Complement factor b analogs, compositions formed therefrom, and uses thereof

Abstract

Disclosed herein are polypeptides that include human complement factor B analogs and fusion proteins formed therefrom. The complement factor B analogs typically have one or more mutations at a factor D cleavage site, and optionally one or more mutations at C3B binding sites or a mutation of a free cysteine site. Also disclosed herein are pharmaceutical compositions containing a complement factor B analog or a complement factor B analog Fc fusion protein, as a homodimer, multimer, or heterodimer. These pharmaceutical compositions include nucleic acids, viral vectors, or cells that encode or express the disclosed composition. Methods for treating complement-mediated diseases are also disclosed and can include administering the pharmaceutical compositions to subjects for modulation of complement activity and treatment of disease symptoms associated with complement pathway dysfunction.

Description

[0001] ATTORNEY DOCKET NO. MSD PC 139 PCT

[0002] COMPLEMENT FACTOR B ANALOGS, COMPOSITIONS FORMED THEREFROM, AND USES THEREOF

[0003] CROSS REFERENCE TO RELATED APPLICATION

[0004] This application claims benefit of and priority to U. S. Provisional Application No. 63 / 791,167, filed April 18, 2025, the contents of which is specifically incorporated by reference herein in its entirety.

[0005] REFERENCE TO THE SEQUENCE LISTING

[0006] The Sequence Listing XML submitted as a file named “MSD_PC139_PCT_ST26.xml”, created on April 17, 2025, and having a file size of 61,436 bytes is hereby incorporated by reference pursuant to 37 C. F. R. § 1.834(c)(1).

[0007] FIELD OF THE INVENTION

[0008] The field generally relates to complement factors and complement pathways, and more specifically to complement factor B analogs and their use for modulating complement pathways.

[0009] BACKGROUND OF THE INVENTION

[0010] The complement system is a component of the innate and adaptive immune system (reviewed by Volanakis, J. E., 1998. Chapter 2. In The Human Complement System in Health and Disease. Edited by J. E. Volanakis, and M. M. Frank. Marcel Dekker, Inc., New York pp 9-32). Complement plays an important role in microbial killing, and for the transport and clearance of immune complexes. Many of the activation products of the complement system are also associated with proinflammatory or immunoregulatory functions. The complement system includes of plasma and membrane-associated proteins that are organized in three enzymatic-activation cascades: the classical, the lectin, and the alternative pathways. All three pathways can lead to the formation of the terminal complement complex (TCC, also called membrane attack complex (MAC)) and an array of biologically active products.

[0011] In some cases, complement activation is initiated either by specific antibodies recognizing and binding to a variety of pathogens and foreign molecules, and / or by direct interaction of complement proteins with foreign substances. On activation, these pathways result in the formation of protease complexes, the C3-convertases. The classical pathway C3-convertase, C4b2a, and the alternative pathway C3-convertase, C3bBb, are both able to cleave the a chain of C3 generating C3b. C3b has the potential to bind covalently to biological surfaces. C3b binding leads to opsonization for phagocytosis by polymorphonuclear cells and macrophages. When additional C3b is available, the C3-convertases can function as C5-convertases, cleaving C5 and initiating the assembly of the 45845704.1 1ATTORNEY DOCKET NO. MSD PC 139 PCT

[0012] TCC, or MAC, which mediates cellular lysis by insertion of pore-forming protein complexes into targeted cell membranes.

[0013] In the classical pathway, Clq, a collagenous subcomponent of the first component (Cl), binds to immunoglobulins within immune complexes, and its associated serine proteases, Clr and Cis, become activated. This complement cascade is initiated by the subsequent cleavage of C4 and C2, followed by C3 activation. The resulting C3b fragment not only acts as an opsonin but also leads to MAC formation in the lytic pathway. In innate immunity, a complex composed of a recognition molecule (lectin) and serine proteases, termed the mannose-binding lectin (MBL)-associated serine protease (MASP), activates C4 and C2 upon binding to carbohydrates on the surface of microorganisms via the lectin pathway. This binding occurs in the absence of immunoglobulins. Recognition molecules of the lectin pathway found in jawed vertebrates are MBLs and ficolins, both of which are characterized by the presence of a collagen- like domain, like Clq, and a carbohydrate binding domain having a common binding specificity for GlcNAc. MASPs and Clr / Cls share the same domain organization and form a subfamily of serine proteases.

