from aryloxymethyl-carbonyl; benzothiazol-2-yl-carbonyl; thiazol-2-yl- carbonyl; oxazol-2-yl-carbonyl; benzooxazol-2-yl-carbonyl; pyridin-2-yl-carbonyl;

pyrimidin-4-yl-carbonyl; pyrimidin-2-yl-carbonyl; isoxazol-5-yl-carbonyl; isoxazol-3-yl- carbonyl; 1,2,4-oxadiazol-3-yl-carbonyl; 1,2,4-oxadiazol-5-yl-carbonyl; cyano; ethynyl; fluoromethyl-carbonyl; acyloxymethyl-carbonyl; alkylsulfonyl-vinyl; and arylsulfonyl-vinyl; wherein Z is optionally substituted with one or more substituents selected from C_1-4 alkyl, C_1-4 alkoxy, C_1-4 haloalkyl, C_1-4 haloalkoxy, halogen, and–N₃; and wherein R³ is selected from C_3-8 cycloalkyl, C_6-10 aryl, 5-to-12 membered heteroaryl, 5-to-12 membered saturated heterocyclyl, and -L-R⁵. In some such embodiments, R¹ and R² are H; B and D are independently selected from hydrogen and fluoro; A is -CH₂-; and R⁴ is selected from hydrogen and C_1-4 alkyl. [0087] In some embodiments, the method includes administering a Kgp inhibitor of Formula Ib as described above, or a pharmaceutically acceptable salt thereof, wherein Z is selected from aryloxymethyl-carbonyl; benzothiazol-2-yl-carbonyl; thiazol-2-yl-carbonyl; oxazol-2-yl-carbonyl; benzooxazol-2-yl-carbonyl; pyridin-2-yl-carbonyl; pyrimidin-4-yl- carbonyl; pyrimidin-2-yl-carbonyl; isoxazol-5-yl-carbonyl; isoxazol-3-yl-carbonyl; 1,2,4- oxadiazol-3-yl-carbonyl; 1,2,4-oxadiazol-5-yl-carbonyl; cyano; ethynyl; fluoromethyl- carbonyl; acyloxymethyl-carbonyl; alkylsulfonyl-vinyl; and arylsulfonyl-vinyl; wherein Z is optionally substituted with one or more substituents selected from C_1-4 alkyl, C_1-4 alkoxy, C_1-4 haloalkyl, C_1-4 haloalkoxy, halogen, and–N₃; and wherein R³ is selected from

C_3-8 cycloalkyl, C_6-10 aryl, 5-to-12 membered heteroaryl, 5-to-12 membered saturated heterocyclyl, and -L-R⁵. In some such embodiments, R¹ and R² are H; B and D are independently selected from hydrogen and fluoro; and A is -CH₂-. [0088] In some embodiments, the method includes administering a Kgp inhibitor of Formula I or Formula Ia as described above, or a pharmaceutically acceptable salt thereof, wherein Z is selected from halogen-substituted aryloxymethyl-carbonyl, pyridin-2-yl- carbonyl, benzothiazol-2-yl-carbonyl, and thiazol-2-yl-carbonyl; and wherein R³ is selected from C_3-8 cycloalkyl, C_6-10 aryl, 5-to-12 membered heteroaryl, 5-to-12 membered saturated heterocyclyl, and -L-R⁵. In some such embodiments, R¹ and R² are H; B and D are independently selected from hydrogen and fluoro; A is -CH₂-; and R⁴ is selected from hydrogen and C_1-4 alkyl. [0089] In some embodiments, the method includes administering a Kgp inhibitor of Formula Ib as described above, or a pharmaceutically acceptable salt thereof, wherein Z is selected from halogen-substituted aryloxymethyl-carbonyl, pyridin-2-yl-carbonyl, benzothiazol-2-yl-carbonyl, pyridin-2-yl-carbonyl, and thiazol-2-yl-carbonyl; and wherein R³ is selected from C_3-8 cycloalkyl, C_6-10 aryl, 5-to-12 membered heteroaryl, 5-to-12 membered saturated heterocyclyl, and -L-R⁵. In some such embodiments, R¹ and R² are H; B and D are independently selected from hydrogen and fluoro; and A is -CH₂-. [0090] In some embodiments, the method includes administering a Kgp inhibitor of Formula I or Formula Ia as described above, or a pharmaceutically acceptable salt thereof, wherein Z is selected from aryloxymethyl-carbonyl; benzothiazol-2-yl-carbonyl; thiazol-2-yl- carbonyl; oxazol-2-yl-carbonyl; benzooxazol-2-yl-carbonyl; pyridin-2-yl-carbonyl;

pyrimidin-4-yl-carbonyl; pyrimidin-2-yl-carbonyl; isoxazol-5-yl-carbonyl; isoxazol-3-yl- carbonyl; 1,2,4-oxadiazol-3-yl-carbonyl; 1,2,4-oxadiazol-5-yl-carbonyl; cyano; ethynyl; fluoromethyl-carbonyl; acyloxymethyl-carbonyl; alkylsulfonyl-vinyl; and arylsulfonyl-vinyl; wherein Z is optionally substituted with one or more substituents selected from C_1-4 alkyl, C_1-4 alkoxy, C_1-4 haloalkyl, C_1-4 haloalkoxy, halogen, and–N₃; and wherein R³ is selected from C_3-8 cycloalkyl, C_6-10 aryl, 5-to-12 membered heteroaryl, 5-to-12 membered saturated heterocyclyl, and -L-R⁵. In some such embodiments, R¹ and R² are H; B and D are independently selected from hydrogen and fluoro; and A is -CH₂-. In some such

embodiments, R⁴ is selected from hydrogen and methyl. [0091] In some embodiments, the method includes administering a Kgp inhibitor of Formula I or Formula Ia as described above, or a pharmaceutically acceptable salt thereof, wherein Z is selected from halogen-substituted aryloxymethyl-carbonyl, pyridin-2-yl- carbonyl, benzothiazol-2-yl-carbonyl, and thiazol-2-yl-carbonyl; and wherein R³ is selected from C_3-8 cycloalkyl, C_6-10 aryl, 5-to-12 membered heteroaryl, 5-to-12 membered saturated heterocyclyl, and -L-R⁵. In some such embodiments, R¹ and R² are H; B and D are independently selected from hydrogen and fluoro; and A is -CH₂-. In some such

embodiments, R⁴ is selected from hydrogen and methyl. [0092] In some embodiments, the method includes administering a Kgp inhibitor of Formula I or Formula Ia as described above, or a pharmaceutically acceptable salt thereof, wherein:

A is -CH₂-;

B and D are hydrogen;

Z is selected from halogen-substituted aryloxymethyl-carbonyl, benzothiazol-2-yl- carbonyl, pyridin-2-yl-carbonyl, and thiazol-2-yl-carbonyl;

R¹ and R² are H; and

R³ is selected from C_3-8 cycloalkyl, C_6-10 aryl, 5-to-12 membered heteroaryl, 5-to-12 membered saturated heterocyclyl, and -L-R⁵. In some such embodiments, R⁴ is hydrogen or methyl. In some such embodiments, R⁴ is hydrogen. [0093] In some embodiments, the method includes administering a Kgp inhibitor of Formula Ib as described above, or a pharmaceutically acceptable salt thereof, wherein:

A is -CH₂-;

B and D are hydrogen;

R¹ and R² are H; and

R³ is selected from C_3-8 cycloalkyl, C_6-10 aryl, 5-to-12 membered heteroaryl, 5-to-12 membered saturated heterocyclyl, and -L-R⁵. [0094] In some embodiments, the method includes administering a Kgp inhibitor of Formula I or Formula Ia as described above, or a pharmaceutically acceptable salt thereof, wherein:

A is -CH₂-;

B is hydrogen;

D is fluoro;

Z is selected from halogen-substituted aryloxymethyl-carbonyl, benzothiazol-2-yl- carbonyl, pyridin-2-yl-carbonyl, and thiazol-2-yl-carbonyl; R¹ and R² are H; and

R³ is selected from C_3-8 cycloalkyl, C_6-10 aryl, 5-to-12 membered heteroaryl, 5-to-12 membered saturated heterocyclyl, and -L-R⁵. In some such embodiments, R⁴ is hydrogen or methyl. In some such embodiments, R⁴ is hydrogen. [0095] In some embodiments, the method includes administering a Kgp inhibitor of Formula Ib as described above, or a pharmaceutically acceptable salt thereof, wherein:

A is -CH₂-;

B is hydrogen;

D is fluoro;

R¹ and R² are H; and

R³ is selected from C_3-8 cycloalkyl, C_6-10 aryl, 5-to-12 membered heteroaryl, 5-to-12 membered saturated heterocyclyl, and -L-R⁵. [0096] In some embodiments, the method includes administering a Kgp inhibitor of Formula I or Formula Ia as described above, or a pharmaceutically acceptable salt thereof, wherein:

A is -CH₂-;

B is hydrogen;

D is hydrogen or fluoro;

Z is halogen-substituted aryloxymethyl-carbonyl or benzothiazol-2-yl-carbonyl; R¹ and R² are H;

R³ is selected from cyclopentyl, cyclohexyl, morpholino, phenyl, piperidinyl, pyridinyl, tetrahydrofuranyl, tetrahydropyranyl, 1,2,3,4-tetrahydronaphthyl, and thiazolyl, each of which is optionally substituted with 1-3 members selected from the group consisting of methyl, methoxy, trifluoromethyl, acetyl, and -N₃; and

R⁴ is hydrogen or methyl. In some such embodiments, R⁴ is hydrogen. In some such embodiments, D and R⁴ are hydrogen. In some such embodiments, D and R⁴ are hydrogen, and Z is (2,3,5,6-tetrafluorophenoxy)methyl-carbonyl. [0097] In some embodiments, the method includes administering a Kgp inhibitor of Formula Ib as described above, or a pharmaceutically acceptable salt thereof, wherein:

A is -CH₂-; B is hydrogen;

D is hydrogen or fluoro;

Z is halogen-substituted aryloxymethyl-carbonyl or benzothiazol-2-yl-carbonyl; R¹ and R² are H; and

R³ is selected from cyclopentyl, cyclohexyl, morpholino, phenyl, piperidinyl, pyridinyl, tetrahydrofuranyl, tetrahydropyranyl, 1,2,3,4-tetrahydronaphthyl, and thiazolyl, each of which is optionally substituted with 1-3 members selected from the group consisting of methyl, methoxy, trifluoromethyl, acetyl, and -N₃. In some such embodiments, D is hydrogen. In some such embodiments, D is hydrogen and Z is (2,3,5,6- tetrafluorophenoxy)methyl-carbonyl. [0098] In some embodiments, the Kgp inhibitor of Formula I has a structure according to Formula Ic:

or a pharmaceutically acceptable salt thereof,

wherein R³ is selected from C_3-8 cycloalkyl, C_6-10 aryl, 5-to-12 membered heteroaryl, 5-to-12 membered saturated heterocyclyl, and -L-R⁵,

wherein L is C_1-4 alkylene. [0099] In some embodiments, the method includes administering a Kgp inhibitor of Formula Ic, or a pharmaceutically acceptable salt thereof, wherein R³ is selected from cyclopentyl, cyclohexyl, morpholino, phenyl, piperidinyl, pyridinyl, tetrahydrofuranyl, tetrahydropyranyl, 1,2,3,4-tetrahydronaphthyl, and thiazolyl, each of which is optionally substituted with 1-3 members selected from methyl, methoxy, trifluoromethyl, acetyl, and -N₃. [0100] In some embodiments, the Kgp inhibitor of Formula I, Formula Ia, Formula Ib, or Formula Ic is selected from:

and pharmaceutically acceptable salts thereof.

[0101] In some embodiments, the Kgp inhibitor of Formula I, Formula Ia, Formula Ib, or Formula Ic i l fr m

, and pharmaceutically acceptable salts thereof. [0102] In some embodiments, the method includes administering a Kgp inhibitor of Formula I, Formula Ia, or Formula Ib wherein A is -O-, including compounds according to Formula C1:

[0103] In some embodiments, the method includes administering a Kgp inhibitor of Formula I, Formula Ia, or Formula Ib wherein B is halo; D is halo; or B and D are halo; including compounds according to Formula C2, Formula C3, and Formula C4:

[0104] In some embodiments, the method includes administering a Kgp inhibitor of Formula I, Formula Ia, or Formula Ib wherein Z is selected from thiazol-2-yl-carbonyl;

oxazol-2-yl-carbonyl; benzooxazol-2-yl-carbonyl; pyridin-2-yl-carbonyl; pyrimidin-4-yl- carbonyl; pyrimidin-2-yl-carbonyl; isoxazol-5-yl-carbonyl; isoxazol-3-yl-carbonyl; 1,2,4- oxadiazol-3-yl-carbonyl; 1,2,4-oxadiazol-5-yl-carbonyl; maleimidyl; pyridinyldisulfanyl (including pyridin-2-yldisulfanyl); cyano; ethynyl; fluoromethyl-carbonyl; acyloxymethyl- carbonyl; aryloxymethyl-carbonyl; alkylsulfonyl-vinyl; and arylsulfonyl-vinyl. [0105] In some embodiments, the method includes administering a Kgp inhibitor of Formula I, Formula Ia, or Formula Ib wherein Z is selected from thiazol-2-yl-carbonyl;

pyridin-2-yl-carbonyl; cyano; ethynyl; fluoromethylcarbonyl; and 2,3,5,6- tetrafluorophenoxymethyl-carbonyl; including compounds according to Formula B1, Formula B2, Formula B3, Formula B4, Formula B5, and Formula B6:

[0106] In some embodiments, the method includes administering a Kgp inhibitor of Formula Id:

or a pharmaceutically acceptable salt thereof,

wherein L is C_1-4 alkylene. [0107] In some embodiments, the method includes administering a Kgp inhibitor of Formula Id, or a pharmaceutically acceptable salt thereof, wherein R³ is selected from cyclopentyl, cyclohexyl, morpholino, phenyl, piperidinyl, pyridinyl, tetrahydrofuranyl, tetrahydropyranyl, 1,2,3,4-tetrahydronaphthyl, and thiazolyl, each of which is optionally substituted with 1-3 members selected from methyl, methoxy, trifluoromethyl, acetyl, and -N₃. In some such embodiments, R³ is cyclopentyl. [0108] In some embodiments, the Kgp inhibitor of Formula Id is selected from:

and pharmaceutically acceptable salts thereof. [0109] In some embodiments, the Kgp inhibitor of Formula Id is selected from:

,

and pharmaceutically acceptable salts thereof.

[0110] In some embodiments, the Kgp inhibitor of Formula Id is selected from:

, and pharmaceutically acceptable salts thereof.

[0111] In some embodiments, the Kgp inhibitor of Formula I, Formula Ia, or Formula Ib is selected from

,

and pharmaceutically acceptable salts thereof.

[0112] In some embodiments, the method includes administering a Kgp inhibitor of Formula I, Formula Ia, or Formula Ib, wherein Z is selected from pyridin-2-yl-carbonyl and thiazol-2-yl-carbonyl, and R³ is selected from C_6-10 aryl and C_3-8 cycloalkyl. In some such embodiments, the com ound is selected from:

, and pharmaceutically acceptable salts thereof. [0113] In some embodiments, the method includes administering a Kgp inhibitor of Formula I or Formula Ia, wherein R⁴ is selected from C_1-4 alkyl and C_1-4 haloalkyl. In some such embodiments, the comp n i

or a pharmaceutically acceptable salt thereof. [0114] In some embodiments, the method includes administering a Kgp inhibitor of Formula I, Formula Ia, Formula Ib, Formula Ic, or Formula Id, or a pharmaceutically acceptable salt thereof, wherein R³ is selected from cyclopentyl; cyclohexyl;

1-methylcyclohexyl; 1-methoxycyclohexyl; morpholin-2-yl; 4-acetylmorpholin-2-yl; phenyl; 2-trifluoromethylphenyl; 3-azidophenyl; piperidine-3-yl; 1-acetyl-piperidine-3-yl; pyridin-2- yl; pyridin-3-yl; pyridin-4-yl; 6-oxo-1,6-dihydropyridin-2-yl; tetrahydrofuran-2-yl;

tetrahydro-2H-pyran-2-yl; tetrahydro-2H-pyran-3-yl; tetrahydro-2H-pyran-4-yl; 1,2,3,4- tetrahydronaphth-1-yl; 1,2,3,4-tetrahydronaphth-2-yl; thiazol-5-yl;and thiazol-2-yl. [0115] In some embodiments, the method includes administering a Kgp inhibitor of Formula I, Formula Ia, Formula Ib, Formula Ic, or Formula Id, or a pharmaceutically acceptable salt thereof, wherein R³ is selected from cyclopentyl; cyclohexyl;

1-methylcyclohexyl; 1-methoxycyclohexyl; 1,2,3,4-tetrahydronaphth-1-yl; and 1,2,3,4- tetrahydronaphth-2-yl; which radicals are shown below. In some such embodiments, R³ is cyclopentyl.

[0116] In some embodiments, the method includes administering a Kgp inhibitor of Formula I, Formula Ia, Formula Ib, Formula Ic, or Formula Id, or a pharmaceutically acceptable salt thereof, wherein R³ is selected from morpholin-2-yl; 4-acetylmorpholin-2-yl; piperidine-3-yl; 1-acetyl-piperidine-3-yl; tetrahydrofuran-2-yl; tetrahydro-2H-pyran-2-yl; tetrahydro-2H-pyran-3-yl; and tetrahydro-2H-pyran-4-yl; which radicals are shown below.

[0117] In some embodiments, the method includes administering a Kgp inhibitor of Formula I, Formula Ia, Formula Ib, Formula Ic, or Formula Id, or a pharmaceutically acceptable salt thereof, wherein R³ is selected from phenyl; 2-trifluoromethylphenyl; 3- azidophenyl; pyridin-2-yl; pyridin-3-yl; pyridin-4-yl; 6-oxo-1,6-dihydropyridin-2-yl; thiazol- 5-yl; and thiazol-2-yl; which radicals are shown below.

[0118] The methods described herein encompass the use of therapeutically active enantiomers or diastereomers of the described compounds. The use of all such enantiomers and diastereomers of these compounds is included in the scope of the invention. Such compounds can be used as mixtures (e.g., racemic mixtures) or as isolated enantiomers or diastereomers. [0119] In further embodiments, the method includes administering a Kgp inhibitor of Formula Ie:

or a pharmaceutically acceptable salt thereof, wherein

Z is a thiol-reactive group or a masked thiol-reactive group;

A is selected from -CH₂- and -O-;

R¹ is selected from hydrogen and an amine protecting group;

R² is hydrogen; and

R³ is selected from C_6-10 aryl, 5-to-12 membered heteroaryl, C_1-8 alkyl, C_3-8 cycloalkyl, 5-to-12 membered saturated heterocyclyl, -L-R⁵, and -OR⁶, wherein L is selected from -O-, -NR-, C_1-4 alkylene, and 2- to 4-membered

heteroalkylene, wherein R is selected from hydrogen and C_1-8 alkyl,

each R^d is independently selected from hydrogen and C_1-8 alkyl, each subscript k is independently selected from 0, 1, 2, 3, 4, 5, and 6, and each subscript u is independently selected from 1, 2, 3, 4, 5, and 6; and R⁴ is selected from hydrogen, halogen, C_1-4 alkyl, C_1-4 alkoxy, C_1-4 haloalkyl, and C_1-4 haloalkoxy. [0120] In some embodiments, the method includes administering a Kgp inhibitor of Formula If:

[0121] Compounds of Formula I are described in U.S. Pat. Appl. Pub. No.2016/0096830, which is incorporated herein by reference in its entirety.