[0014] The lectin complement pathway in innate immunity is closely related to the classical complement pathway in adaptive immunity, e.g., with respect to the structures and functions of their components. Both pathways are typically initiated by complexes including of collagenous proteins and serine proteases of the mannose-binding lectin (MBL)-associated serine protease (MASP) / Clr / Cls family. It has been speculated that the classical pathway emerged evolutionarily after the lectin pathway.

[0015] Activation of the alternative complement pathway typically begins when C3b protein binds to a cell and other surface components, e.g., of microbes. Factor B protein is an essential component of the alternative complement pathway. One of the key constituents of the alternative complement pathway is C3 convertase. C3 convertase is formed by the binding of factor B protein to C3b protein, causing a conformation change in C3b bound factor B protein. Following the conformation change, factor B protein is proteolyzed by factor D protein, resulting in the formation of fragments Ba and Bb protein. While fragment Ba protein dissociates from the complex, fragment Bb protein remains bound to C3b protein forming the C3bBb complex, which serves as the C3 convertase. Properdin can bind C3bBb and stabilizes the C3 convertase. Thereafter, factor D protein is dissociated from the C3bBb complex, promoting the AP cascade (Gros, P et al., 2008). Factor D protein functions as a catalyst and can be recycled in the pathway.

[0016] 45845704.1 2ATTORNEY DOCKET NO. MSD PC 139 PCT

[0017] Since C3b is free in the plasma, it can bind to either a host cell or pathogen surface. To prevent complement activation from proceeding on the host cell, there are several different kinds of regulatory proteins that disrupt the complement activation process.

[0018] Complement Receptor 1 (CR1 or CD35) and DAE (also known as CD55) compete with Factor B in binding with C3b on the cell surface and can even remove Bb from an already formed C3bBb complex. The formation of a C3 convertase can also be prevented when a plasma protease called Factor I cleaves C3b into its inactive form, iC3b. Factor I works with C3b-binding protein cofactors such as CR1 and Membrane Cofactor of Proteolysis (MCP or CD46). Another complement regulatory protein is Factor H which either competes with factor B, displaces Bb from the convertase, acts as a cofactor for Factor I, or preferentially binds to C3b bound to vertebrate cells.

[0019] The precise function of the complement system depends on its regulation, as activation of the complement cascade leads to the production of a number of proteins that contribute to inflammation. This is beneficial when contributing to a host defense, but can be detrimental if activated on self tissue. Typically, activation of C3 in the blood is kept at a low level, and C3b deposition is limited to the surface of pathogens.

[0020] The human wild type complement factor B protein is a 764 amino acid, single-chain glycoprotein (approximately 90-100 KDa) composed of five protein domains (Mole et al., 1984 The J. Biol Chem, 259:6, 3407-3412). A human wild type complement factor B protein (also called fB, or Wt fB, or Wt hfB) is typically expressed with an N-terminal 25 amino acid signal peptide, e.g., see SEQ ID NO:1. The amino-terminal region (Ba) of human wild type complement factor B protein includes primarily of three short consensus repeats. The middle region is a type A domain similar to those found in von Willebrand factor (Colombatti et al., Blood (1991) 77( 11):2305- 15). The carboxy terminus is a serine protease (SP) domain (Perkins and Smith, Biochem J. (1993) 295( Pt 1): 109-14; Hourcade et al., JBC (1998) 273(40):25996-6000; Ilourcade et al. J Immunol. (1999) 162(5):2906-ll; Xu et al., J Biol Chem. 2000275(l):378-85; Milder et al. Nat Struct Mol Biol (2007) 14(3):224-8).