[0122] In some embodiments, the gingipain blocking agent has a structure according to Formula II:

(II)

wherein

R¹ or R² is unsubstituted or substituted benzyloxycarbonyl;

R³ and R⁴ is each independently selected from the group consisting of a bond, hydrogen, hydroxyl, carboxyl, an aminoalkyl, and a side chain of an α-amino acid, wherein the hydroxyl, the carboxyl, the aminoalkyl, and the side chain of the α-amino acid are unsubstituted or substituted;

R⁵ and R⁶ is each independently selected from the group consisting of a bond, H, hydroxyl, carboxyl, a lower alkyl, and alkylaryl, wherein the hydroxyl, the carboxyl, the lower alkyl, and the alkylaryl are unsubstituted or substituted;

R⁷ is selected from the group consisting of alkyl amine, 1-methyl-1-phenyl- hydrozinocarbonyl, and alkylcarbonyl, wherein the alkyl amine, the 1-methyl-1-phenyl- hydrozinocarbonyl, and the alkylcarbonyl are unsubstituted or substituted;

X¹ is CH;

X² and X³ are both CO;

p is an integer from 1 to 4; and

q is 1. [0123] In some embodiments, the compound is selected from the group consisting of KYT- 1, KYT-36, KYT-41, and combinations thereof.

[0124] In some embodiments, the compound is a combination of KYT-36 and KYT-1. [0125] KYT-36, KYT-41, and related compounds are described in U.S. Pat. Nos.6,954,843 and 7,067,476, which are incorporated herein by reference in their entirety. B. Antibacterial agents [0126] Bacteriocidal and bacteriostatic compounds like antibiotics can be used to reduce bacterial levels and resulting gingipain- and inflammation-induced osteoarthritis. In certain embodiments, the antibiotic used for treatment of osteoarthritis is selective for P. gingivalis over other bacteria so as to preserve beneficial bacteria. Examples of useful antibiotics include, but are not limited to, quinolones (e.g., moxifloxacin, gemifloxacin, ciprofloxacin, oflaxacin, trovafloxacin, sitafloxacin, etc.), β-lactams (e.g., a penicillin (e.g., amoxicillin, amoxacilin-clavulanate, piperacillin-tazobactam, penicillin G, etc.), cephalosporins (e.g., ceftriaxone, etc.)), macrolides (e.g., erythromycin, azithromycin, clarithromycin, etc.), carbapenems (e.g., doripenem, imipenem, meropinem, ertapenem, etc.), thiazolides (e.g., tizoxanidine, nitazoxanidine, RM 4807, RM 4809, etc.), tetracyclines (e.g., tetracycline, minocycline, doxycycline, eravacycline, etc.), clindamycin, metronidazole, satranidazole, and agents that inhibit/interfere with formation of biofilm of anaerobic gram negative bacteria (e.g., oxantel, morantel or thiabendazole, etc). Combinations of two, three, four, five, six, or more of any of the foregoing agents, etc, can also be used in the methods of the invention. In certain embodiments, the compound is selected from the group consisting of tetracyclines (e.g., minocycline, doxycycline, etc.), penicillins (e.g., amoxicillin/clavulanic acid

combinations), metronidazole, eravacycline, clindamycin, amoxicillin, eravacycline, satranidazole, and combinations of the foregoing. In some embodiments, the antibiotic is moxifloxacin. [0127] FA-70C1, isolated from the culture supernatant of Streptomyces species strain FA- 70, is a potent Rgp inhibitor and also exhibits growth-inhibitory activity against P. gingivalis. Experiments have shown that the dipeptide bestatin selectively inhibits growth

of P. gingivalis by affecting the intracellular uptake of amino acids and peptides, which serve as energy and nitrogen sources for this bacterial species (Labbe, et al. J Periodontol, 2001. 72(6): 714-21). Bestatin or similar compounds could be used to treat osteoarthritis.

Alternatively, a treatment can be targeted to inhibit the gingipains in order to simultaneously block gingipain-induced cell death and act as a narrow spectrum antibiotic. [0128] Similarly, dogs with gingipains in their joints may experience osteoarthritis, which could be treated or prevented with compounds and compositions that inhibit gingipains or act as bacteriocidal or bacteriostatic agents of P. gingivalis. Stathopoulou et al. found that small peptide derived inhibitors of Rgp or Kgp can prevent gingipain-induced epithelial cell death. Rgp and Kgp induced cell death has also been demonstrated in endothelial cells and other cell types. See, Stathopoulou, et al. BMC Microbiol, 2009.9: 107; Sheets, et al. Infect Immun, 2005.73(3): 1543-52; Sheets, et al. Infect Immun, 2006.74(10): 5667-78. [0129] In some embodiments, the gingipain blocking agent is a an antibacterial agent which is bacteriostatic or bacteriocidal with respect to P. gingivalis. [0130] In some embodiments, the antibacterial agent is bestatin or an analog thereof. [0131] In some embodiments, the bacteriocidal agent is selected from the group consisting of a quinolone; a floroquinolone; a β-lactam; a cephalosporin; a macrolide; a carbapenem; a thiazolide; a tetracycline; a lincomycin; an agent that inhibits/interferes with formation of a biofilm of anaerobic gram negative bacteria; and combinations thereof. [0132] In some embodiments, the bacteriocidal agent is selected from the group consisting of gemifloxacin, ciprofloxacin, oflaxacin, trovafloxacin, sitafloxacin, moxifloxacin, amoxicillin, amoxacilin-clavulanate, piperacillin-tazobactam, penicillin G, ceftriaxone, erythromycin, azithromycin, clarithromycin, doripenem, imipenem, meropinem, ertapenem, tizoxanidine, nitazoxanidine, RM 4807, RM 4809, tetracycline, minocycline, doxycycline, eravacycline, clindamycin, metronidazole, satranidazole, oxantel, morantel, thiabendazole, and combinations thereof. C. Antibodies [0133] In some embodiments, the gingipain blocking agent is an antibody. Antibodies may rely on damage to the joint tissues and vasculature for access to P. gingivalis and gingipains residing within intraarticular tissues. Antibodies may also help to stimulate the efficacy of the immune system in clearing the bacteria. Antibodies to RgpA and/or RgpB and/or Kgp can be utilized including, e.g., 18E6, 7B9, 61Bg 1.3, 1B5, 7B4, 15C8, humanized versions thereof, and other structurally or functionally similar antibodies. The RgpB-specific monoclonal antibody, 18E6, which binds to the first half of the immunoglobulin domain of RgpB. The Kgp-specific monoclonal antibody, 7B9, recognizes an epitope within the Kgp catalytic domain. The RgpA antibody 61Bg 1.3 has been shown in humans to reduce reinfection with P. gingivalis with respect to periodontal disease. See, Nguyen, et al. J Bacteriol, 2007.

189(3): 833-43; Sztukowska, et al. Mol Microbiol, 2004.54(5): 1393-408; Booth, et al. Infect Immun, 1996.64(2): 422-7. It has been demonstrated that 18E6 and 7B9 protect cells from gingipain-induced cell death. Additional antibodies which may be used in the methods of present invention include, e.g., RgpA MAb 1B5, RgpA Mab 7B4, and Kgp antibody 15C8, as well as structurally and/or functionally similar antibodies. Antibodies specific for gingipain epitopes or other proteins expressed by P. gingivalis can also be used in the methods of the invention. Antibodies would preferably be humanized for use in humans. [0134] Methods known to those in the field for delivery of biologics to improve half-life and joint penetration can be used including, but not limited to, intravenous delivery, subcutaneous delivery, intranasal delivery, vector transport, and direct joint delivery. [0135] In some embodiments, the gingipain blocking agent is an antibody which binds to a P. gingivalis protein. [0136] In some embodiments, the antibody binds to at least one protein selected from the group consisting of Kgp, RgpA, and RgpB. [0137] In some embodiments, the antibody is selected from the group consisting of 7B9 ,18E6, 61Bg 1.3, 1B5, 7B4, 15C8, fragments thereof, and combinations thereof. [0138] In some embodiments, the antibody is humanized. D. Vaccines [0139] Vaccines can be administered to a subject according to the methods of the invention, so as to disrupt progression of osteoarthritis. A variety of vaccine strategies are known to those in the art. These strategies could be used for the treatment and prevention of osteoarthritis as described in the present specification. See, Guo, et al. Periodontol 2000, 2010.54(1): 15-44. [0140] Genco et al. immunized mice with a 20 amino acid synthetic peptide derived from the catalytic domain of RgpA having the amino acid sequence

YTPVEEKQNGRMIVIVAKKY. Mice vaccinated with this synthetic gingipain epitope were protected from P. gingivalis invasion in the mouse chamber model. In another study, mice immunized with purified RgpA protein were protected from P. gingivalis-mediated periodontal disease, suggesting that it was the production of antibodies against the hemaglutinin domain of RgpA that were protective. See, Genco, et al. Infect Immun, 1998. 66(9): p.4108-14; Gibson, et al. Infect Immun, 2001.69(12): p.7959-63. If one or more gingipains are used for immunization, it may be preferable to inactivate their proteolytic activity, using iodoacetamide or another method, prior to administering. Recombinant gingipains, produced by E. coli for example, have little or no activity compared to gingipains produced by P. gingivalis and can be used for this purpose. [0141] Page et al. have shown that immunization of nonhuman primates with purified gingipains inhibited alveolar bone destruction, and that the vaccine was well tolerated by the animals. Gingipain DNA vaccines were tested by Guo et al. who found that Kgp and RgpA, but not RgpB DNA vaccines were effective in preventing periodontal symptoms in dogs. The kgp, rgpA, and rgpB genes were amplified by polymerase chain reaction (PCR) from P. gingivalis ATCC 33277 and cloned into the pVAX1 vector. See, Page, et al. Oral Microbiol Immunol, 2007.22(3): 162-8; Guo, et al. J Periodontol, 2014.85(11): 1575-81. [0142] Lee et al.2006 immunized rats with P. gingivalis HSP60, and experimental alveolar bone loss was induced by infection with multiple periodontopathogenic bacteria. There was a very strong inverse relationship between postimmune anti-P. gingivalis HSP immunoglobulin G (IgG) levels and the amount of alveolar bone loss induced by either P. gingivalis or multiple bacterial infection (p=0.007). Polymerase chain reaction data indicated that the vaccine successfully eradicated the multiple pathogenic species. [0143] Intranasal administration of P. gingivalis fimbrial antigen with recombinant cholera toxin B subunit also induced a significant immune response (fimbrial-specific secretory IgA- sIgA) in mice, which could reduce P. gingivalis-mediated alveolar bone loss. It is also possible that this mucosal immunization resulted in peripheral tolerance and hence a reduced inflammatory response and alveolar bone loss. However, it has further been demonstrated that immunization with 43-kDa fimbrillin polymer of P. gingivalis did not show satisfactory levels of protection against all strains of P. gingivalis tested. The feasibility of this fimbrial protein of P. gingivalis as a vaccine candidate antigen may therefore be dependent on its effectiveness in protecting against all the P. gingivalis strains. See, Travis, et al. Adv Exp Med Biol, 2000.477: p.455-65. [0144] A conjugate vaccine incorporating both fimbriae and P. gingivalis capsular polysaccharide (CPS) has been introduced in a study that led to the production of a high IgG response and which was effective in protecting against P. gingivalis infection. See, Byrne, et al. Oral Microbiol Immunol, 2009.24(6): 469-77. However, in this study it was not clear whether the protection came from the CPS or fimbriae. CPS, by virtue of its encapsulation and antigenic shift, constitutes a robust strategy for P. gingivalis survival against

opsonophagocytic activity. Due to its poor T-cell stimulating ability, however, CPS of other Gram-negative bacteria is usually conjugated to a protein antigen (for stimulating helper T- cells) in many vaccine trials in infectious diseases, such as pneumonia and meningitis. More recently, P. gingivalis CPS alone has nevertheless, been used as an immunogen, and it has been reported to result in an elevated production of serum IgG and IgM that provided protection against P. gingivalis-induced bone loss. [0145] Zhu et al.2013 tested a vaccine of peptidylarginine deiminase (PAD) from P. gingivalis in a mouse model. Compared with animal immunization with incomplete Freund's adjuvant (IFA) alone, PAD group significantly inhibited (P<0.05) bone resorption. It is contemplated that these vaccine strategies could be used in the methods of the present invention, e.g., to treat or prevent osteoarthritis. See, Zhu, et al. Arch Oral Biol, 2013.

58(12): 1777-83. [0146] Vaccination can also be accomplished with live attenuated or killed P. gingivalis. Comparisons of the protective effects of subcutaneous immunization among formalin-killed P. gingivalis, heat-killed P. gingivalis, outer membrane fraction, and lipopolysaccharide revealed that immunization with killed P. gingivalis provides the greatest protection from lesion formation induced by P. gingivalis. Preparation of killed bacteria for vaccination involves growth of the bacteria in standard conditions, and collection during the logarithmic growth phase. The bacteria are then centrifuged, washed three times, and resuspended in sterile phosphate-buffered saline (PBS, pH 7.4). Bacteria can be killed by fixation with 0.8% formalin at 4 °C for 24 h followed by washing, and resuspension in sterile PBS or heated to 95 °C for 10 minutes. Bacteria can be plated and incubated for 7 days to ensure effective killing. Approximately 2.5 × 109 cells/mL or other effective dose can be used for vaccination. Live attenuated bacteria may be the most effective vaccine for intracellular bacteria as is the case for tuberculosis. P. gingivalis may be attenuated by knocking out gingipains or other methods known to those in the art. See, Kesavalu, et al., Infect Immun, 1992.60(4): 1455-64; Wang, et al., Int Immunopharmacol, 2015. 25(1): 65-73; Genco, et al., Infection and Immunity, 1992.60(4): 1447-1454. [0147] Vaccination in accordance with the present invention also encompasses passive immunization, namely direct administration of antibodies against gingipains. The antibodies 7B9, 18E6 or 61Bg 1.3, 1B5, 7B4, 15C8, or a structurally and/or functionally similar antibodies, could be used in the methods of the present invention, e.g., to treat or prevent osteoarthritis or determine if a subject possibly has osteoarthritis, is at risk of developing osteoarthritis, as well as to monitor the efficacy of the treatment of osteoarthritis. Humanized versions of these antibodies, nanobodies, or antibody fragments of these antibodies could also be used. [0148] In some of the embodiments, the passive immunization prevents or treats infection of P. gingivalis and therefore prevents joint infiltration of gingipains. Since colonization with P. gingivalis can occur during the first few years of life, a vaccine against gingipains or other components of P. gingivalis may provide life-long protection against gingipain-induced osteoarthritis. See, McClellan, et al. J Clin Microbiol, 1996.34(8): 2017-9. [0149] Accordingly, some embodiments of the invention provide methods for treating osteoarthritis as described above wherein the gingipain blocking agent is a vaccine. In some embodiments, the vaccine comprises at least one member selected from the group consisting of Kgp, RgpA, RgpB, and epitopes thereof. In some such embodiments, the Kgp, RgpA, RgpB, and epitopes thereof are inactivated. [0150] In some embodiments, the vaccine contains P. gingivalis. In some such

embodiments, the P. gingivalis is live attenuated P. gingivalis or killed P. gingivalis. [0151] In some embodiments, the vaccine is an active vaccine comprising a P. gingivalis protein other than RgpA, RgpB and Kgp, or an immunogenic fragment thereof. [0152] Other gingipain blocking agents can also be used in the methods of the invention. Examples include, but are not limited to, lysine derivatives, arginine derivatives, histatin 5; baculovirus p35; a single point mutant of cowpox viral cytokine-response modifier (CrmA (Asp > Lys)); phenylalanyl-ureido-citrullinyl-valyl-cycloarginal (FA-70C1);

(acycloxy)methyl ketone (Cbz-Phe-Lys-CH₂OCO-2,4,6-Me₃Ph); peptidyl chloro-methyl ketones (e.g., chloromethyl ketone derivatives of arginine, chloromethyl ketone derivatives of lysine, and the like); fluoro-methyl ketones; bromo-methyl ketones; ketopeptides; 1-(3- phenylpropionyl)piperidine-3(R,S)-carboxylic acid [4-amino-1(S)-(benzothiazole-2- carbonyl)butyl]amide (A71561); azapeptide fumaramide; aza-peptide Michael acceptors; benzamidine compounds; acyclomethylketone; activated factor X inhibitors (e.g., DX- 9065a); cranberry nondialysable fraction; cranberry polyphenol fraction; pancreatic trypsin inhibitor; Cbz-Phe-Lys-CH₂O-CO-2,4,6-Me₃-Ph; E-64; chlorhexidine; and zinc (e.g., zinc acetate). [0153] In some of these embodiments, Zn can enhance potency and selectivity of the compounds (e.g., chlorhexidine, benzamidine, etc.) used in the methods of the invention. Benzamidine compounds include, e.g., the following compounds and derivatives thereof:

[0154] In some embodiments, the gingipain blocking agent is a naturally-occurring gingipain inhibitor. Examples of naturally-occurring gingipain inhibitors include, but are not limited to, melabaricone C, isolated from nutmeg or polyphenolic compounds derived from plants, such as cranberry, green tea, apple, and hops. In some embodiments, the gingipain blocking agent is an antimicrobial peptide. Examples of naturally and unnaturally occurring antimicrobial peptides include, but are not limited to: κ-casein peptide (109–137) 34, histatin 5, and CL(14-25), CL(K25A) and CL(R24A, K25A) (see, e.g., Taniguchi et al., Biopolymers, 2014.102(5): 379-89). κ-casein(109-107) is known to inhibit proteolytic activity associated with P. gingivalis whole cells, purified RgpA-gp proteinase-adhesion complexes, and purified RgpB. It has exhibited synergism with ZN(ii) against both Arg- and Lys-specific proteinases. Antimicrob Agents Chemother.2011 Mar; 55(3):155-61. Administration of such inhibiting peptides, with or without synergistic ingredients such as (ZN_(II)) for the treatment of osteoarthritis is encompassed by the present invention. [0155] Bacteriophage therapy against P. gingivalis can also be used for osteoarthritis in the methods of the invention. Bacteriophages (i.e.,“phages”) specifically infect target bacteria, replicate inside of the target bacteria, and lyse the target bacteria, releasing progeny phages that can continue the cycle. The progeny phages can migrate to other sites of infection anywhere in the body, including joint tissues. Typically, phages only minimally impact non- target bacteria or body tissues. Phage therapy for osteoarthritis can be cocktails of phages purified from oral preparations that display activity against a range of bacterial strains, or the phages can be highly specific for P. gingivalis. Lytic (as opposed to temperate) phages suitable for therapeutic purposes can be isolated from oral tissue or saliva of periodontal patients by methods known to those in the art and as described in Mancuca et al.2010.

Briefly, P. gingivalis and its phages can be isolated by culturing the human samples in selective P. gingivalis agar or by enriching for P. gingivalis by adding a culture of P.

gingivalis to the sample to amplify the specific phages. Following bacterial lysis, the phages are separated from host cell material by centrifugation followed by filtration or extraction with chloroform to kill any remaining bacteria. The phages are then applied to a lawn of bacteria and lytic plaques are selected for further characterization. In certain instances, multiple phages from diverse strains of P. gingivalis, or multiple types of oral bacteria, are combined to increase the efficacy of the phage therapy. The choice of phage strain and the methods of phage preparation are critical to the success or failure of phage therapy.