[0021] Some complement factor B analogs and their use for inhibiting complement and treating complement mediated diseases are described in U. S. Patent US 9,228,003. For example, the human complement factor B protein analog (referred to herein as PC 113) is a dominant negative human factor B protein variant that efficiently inhibits the alternative complement (AP) activity. PCI 13 protein (SEQ ID NO: 2) has six amino acid changes compared to a human wild type factor B protein (SEQ ID NO:1). The six amino acid changes facilitate PCI 13 protein to (1) bind much tighter to C3b protein, (2) resist C3b- 45845704.1 3ATTORNEY DOCKET NO. MSD PC 139 PCT

[0022] dependent cleavage by factor D protein, (3) bind tighter to factor D protein when compared to the wild type factor B protein, and (4) a free cysteine, C292, was substituted with a serine. The tighter binding of PCI 13 with C3b protein and factor D protein sequester two important components of the alternative complement pathway (AP) in an inactive C3 convcrtasc (C3bPCl 13), blocking the AP activity. Since C3b-bound PCI 13 protein cannot be cleaved by factor D protein, the serine protease at the C-terminus of PCI 13 protein is not activated, blocking AP pathway activity.

[0023] However, there remains a need for additional complement factor B analogs.

[0024] Thus, it is the object of the present application to provide additional complement factor B analogs and other compositions formed therefrom that modulate a complement pathway for the study and / or treatment of various conditions or diseases related to a complement pathway.

[0025] BRIEF SUMMARY OF THE INVENTION

[0026] The present disclosure provides polypeptides including a human complement factor B analog. The disclosure also provides Fc fusion protein with the human complement factor B analog. In some forms, a complement factor B analog includes a mutation in factor D cleavage site.

[0027] For example, in some forms, a disclosed polypeptide includes a complement factor B protein analog including the substitutions Lysine to Asparagine at position 258, Arginine to Alanine, Leucine, Glycine, or Aspartic Acid at position 259, and Lysine to Threonine or Serine at position 260 relative to SEQ ID NO:1. In a particular form, the substitution at position 258 is Asparagine, the substitution at position 259 is Leucine, and the substitution at position 260 is Threonine. Such polypeptides typically inhibit complement activity.

[0028] Also provided are polypeptides including a complement factor B protein analog including an aspartic acid substitution at the position corresponding to the arginine at position 259 of SEQ ID NO: 1. Such polypeptides typically enhance complement activity.

[0029] Any of the polypeptides can include additional mutations. For example, in some forms, the polypeptides include an additional mutation in a complement factor D cleavage site. Exemplary mutations include: (a) a mutation of a free cysteine amino acid, and / or (b) a mutation in a C3b binding site.

[0030] In some forms, (a) includes a substitution of the free cysteine, optionally wherein the free cysteine is substituted with more than one amino acid. In some forms, the complement factor B protein analog is an analog of SEQ ID NO: 1 and the complement factor B protein 45845704.1 4ATTORNEY DOCKET NO. MSD PC 139 PCT

[0031] analog has cysteine amino acids that fomi disulfide bonds and the free cysteine amino acid has been substituted by another amino acid. In some forms, the free cysteine is substituted with an amino acid selected from a group consisting of alanine, histidine, isoleucine, leucine, methionine, phenylalanine, serine, threonine, tyrosine and valine. The free cysteine amino acid mutation can be a deletion of the free cysteine. In some forms, the free cysteine corresponds to amino acid 292 of SEQ ID NO:1.

[0032] In some forms, (b) includes: (i) a substitution or deletion of an aspartic acid corresponding to amino acid 279 of SEQ ID NO:1, a substitution or deletion of an asparagine corresponding to amino acid 285 of SEQ ID NO:1 or both; or (ii) an insertion of at least one amino acid next to the aspartic acid or the asparagine. In some forms, the aspartic acid, the asparagine or both are substituted with one or more amino acids, optionally glycine, alanine or asparagine. In specific examples, the substitution includes replacing the aspartic acid with glycine and the asparagine with aspartic acid.