Insufficiently virulent phages or poorly prepared phage stocks can result in ineffective therapy. See, Abedon, Bacteriophage, 2011.1(2): 66-85; Dubos, et al. J Exp Med, 1943. 78(3): 161-8; Machuca, et al. Appl Environ Microbiol, 2010.76(21): 7243-50; Hunt, et al. Journal of Clinical Microbiology, 1986.23(3): 441-445; Gill, et al. Curr Pharm Biotechnol, 2010.11(1): 2-14. [0156] In some embodiments, the invention provides a method of treating infectious arthritis or psoriatic arthritis. The method includes administering a therapeutically effective amount of one or more gingipain-blocking agents (e.g., a compound of Formula I, Formula Ia, or Formula Ib, Formula Ic; an antibacterial agent; an antibody; or a vaccine as described herein) to a patient in need thereof. In some embodiments, the method is used for treating infectious arthritis. Infectious arthritis (or“septic arthritis”) refers to the infection of a joint cavity with microorganisms, typically bacteria, which can initiate a process of inflammation and cause irreversible damage to a joint cavity. In some embodiments, the method is used for treating psoriatic arthritis. Psoriatic arthritis refers to chronic inflammatory arthritis which is associated with psoriasis, a common chronic skin condition that causes red patches on the body. Certain individuals with psoriasis will develop arthritis along with the skin condition, with psoriasis often preceding the arthritis. Psoriatic arthritis exhibits itself in a variety of ways, ranging from mild to severe arthritis, wherein the arthritis usually affects the fingers and the spine. When the spine is affected, the symptoms are similar to those of ankylosing spondylitis. Psoriatic arthritis is sometimes associated with arthritis mutilans, a disorder which is characterized by excessive bone erosion resulting in a gross, erosive deformity which mutilates the joint. IV. Administration of gingipain blocking agents [0157] Gingipain blocking agents as described herein can be administered at any suitable dose in the methods of the invention. In general, a gingipain blocking agent is administered at a dose ranging from about 0.01 milligrams to about 1000 milligrams per kilogram of a subject’s body weight (i.e., about 0.01-1000 mg/kg). The dose of gingipain blocking agent can be, for example, about 0.01-100 mg/kg, , or about 0.01-10 mg/kg, or about 0.1-1 mg/kg, or about 0.1-50 mg/kg, or about 2.5-25 mg/kg, or about 5-10 mg/kg. The dose of gingipain blocking agent can be about 0.01, 0.05, 0.1, 0.25, 0.5, 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 85, 90, 95, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950 or 1000 mg/kg. The dosages can be varied depending upon the requirements of the patient, the severity of the osteoarthritis being treated, and the particular formulation being administered. The dose administered to a patient should be sufficient to result in a beneficial therapeutic response in the patient. The size of the dose will also be determined by the existence, nature, and extent of any adverse side-effects that accompany the administration of the drug in a particular patient. Determination of the proper dosage for a particular situation is within the skill of the typical practitioner. The total dosage can be divided and administered in portions over a period of time suitable to treat to the seizure disorder. [0158] Gingipain blocking agents can be administered for periods of time which will vary depending upon the severity of the osteoarthritis and the overall condition of the subject to whom the gingipain blocking agent is administered. Administration can be conducted, for example, hourly, every 2 hours, three hours, four hours, six hours, eight hours, or twice daily including every 12 hours, or any intervening interval thereof. Administration can be conducted once daily, or once every 36 hours or 48 hours, or once every month or several months. Following treatment, a subject can be monitored for changes in his or her condition and for alleviation of the symptoms of the disorder. The dosage of the gingipain blocking agent can either be increased in the event the subject does not respond significantly to a particular dosage level, or the dose can be decreased if an alleviation of the symptoms of the disorder is observed, or if the disorder has been remedied, or if unacceptable side effects are seen with a particular dosage. [0159] A therapeutically effective amount of a gingipain blocking agent can be

administered to the subject in a treatment regimen comprising intervals of at least 1 hour, or 6 hours, or 12 hours, or 24 hours, or 36 hours, or 48 hours between dosages. Administration can be conducted at intervals of at least 72, 96, 120, 144, 168, 192, 216, or 240 hours (i.e., 3, 4, 5, 6, 7, 8, 9, or 10 days). In certain embodiments, administration of one or more gingipain blocking agents is conducted in a chronic fashion over periods ranging from several months to several years. Accordingly, some embodiments of the invention provide a method of treating osteoarthritis as described above, wherein the gingipain blocking agent is

administered to the subject for at least one year. In some embodiments, the gingipain blocking agent is administered to the subject for at least 10 years. In some embodiments, the gingipain blocking agent is administered to the subject for at least 60 years. Treatment efficacy and/or successful administration can be assessed by measuring levels of circulating levels of RgpA and/or RgpB and/or Kgp and/or P. gingivalis in plasma and/or synovial fluid. Based on this assessment, the dose and/or frequency of administration may be adjusted. [0160] Administration of gingipain blocking agents according to the methods of the invention typically results in the reduction gingipain levels and/or P. gingivalis levels in the joint tissue and/or the circulatory system of the subject to whom the gingipain blocking agents are administered. In certain embodiments, administration of a gingipain blocking agent according to the methods of the invention results in at least a 20% reduction of gingipain levels in joint tissue or in the circulatory system. For example, the circulating levels of P. gingivalis or gingipains and/or the levels of P. gingivalis or gingipains in joint tissue are preferably reduced by from about 25% to about 95%, or from about 35% to about 95%, or from about 40% to about 85%, or from about 40% to about 80% as compared to the corresponding levels of gingipains 24 hours prior to the first administration of the gingipain blocking agent. [0161] A gingipain blocking agent of the invention can be administered in the same composition as an additional therapeutically active agent. Alternatively, the additional therapeutically active agent can be administered separately before, concurrently with, or after administration of the gingipain blocking agent. Examples of therapeutic agents that can be combined with the gingipain blocking agents include, but are not limited to: acetaminophen, oral and topical non-steroidal anti-inflammatory drugs (NSAIDS, including naproxen, diclofenac, and ketoprofen, as well as COX-2 selective NSAIDS such as celecoxib), oral opioids (such as tramadol, oxycodone, and the like), and intra-articular injection of glucocorticoids such as hydrocortisone. Combination treatments are also envisioned with treatments that promote joint tissue recovery, including but not limited to growth factors, growth factor mimetics, stem cells, gene therapy and encapsulated cell therapy. In addition, combination treatments are also envisioned for use with surgical treatments, including but not limited to joint replacement for both knees and hips, and surgical transfer of articular cartilage from a non-weight-bearing area to the damaged area. [0162] In another embodiment,“boosting” of gingipain protease inhibitor compounds with ritonavir (RTV) may be used to increase bioavailability and increase intraarticular penetration. For example, ritonavir is commonly combined with oral peptidic HIV protease inhibitors to increase plasma levels by inhibiting the P4503A4 enzyme and thus decreasing first-pass metabolism. In addition, RTV binds to P-glycoprotein, a transmembrane efflux pump that is found in many tissues, including the blood brain barrier, allowing co- administered compounds better access to tissues. Expression of the P-glycoprotein gene (MDR1/ABCB1) has been demonstrated in arthritic synovial tissue membrane. See, Walmsley, et al. N Engl J Med, 2002.346(26): 2039-46; Marzolini, et al. Mol Pharm, 2013. 10(6): 2340-9; Stamp, et al. J Rheumatol, 2013.40(9): 1519-22. Therefore, a combination of RTV and gingipain protease inhibitors might be used to increase plasma concentrations and intra-articular levels of the gingipain inhibitors. It has been shown that oral administration of RTV 15 minutes prior to Kyt-36 increases the half-life. In another embodiment, a course of antibiotics might be paired with gingipain inhibitors to jump start treatment. [0163] Gingipain blocking agents can be administered orally in the methods of the invention. Suitable compositions for oral administration include, but are not limited to, tablets, troches, lozenges, aqueous or oily suspensions, dispersible powders or granules, emulsions, hard or soft capsules, syrups, elixirs, solutions, buccal patches, oral gels, chewing gums, chewable tablets, effervescent powders, and effervescent tablets. Compositions for oral administration can be formulated according to any method known to those of skill in the art. Such compositions can contain one or more agents selected from sweetening agents, flavoring agents, coloring agents, antioxidants, and preserving agents in order to provide pharmaceutically elegant and palatable preparations. [0164] Tablets generally contain the active ingredient in admixture with non-toxic pharmaceutically acceptable excipients, including: inert diluents, such as cellulose, silicon dioxide, aluminum oxide, calcium carbonate, sodium carbonate, glucose, mannitol, sorbitol, lactose, calcium phosphate, and sodium phosphate; granulating and disintegrating agents, such as corn starch and alginic acid; binding agents, such as polyvinylpyrrolidone (PVP), cellulose, polyethylene glycol (PEG), starch, gelatin, and acacia; and lubricating agents such as magnesium stearate, stearic acid, and talc. The tablets can be uncoated or coated, enterically or otherwise, by known techniques to delay disintegration and absorption in the gastrointestinal tract and thereby provide a sustained action over a longer period. For example, a time delay material such as glyceryl monostearate or glyceryl distearate can be employed. Tablets can also be coated with a semi-permeable membrane and optional polymeric osmogents according to known techniques to form osmotic pump compositions for controlled release. [0165] Compositions for oral administration can be formulated as hard gelatin capsules wherein the active ingredient is mixed with an inert solid diluent (such as calcium carbonate, calcium phosphate, or kaolin), or as soft gelatin capsules wherein the active ingredient is mixed with water or an oil medium (such as peanut oil, liquid paraffin, or olive oil). [0166] Gingipain blocking agents can also be administered topically as a solution, ointment, cream, gel, or suspension, as well as in mouth washes, eye-drops, and the like. Still further, transdermal delivery of gingipain blocking agents can be accomplished by means of iontophoretic patches and the like. [0167] Gingipain blocking agents can be administered by injection in the methods of the invention. Sterile injectable preparations can be formulated using non-toxic parenterally- acceptable vehicles including water, Ringer’s solution, and isotonic sodium chloride solution, and acceptable solvents such as 1,3-butane diol. In addition, sterile, fixed oils can be used as a solvent or suspending medium. For this purpose, any bland fixed oil can be employed including synthetic monoglycerides, diglycerides, or triglycerides. [0168] Aqueous suspensions can contain one or more gingipain blocking agents in admixture with excipients including, but not limited to: suspending agents such as sodium carboxymethylcellulose, methylcellulose, oleagino-propylmethylcellulose, sodium alginate, polyvinyl-pyrrolidone, gum tragacanth and gum acacia; dispersing or wetting agents such as lecithin, polyoxyethylene stearate, and polyethylene sorbitan monooleate; and preservatives such as ethyl, n-propyl, and p-hydroxybenzoate. Dispersible powders and granules (suitable for preparation of an aqueous suspension by the addition of water) can contain one or more gingipain blocking agents in admixture with a dispersing agent, wetting agent, suspending agent, or combinations thereof. Oily suspensions can be formulated by suspending a gingipain blocking agent in a vegetable oil (e.g., arachis oil, olive oil, sesame oil or coconut oil), or in a mineral oil (e.g., liquid paraffin). Oily suspensions can contain one or more thickening agents, for example beeswax, hard paraffin, or cetyl alcohol. These compositions can be preserved by the addition of an anti-oxidant such as ascorbic acid. [0169] The pharmaceutical compositions containing gingipain blocking agents can also be administered in the form of oil-in-water emulsions. The oily phase can be a vegetable oil, for example olive oil or arachis oil, or a mineral oil, for example liquid paraffin or mixtures of these. Suitable emulsifying agents can be naturally-occurring gums, such as gum acacia or gum tragacanth; naturally-occurring phospholipids, such as soy lecithin; esters or partial esters derived from fatty acids and hexitol anhydrides, such as sorbitan monooleate; and condensation products of said partial esters with ethylene oxide, such as polyoxyethylene sorbitan monooleate. [0170] Additionally, the gingipain blocking agents can be administered so as to increase bioavailability. Time release technology can be used to increase bioavailability including formulations for sustained-release (SR), sustained-action (SA), extended-release (ER, XR, XL) timed-release (TR), controlled-release (CR), modified release (MR), continuous-release, osmotic release and slow release implants. [0171] In some embodiments, the gingipain blocking agent is administered orally. In some embodiments, the gingipain blocking agent has been modified to increase bioavailability. [0172] In some embodiments, the gingipain blocking agent is administered intranasally. In some embodiments, the gingipain blocking agent is administered subcutaneously. In some embodiments, the gingipain blocking agent is administered intravenously. In some embodiments, the gingipain blocking agent is administered intraarticularly. [0173] In some embodiments, the subject is an animal or a human. In some embodiments, the subject is a canine, a feline, a horse, or a rodent. In some embodiments, the subject is a canine. In some embodiments, the treatment is preventative. In some embodiments, the treatment is delivered in food. V. Identification and treatment of subjects with osteoarthritis [0174] In another aspect, the invention provides a method for treating osteoarthritis, wherein the method includes: identifying a subject having P. gingivalis antigens or P.

gingivalis DNA in synovial fluid or tissue, and administering a therapeutically effective amount of a gingipain blocking agent to the subject having the P. gingivalis antigens or the P. gingivalis DNA in synovial fluid or tissue. In some such embodiments, the method further comprises periodically determining whether the subject has P. gingivalis antigens or P.

gingivalis DNA in synovial fluid or tissue over the course of an evaluation period, and adjusting the treatment if the P. gingivalis antigens or P. gingivalis DNA levels in synovial fluid are observed to change over the course of the evaluation period. [0175] A variety of primers and probes can be used for detecting P. gingivalis nucleic acids including, but not limited to, oligonucleotides having at least 80% sequence complementarity to nucleic acids for P. gingivalis 16S RNA, P. gingivalis RgpB nucleic acid sequences encoding P. gingivalis RgpB polypeptides, and nucleic acid sequences encoding polypeptides of P. gingivalis fimbria, such that the oligonucleotides can hybridize to said nucleic acids. Known techniques, including Western blots or ELISA conducted with P. gingivalis-specific antibodies (e.g., 7B9 for detection of Kgp, 18E6 for detection of Rgp), can be used to detect P. gingivalis in synovial fluid or tissue. Mass-spectrometry techniques, including MS/MS, and other proteomic methodology can also be used to identify P. gingivalis antigens. [0176] Another embodiment of the invention encompasses the use of P. gingivalis exposed or infected rodent and dog as models of osteoarthritis. These models are valuable for the understanding of osteoarthritis and the testing of therapeutics for efficacy. As described previously, dogs are naturally predisposed to infection with P. gingivalis and incidence of this infection is increased through direct exposure, feeding of soft food, and/or lack of dental care. See, Berglundh, supra, and Albuquerque, supra. Aged dogs spontaneously develop many features of osteoarthritis. See, Sanderson, et al. Vet Rec, 2009.164(14): 418-24.

Analysis of the joints of an aged dog with osteoarthritis show the presence of P. gingivalis DNA in osteoarthritic tissue, as shown in Fig.3. One embodiment of the invention encompasses the use of gingipain inhibitors to treat or prevent osteoarthritis in dogs.

Additionally, dogs with natural or purposeful P. gingivalis infection can be useful as models for studying the efficacy of therapeutics for humans. VI. Examples Example 1: P. gingivalis markers found in human joint tissue. [0177] Human autopsy joint tissues were obtained from Advanced Tissue Solutions.

Osteoarthritic joint tissue and normal joint tissue were embedded in paraffin, sectioned at 5 µm with a microtome, and mounted on coverslips. Paraffin was removed from the sections with xylenes, and the sections were hydrated in alcohol series. Endogenous peroxidase was blocked with Bloxall (Vector Laboratories, Burlingame, CA) and washed in TBS. After blocking unspecific antigens with normal horse serum (Vector Laboratories), sections were incubated with primary antibody 18E6 (University of Georgia, Athens, GA) (7.5 µg/ml; 0.3% Triton-X-100 in TBS) overnight at 4 °C. The primary antibody was detected using ImmPRESS™ Excel Amplified HRP Polymer Staining Kit (Anti-Mouse IgG) (Vector Laboratories) following the manufacturer’s instructions followed by counterstaining with Hematoxylin. Samples were coverslipped with DPX Mounting Medium (Sigma, St. Louis, MO). OA joints showed strong arginine gingipain staining (evidenced by the rust color) while normal joints did not. Staining was seen in osteoclasts near bone pathology (Fig.1), synovial cells (Fig.2), and other compartments. Example 2: P. gingivalis is found in osteoarthritic dog tissues. [0178] Joints from a 19 year old beagle dog were purchased from Intervivo. The dog had been diagnosed with osteoarthritis by a veterinarian in three joints (left shoulder, right shoulder, left stifle). Joints were sampled and analyzed by PCR for P. gingivalis arginine gingipain.100 mg of dog shoulder, stifle or elbow tissues were lysed to extract DNA using QiAmp Cador pathogen kit (Qiagen).250 ng of extracted DNA from each sample were used for polymerase chain reaction (PCR), using EconoTaq plus Green Master Mix (Lucigen) with 200 nM of each primer. Forward primer: 5′-AGCAACCAGCTACCGTTTAT-3′. Reverse primer: 5′-GTACCTGTCGGTTTACCATCTT-3′. PCR reactions were programmed with a denaturing step at 95°C for 5 min, 30 cycles of (95°C 30 sec denature, 56°C 30 sec annealing, 72°C 30 sec extension), and a final extension step at 72°C 5 min.20 μl of each PCR product was applied to a 2% SYBR agarose gel, run for 30 min, then visualized with an Amersham Imager 600. [0179] As shown in Fig.3, the P. gingivalis band was observed at 118 nt in the three osteoarthritic joints (left shoulder, right shoulder, and left stifle). No P. gingivalis DNA was observed in the three non-arthritic joints. Example 3: Gingipain inhibitors prevent degradation of human collagen. [0180] P. gingivalis was grown to exponential phase (OD 600 nm = 0.6) in a Coy's anaerobic chamber under 5% hydrogen, 10% carbon dioxide, and 95% nitrogen. The bacteria were centrifuged at 5000 × g for 10 min at 4°C, and then the supernatant was collected. The supernatant was concentrated by centrifugation at 5000 × g for 60 min at 4°C min using Corning Spin-X UF-20 concentrator tubes and then at 17,000 × g for 30 min using Corning Spin-X UF500 concentrator tubes.10 µg of collagen was incubated with 0.6 µg of P.

gingivalis culture supernatant for 1h in the absence or presence of 50 µM Rgp inhibitor (Compound 13-R, Table 1), 50 µM Kgp inhibitor (Compound 43, Table 1), or both. Reaction mixtures contained 5 mM cysteine, 20 mM sodium phosphate buffer, pH 7.5. After incubation, the reaction was terminated by the addition of protease inhibitor cocktail (Sigma). The samples were then analyzed by SDS-polyacrylamide gel electrophoresis. Following separation, the gels were stained with Biosafe Coomassie (Bio-Rad). The gel data (e.g., Fig. 4) showed that the Rgp inhibitor and Kgp inhibitor prevent degradation of collagen by the gingipain-containing P. gingivalis supernatant. Administration of gingipain inhibitors can be used to prevent collagen degradation in osteoarthritic subjects. VII. Exemplary Embodiments [0181] Exemplary embodiments provided in accordance with the presently disclosed subject matter include, but are not limited to, the claims and the following embodiments: 1. A method of treating osteoarthritis comprising administering a therapeutically effective amount of one or more gingipain-blocking agents to a patient in need thereof. 2. The method of embodiment 1, wherein the gingipain blocking agent is a compound which inhibits Lysine Gingipain (Kgp) activity or production; a compound which inhibits translocation of Kgp into joint tissue or into systemic circulation; and/or a compound which inhibits the pathological effects of Kgp in a mammal. 3. The method of embodiment 2, wherein the compound has an IC₅₀ of Lysine Gingipain (Kgp) of less than or equal to 10 nanomolar (nM). 4. The method of embodiment 1, wherein the gingipain blocking agent is a compound which inhibits Arginine Gingipain A (RgpA) activity or production; a compound which inhibits translocation of RgpA into joint tissue or into systemic circulation; and/or a compound which inhibits the pathological effects of RgpA in a mammal. 5. The method of embodiment 4, wherein the compound has an IC₅₀ of Arginine Gingipain A (RgpA) of less than or equal to 10 nanomolar (nM). 6. The method of embodiment 1, wherein the gingipain blocking agent is a compound which inhibits Arginine Gingipain B (RgpB) activity or production; a compound which inhibits translocation of RgpA into joint tissue or into systemic circulation; and/or a compound which inhibits the pathological effects of RgpB in a mammal. 7. The method of embodiment 6, wherein the compound has an IC₅₀ of Arginine Gingipain B (RgpB) of less than or equal to 10 nanomolar (nM). 8. The method of any one of embodiments 2-7, wherein the gingipain blocking agent is a compound or combination of compounds that inhibits Kgp and RgpA/B activity. 9. The method of embodiment 2, wherein the compound has a structure according to Formula Ib:

or a pharmaceutically acceptable salt thereof, wherein

Z is selected from the group consisting of halogenated substituted aryloxymethyl-carbonyl, benzothiazol-2-yl-carbonyl; thiazol-2-yl-carbonyl; oxazol-2-yl- carbonyl; benzooxazol-2-yl-carbonyl; pyridin-2-yl-carbonyl; pyrimidin-4-yl-carbonyl;

pyrimidin-2-yl-carbonyl; isoxazol-5-yl-carbonyl; isoxazol-3-yl-carbonyl; 1,2,4-oxadiazol-3- yl-carbonyl; 1,2,4-oxadiazol-5-yl-carbonyl; cyano; ethynyl; fluoromethyl-carbonyl;

acyloxymethyl-carbonyl; aryloxymethyl-carbonyl; alkylsulfonyl-vinyl; and arylsulfonyl- vinyl; each of which is optionally substituted with one or more substituents selected from the group consisting of C_1-4 alkyl, C_1-4 alkoxy, C_1-4 haloalkyl, C_1-4 haloalkoxy, halogen, and –N₃;