[0033] The complement factor B protein analog can exhibit increased binding affinity to C3b as compared to a binding affinity of a corresponding native complement factor B protein to C3b, e.g., SEQ ID NO:1. In some forms, the complement factor B protein analog has increased C3b binding affinity as compared to a corresponding native complement factor B protein and the complement factor B protein analog includes (i) diminished protease activity as compared to the corresponding native complement factor B protein; (ii) diminished ability to be cleaved by a factor D protein as compared to the corresponding native complement factor B protein; or (iii) diminished protease activity as compared to the corresponding native complement factor B protein and diminished ability to be cleaved by a factor D protein as compared to the corresponding native complement factor B protein.

[0034] In some forms, mutation of the complement factor D cleavage site includes an insertion next to one or more of positions 258, 259, and 260 relative to SEQ ID NO:1. For example, in some forms including aspartic acid position 259, the mutation in the complement factor D cleavage site further includes a substitution or deletion of one or both lysines corresponding to amino acid 258 or 260 of SEQ ID NO: 1, optionally wherein the amino acids corresponding to amino acids 258 and 260 of SEQ ID NO:1 are each substituted with alanine.

[0035] In some forms, the complement factor B analog competes with binding of the native complement factor B. The complement factor B protein analog can be an analog of human complement factor B protein such as SEQ ID NO:1. In some forms, the complement factor B protein analog includes at least one mutation corresponding to a mutation of SEQ ID NO:1 selected from a group consisting of D279G, N285D and C292S.

[0036] 45845704.1 5ATTORNEY DOCKET NO. MSD PC 139 PCT

[0037] In particular examples, the polypeptide includes the amino acid sequence of SEQ ID NO:3 or 12 with or without a signal sequence, or a variant thereof with at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO:3 or 12.

[0038] In some forms, the complement factor B protein analog includes mutations corresponding to K258N, R259L, K260T, D279G, N285D and C292S of SEQ ID NO:1.

[0039] In some forms, the complement factor B protein analog includes at least one mutation corresponding to a mutation of SEQ ID NO: 1 selected from a group consisting of K258A, K260A, D279G, N285D and C292S.

[0040] In some forms, the amino acid corresponding to amino acids 259 of SEQ ID NO:1 is substituted with a glycine, optionally wherein the polypeptide includes the amino acid sequence of SEQ ID NO:30 with or without the signal sequence, or a variant thereof with at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO:30. The glycine substitution can decrease or ablate cleavage of the complement factor B protein analog by factor D protein. In some forms, the complement factor B protein analog includes mutations corresponding to K258A, R259G, K260A, D279G, N285D and C292S relative to SEQ ID NO: 1.

[0041] In some forms, amino acid 259 of SEQ ID NO: 1 is substituted with an aspartic acid, optionally wherein the polypeptide includes the amino acid sequence of SEQ ID NO:31 with or without the signal sequence, or a variant thereof with at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO:31. In some forms, the complement factor B protein analog includes mutations corresponding to K258A, R259D, K260A, D279G, N285D and C292S of SEQ ID NO:1.

[0042] Thus provided are polypeptides that have decreased cleavage by factor D protein, inhibit or reduce complement activity, and / or inhibit the alternative complement pathway. Also provided are polypeptides that have enhanced cleavage of the complement factor B protein analog by factor D protein, increased complement activity, and / or an increase the alternative complement pathway.

[0043] In specific examples, the complement factor B protein analog is at least 90%, at least 95%, at least 98% or at least 99% identical to SEQ ID NO:1, 2, 3, 5, 11, 12, 26, 28, 30, or 31, with or without the signal sequence.

[0044] Also provided are complement factor B fusion proteins. In some forms, the fusion protein includes a first fusion partner including a complement factor B analog and a second fusion partner, wherein the N-terminus of the first fusion partner is fused directly or linked by a linker peptide or polypeptide sequence to the C-terminus of the second fusion partner. In 45845704.1 gATTORNEY DOCKET NO. MSD PC 139 PCT

[0045] some forms, the complement factor B analog is one provided herein fused directly or linked by a linker peptide or polypeptide sequence to the second fusion partner.