A is selected from the group consisting of -CH₂- and -O-;

B and D are independently selected from the group consisting of hydrogen, halogen, halomethyl, and halomethoxy

R¹ is selected from the group consisting of hydrogen and an amine protecting group;

R² is hydrogen; and

R³ is selected from the group consisting of C_3-8 cycloalkyl, C_6-10 aryl, 5-to-12 membered heteroaryl, C_1-8 alkyl, 5-to-12 membered saturated heterocyclyl, -L-R⁵, and -OR⁶, wherein

L is selected from the group consisting of -O-, -NR-, C_1-4 alkylene, and 2- to 4-membered heteroalkylene, wherein R is selected from the group consisting of hydrogen and C_1-8 alkyl,

R⁵ is selected from the group consisting of C_6-10 aryl, 5-to-12 membered heteroaryl, C_3-8 cycloalkyl, and 5-to-12 membered saturated heterocyclyl, and

-OR⁶ and the carbonyl to which it is bonded form an amine protecting group, and wherein R³ is optionally substituted with one or more substituents selected from the group consisting of halo, -CN, -NO₂, -N₃, -OH, R^a, R^b, -OR^a, -OR^b, -(CH₂)_kC(O)R^c, -NR^d(CH₂)_uC(O)R^c, -O(CH₂)_uC(O)R^c, -(CH₂)_kCONR^dR^d, -(CH₂)_kNR^dC(O)R^c, -NR^d(CH₂)_uCONR^dR^d, -NR^d(CH₂)_uNR^dC(O)R^c, -O(CH₂)_uCONR^dR^d, -O(CH₂)_uNR^dC(O)R^c, -(CH₂)_kS(O)₂NR^dR^d, -(CH₂)_kNR^dS(O)₂R^c, -(CH₂)_kS(O)₂R^c, -(CH₂)_kS(O)R^c, -(CH₂)_kSR^d, -NR^d(CH₂)_uS(O)₂NR^dR^d, -NR^d(CH₂)_uNR^dS(O)₂R^c, -NR^d(CH₂)_uS(O)₂R^c, -NR^d(CH₂)_uS(O)R^c, -NR^d(CH₂)_uSR^d, -O(CH₂)_uS(O)₂NR^dR^d, -O(CH₂)_uNR^dS(O)₂R^c, -O(CH₂)_uS(O)₂R^c,

-O(CH₂)_uS(O)R^c, and -O(CH₂)_uSR^c, wherein:

each R^a is independently selected from the group consisting of C_1-4 alkyl and C_1-4 haloalkyl,

each R^b is independently selected from the group consisting of C_3-6 cycloalkyl, C_3-6 halocycloalkyl, C_6-10 aryl, 5-to-12 membered heteroaryl, and 5-to-12 membered saturated heterocyclyl,

each R^c is independently selected from the group consisting of -OH, C_1-8 alkyl, C_1-8 haloalkyl, C_3-8 cycloalkyl, C_3-8 halocycloalkyl, C_6-10 aryl, (C_6-10 aryl)-(C_1-8 alkyl), 5-to-12 membered heteroaryl, and 5-to-12 membered saturated heterocyclyl,

each R^d is independently selected from the group consisting of hydrogen and C_1-8 alkyl,

each subscript k is independently selected from 0, 1, 2, 3, 4, 5, and 6, and each subscript u is independently selected from 1, 2, 3, 4, 5, and 6. 10. The method of embodiment 9, wherein the compound has a structure according to Formula Id:

or a pharmaceutically acceptable salt thereof,

wherein R³ is selected from the group consisting of C_3-8 cycloalkyl, C_6-10 aryl, 5-to-12 membered heteroaryl, 5-to-12 membered saturated heterocyclyl, and -L-R⁵,

wherein L is C_1-4 alkylene. 11. The method of embodiment 9, wherein the compound has a structure according to Formula Ic:

(Ic)

or a pharmaceutically acceptable salt thereof,

wherein R³ is selected from the group consisting of C_6-10 aryl, 5-to-12 membered heteroaryl, C_3-8 cycloalkyl, 5-to-12 membered saturated heterocyclyl, and -L-R⁵, wherein L is C_1-4 alkylene. 12. The method of embodiment 2, wherein the compound has a structure according to Formula II:

(II) wherein

R¹ or R² is unsubstituted or substituted benzyloxycarbonyl;

X¹ is CH;

X² and X³ are both CO;

p is an integer from 1 to 4; and

q is 1. 13. The method of embodiment 12, wherein the compound is selected from the group consisting of KYT-1, KYT-36, KYT-41, and combinations thereof. 14. The method of embodiment 13, wherein the compound is a combination of KYT-36 and KYT-1. 15. The method of embodiment 1, wherein the gingipain blocking agent is a an antibacterial agent which is bacteriostatic or bacteriocidal with respect to P. gingivalis. 16. The method of embodiment 15, wherein the antibacterial agent is bestatin or an analog thereof. 17. The method of embodiment 15, wherein the bacteriocidal agent is selected from the group consisting of a quinolone; a floroquinolone; a β-lactam; a

cephalosporin; a macrolide; a carbapenem; a thiazolide; a tetracycline; a lincomycin; an agent that inhibits/interferes with formation of a biofilm of anaerobic gram negative bacteria; and combinations thereof. 18. The method of embodiment 15, wherein the bacteriocidal agent is selected from the group consisting of gemifloxacin, ciprofloxacin, oflaxacin, trovafloxacin, sitafloxacin, moxifloxacin, amoxicillin, amoxacilin-clavulanate, piperacillin-tazobactam, penicillin G, ceftriaxone, erythromycin, azithromycin, clarithromycin, doripenem, imipenem, meropinem, ertapenem, tizoxanidine, nitazoxanidine, RM 4807, RM 4809, tetracycline, minocycline, doxycycline, eravacycline, clindamycin, metronidazole, satranidazole, oxantel, morantel, thiabendazole, and combinations thereof. 19. The method of embodiment 1, wherein the gingipain blocking agent is an antibody which binds to a P. gingivalis protein. 20. The method of embodiment 19, wherein the antibody binds to at least one protein selected from the group consisting of Kgp, RgpA, and RgpB. 21. The method of embodiment 19, wherein the antibody is selected from the group consisting of 7B9 ,18E6, 61Bg 1.3, 1B5, 7B4, 15C8, fragments thereof, and combinations thereof. 22. The method of embodiment 19 or embodiment 21, wherein the antibody is humanized. 23. The method of embodiment 1, wherein the gingipain blocking agent is a vaccine. 24. The method of embodiment 23, wherein the vaccine comprises at least one member selected from the group consisting of Kgp, RgpA, RgpB, and epitopes thereof. 25. The method of embodiment 24, wherein the Kgp, RgpA, RgpB, and epitopes thereof are inactivated. 26. The method of embodiment 23, wherein the vaccine is comprises P. gingivalis. 27. The method of embodiment 26, where in the P. gingivalis is live attenuated P. gingivalis or killed P. gingivalis. 28. The method of embodiment 23, wherein the vaccine is an active vaccine comprising a P. gingivalis protein other than RgpA, RgpB and Kgp, or an immunogenic fragment thereof. 29. The method of any one of the preceding embodiments, further comprising administration of one or more additional therapeutic agent(s) indicated for the treatment and/or prevention osteoarthritis. 30. The method of any one of the preceding embodiments, wherein the gingipain blocking agent has been modified to increase bioavailability. 31. The method of any one of the preceding embodiments, wherein the gingipain blocking agent is administered orally. 32. The method of any one of the preceding embodiments, wherein the gingipain blocking agent is administered intranasally. 33. The method of any one of the preceding embodiments, wherein the gingipain blocking agent is administered subcutaneously. 34. The method of any one of the preceding embodiments, wherein the gingipain blocking agent is administered intravenously. 35. The method of any one of the preceding embodiments, wherein the gingipain blocking agent is administered intraarticularly. 36. The method of any one of the preceding embodiments, wherein the subject is an animal or a human. 37. The method of embodiment 36, wherein the subject is a canine, a feline, a horse, or a rodent. 38. The method of embodiment 37, wherein the subject is a canine. 39. The method of embodiment 38, wherein the treatment is preventative. 40. The method of embodiment 38, wherein the treatment is delivered in food. 41. A method of treating osteoarthritis, the method comprising:

identifying a subject having P. gingivalis antigens or P. gingivalis DNA in synovial fluid or tissue, and

administering a therapeutically effective amount of a gingipain blocking agent to the subject having the P. gingivalis antigens or the P. gingivalis DNA in synovial fluid or tissue. 42. The method of embodiment 41, further comprising periodically determining whether the subject has P. gingivalis antigens or P. gingivalis DNA in synovial fluid or tissue over the course of an evaluation period, and adjusting the treatment if the P. gingivalis antigens or P. gingivalis DNA levels in synovial fluid or tissue are observed to change over the course of the evaluation period. 43. A rodent model of osteoarthritis generated by administration of P. gingivalis to a rodent. 44. The rodent model of embodiment 43, wherein the P. gingivalis is administered orally. 45. The rodent model of embodiment 43, wherein the P. gingivalis is administered intra-articularly. 46. The rodent model of embodiment 43, wherein the P. gingivalis is administered by chamber method. 47. The rodent model of embodiment any one of embodiments 43-46, wherein the rodent is a mouse. 48. The rodent model of embodiment any one of embodiments 43-46, wherein the rodent is a rat. 49. A dog model of osteoarthritis generated by establishment of P.

gingivalis infection in a dog. 50. The dog model of embodiment 49, wherein the P. gingivalis infection is established by administering P. gingivalis to the dog. 51. The dog model of embodiment 49, wherein the P. gingivalis infection is established by feeding soft food to the dog and allowing the dog to develop gingivitis. 52. The dog model of embodiment 49, wherein the P. gingivalis infection is established by withholding dental care from the dog and allowing the dog to develop gingivitis. 53. The dog model of any one of embodiments 49-52, wherein the dog is aged. [0182] Although the foregoing has been described in some detail by way of illustration and example for purposes of clarity and understanding, one of skill in the art will appreciate that certain changes and modifications can be practiced within the scope of the appended claims. In addition, each reference provided herein is incorporated by reference in its entirety to the same extent as if each reference was individually incorporated by reference.

Claims

WHAT IS CLAIMED IS: 1. A method of treating osteoarthritis comprising administering a therapeutically effective amount of one or more gingipain-blocking agents to a patient in need thereof.

2. The method of claim 1, wherein the gingipain blocking agent is a compound which inhibits Lysine Gingipain (Kgp) activity or production; a compound which inhibits translocation of Kgp into joint tissue or into systemic circulation; and/or a compound which inhibits the pathological effects of Kgp in a mammal.

3. The method of claim 2, wherein the compound has an IC₅₀ of Lysine Gingipain (Kgp) of less than or equal to 10 nanomolar (nM).

4. The method of claim 1, wherein the gingipain blocking agent is a compound which inhibits Arginine Gingipain A (RgpA) activity or production; a compound which inhibits translocation of RgpA into joint tissue or into systemic circulation; and/or a compound which inhibits the pathological effects of RgpA in a mammal.

5. The method of claim 4, wherein the compound has an IC₅₀ of Arginine Gingipain A (RgpA) of less than or equal to 10 nanomolar (nM).

6. The method of claim 1, wherein the gingipain blocking agent is a compound which inhibits Arginine Gingipain B (RgpB) activity or production; a compound which inhibits translocation of RgpA into joint tissue or into systemic circulation; and/or a compound which inhibits the pathological effects of RgpB in a mammal.

7. The method of claim 6, wherein the compound has an IC₅₀ of Arginine Gingipain B (RgpB) of less than or equal to 10 nanomolar (nM).

8. The method of claim 2, wherein the gingipain blocking agent is a compound or combination of compounds that inhibits Kgp and RgpA/B activity.

9. The method of claim 2, wherein the compound has a structure according to Formula Ib:

or a pharmaceutically acceptable salt thereof, wherein

Z is selected from the group consisting of halogen-substituted aryloxymethyl- carbonyl; benzothiazol-2-yl-carbonyl; thiazol-2-yl-carbonyl; oxazol-2-yl-carbonyl;

benzooxazol-2-yl-carbonyl; pyridin-2-yl-carbonyl; pyrimidin-4-yl-carbonyl; pyrimidin-2-yl- carbonyl; isoxazol-5-yl-carbonyl; isoxazol-3-yl-carbonyl; 1,2,4-oxadiazol-3-yl-carbonyl; 1,2,4-oxadiazol-5-yl-carbonyl; cyano; ethynyl; fluoromethyl-carbonyl; acyloxymethyl- carbonyl; aryloxymethyl-carbonyl; alkylsulfonyl-vinyl; and arylsulfonyl-vinyl; each of which is optionally substituted with one or more substituents selected from the group consisting of C_1-4 alkyl, C_1-4 alkoxy, C_1-4 haloalkyl, C_1-4 haloalkoxy, halogen, and–N₃;

A is selected from the group consisting of -CH₂- and -O-;

R² is hydrogen; and

-O(CH₂)_uS(O)R^c, and -O(CH₂)_uSR^c, wherein:

each subscript k is independently selected from 0, 1, 2, 3, 4, 5, and 6, and each subscript u is independently selected from 1, 2, 3, 4, 5, and 6.

10. The method of claim 9, wherein the compound has a structure according to Formula Id:

or a pharmaceutically acceptable salt thereof,

wherein L is C_1-4 alkylene.

11. The method of claim 9, wherein the compound has a structure according to Formula Ic:

or a pharmaceutically acceptable salt thereof,

wherein R³ is selected from the group consisting of C_6-10 aryl, 5-to-12 membered heteroaryl, C_3-8 cycloalkyl, 5-to-12 membered saturated heterocyclyl, and -L-R⁵, wherein L is C_1-4 alkylene.

12. The method of claim 2, wherein the compound has a structure according to Formula II:

(II) wherein

R¹ or R² is unsubstituted or substituted benzyloxycarbonyl;

X¹ is CH;

X² and X³ are both CO;

p is an integer from 1 to 4; and

q is 1.

13. The method of claim 12, wherein the compound is selected from the group consisting of KYT-1, KYT-36, KYT-41, and combinations thereof.

14. The method of claim 13, wherein the compound is a combination of KYT-36 and KYT-1.

15. The method of claim 1, wherein the gingipain blocking agent is a an antibacterial agent which is bacteriostatic or bacteriocidal with respect to P. gingivalis.

16. The method of claim 15, wherein the antibacterial agent is bestatin or an analog thereof.

17. The method of claim 15, wherein the bacteriocidal agent is selected from the group consisting of a quinolone; a floroquinolone; a β-lactam; a cephalosporin; a macrolide; a carbapenem; a thiazolide; a tetracycline; a lincomycin; an agent that

inhibits/interferes with formation of a biofilm of anaerobic gram negative bacteria; and combinations thereof.

18. The method of claim 15, wherein the bacteriocidal agent is selected from the group consisting of gemifloxacin, ciprofloxacin, oflaxacin, trovafloxacin, sitafloxacin, moxifloxacin, amoxicillin, amoxacilin-clavulanate, piperacillin-tazobactam, penicillin G, ceftriaxone, erythromycin, azithromycin, clarithromycin, doripenem, imipenem, meropinem, ertapenem, tizoxanidine, nitazoxanidine, RM 4807, RM 4809, tetracycline, minocycline, doxycycline, eravacycline, clindamycin, metronidazole, satranidazole, oxantel, morantel, thiabendazole, and combinations thereof.

19. The method of claim 1, wherein the gingipain blocking agent is an antibody which binds to a P. gingivalis protein.

20. The method of claim 19, wherein the antibody binds to at least one protein selected from the group consisting of Kgp, RgpA, and RgpB.

21. The method of claim 19, wherein the antibody is selected from the group consisting of 7B9 ,18E6, 61Bg 1.3, 1B5, 7B4, 15C8, fragments thereof, and combinations thereof.

22. The method of claim 19, wherein the antibody is humanized.

23. The method of claim 1, wherein the gingipain blocking agent is a vaccine.

24. The method of claim 23, wherein the vaccine comprises at least one member selected from the group consisting of Kgp, RgpA, RgpB, and epitopes thereof.

25. The method of claim 24, wherein the Kgp, RgpA, RgpB, and epitopes thereof are inactivated.

26. The method of claim 23, wherein the vaccine is comprises P.

gingivalis.

27. The method of claim 26, where in the P. gingivalis is live attenuated P. gingivalis or killed P. gingivalis.

28. The method of claim 23, wherein the vaccine is an active vaccine comprising a P. gingivalis protein other than RgpA, RgpB and Kgp, or an immunogenic fragment thereof.

29. The method of claim 1, further comprising administration of one or more additional therapeutic agent(s) indicated for the treatment and/or prevention

osteoarthritis.

30. The method of claim 1, wherein the gingipain blocking agent has been modified to increase bioavailability.

31. The method of claim 1, wherein the gingipain blocking agent is administered orally.

32. The method of claim 1, wherein the gingipain blocking agent is administered intranasally.

33. The method of claim 1, wherein the gingipain blocking agent is administered subcutaneously.

34. The method of claim 1, wherein the gingipain blocking agent is administered intravenously.

35. The method of claim 1, wherein the gingipain blocking agent is administered intraarticularly.

36. The method of claim 1, wherein the subject is an animal or a human.

37. The method of claim 36, wherein the subject is a canine, a feline, a horse, or a rodent.

38. The method of claim 37, wherein the subject is a canine.

39. The method of claim 38, wherein the treatment is preventative.

40. The method of claim 38, wherein the treatment is delivered in food.

41. A method of treating osteoarthritis, the method comprising:

administering a therapeutically effective amount of a gingipain blocking agent to the subject having the P. gingivalis antigens or the P. gingivalis DNA in synovial fluid or tissue.

42. The method of claim 41, further comprising periodically determining whether the subject has P. gingivalis antigens or P. gingivalis DNA in synovial fluid or tissue over the course of an evaluation period, and adjusting the treatment if the P. gingivalis antigens or P. gingivalis DNA levels in synovial fluid or tissue are observed to change over the course of the evaluation period.

43. A rodent model of osteoarthritis generated by administration of P. gingivalis to a rodent.

44. The rodent model of claim 43, wherein the P. gingivalis is administered orally.

45. The rodent model of claim 43, wherein the P. gingivalis is administered intra-articularly.

46. The rodent model of claim 43, wherein the P. gingivalis is administered by chamber method.

47. The rodent model of claim 43, wherein the rodent is a mouse.

48. The rodent model of claim 43, wherein the rodent is a rat.

49. A dog model of osteoarthritis generated by establishment of P. gingivalis infection in a dog.

50. The dog model of claim 49, wherein the P. gingivalis infection is established by administering P. gingivalis to the dog.

51. The dog model of claim 49, wherein the P. gingivalis infection is established by feeding soft food to the dog and allowing the dog to develop gingivitis.

52. The dog model of claim 49, wherein the P. gingivalis infection is established by withholding dental care from the dog and allowing the dog to develop gingivitis.

53. The dog model of claim 49, wherein the dog is aged.