[0046] In some forms, the first fusion partner is contiguous with the carboxyl terminus of the second fusion partner, or the second fusion partner is contiguous with the carboxyl terminus of the first fusion partner. The first fusion partner can be contiguous with the carboxyl terminus of the second fusion partner, such as an immunoglobulin Pc region, e.g., an IgG4 Fc.

[0047] In exemplary forms, the fusion protein includes the amino acid sequence of SEQ ID NO:5 and SEQ ID NO: 17 with or without a signal sequence, or a variant thereof with at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO:5 and SEQ ID NO: 17.

[0048] The fusion proteins can include a domain that mediates dimerization or multimerization of the fusion protein to form homodimers, heterodimers, homomultimers, or heteromultimers. Such domains include, but are not limited to, one or more cysteines that are capable of forming an intermolecular disulfide bond with a cysteine on the partner fusion protein, a coiled-coil domain, an acid patch, a zinc finger domain, a calcium hand domain, a CHI region, a CL region, a leucine zipper domain, an SH2 (sre homology 2) domain, an SH3 (sre Homology 3) domain, a PTB (phosphotyrosine binding) domain, a WW domain, a PDZ domain, a 14-3-3 domain, a WD40 domain, an EH domain, a Lim domain, an isoleucine zipper domain, and a dimerization domain of a receptor dimer pair.

[0049] For example, provided are dimeric proteins including a first and a second fusion protein, such as homo- and heterodimers formed of the provided complement factor B analog polypeptides. The dimers can be fomred when first and second fusion proteins are bound to one another by covalent or noncovalent bonds. In some forms, the fusion proteins include at least two proteins (i.e., first and second fusion proteins) selected from those having the amino acid sequence of SEQ ID NO:3, 5, 11, 12, 26, 28, 30, and 31 with or without a signal sequence, and variants thereof with at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO:3, 5, 11, 12, 26, 28, 30, or 31.

[0050] Multimeric proteins including three of more fusion proteins are also provided. The multimeric proteins can be homo- or heteromultimers (e.g., formed from two or more different fusion proteins).

[0051] In some forms, a heterodimeric protein includes a first and a second fusion protein, wherein (i) the first fusion protein includes a first fusion partner fused to a second fusion partner, wherein the first fusion partner of the first fusion protein includes a complement 45845704.1 7ATTORNEY DOCKET NO. MSD PC 139 PCT

[0052] Factor B analog fused directly or linked by a linker peptide or polypeptide sequence to the second fusion partner of the first fusion protein; and (ii) the second fusion protein includes a first fusion partner fused to a second fusion partner, wherein the first fusion partner of the second fusion protein includes an anti-inflammatory molecule fused directly to a second fusion partner of the second fusion or linked by a linker peptide or polypeptide sequence to the second fusion partner of the second fusion protein.

[0053] In some forms the first fusion protein includes the fusion protein selected from the disclosed complement factor B analog fusion proteins. The anti-inflammatory molecule can be, for example, a blocker of an inflammatory pathway initiated by IL4, IL6, IL13, IL17, IL22, IL23, IL31, Thymic Stromal lymphopoietin (TSLP), or OX40-OX40L axis, optionally an antigen binding fragment that binds to IL4, IL6, IL 13, IL 17, IL22, IL23, IL31, TSLP, and 0X40 or a soluble receptor that can bind these inflammatory molecules that include, but are not limited to, IL4, IL6, IL13, IL17, IL22, IL23, IL31, TSLP, and 0X40. In a specific form, the anti-inflammatory molecule is soluble IL-17 receptor A (sIL-17RA). The second fusion partner of the second fusion protein can be an immunoglobulin Fc region such as an immunoglobulin Fc region of an IgG4 Fc. In some forms, the first and the second fusion proteins arc bound to one another by covalent or noncovalcnt bonds. In particular forms, the heterodimeric protein includes a first fusion protein having the amino acid sequence of SEQ ID NO:3, 5, 11, 12, 26, 28, 30, or 31 with or without a signal sequence, or a variant thereof with at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO:3, 5, 11, 12, 26, 28, 30, or 31 and a second fusion protein including the amino acid sequence of SEQ ID NO:7 with or without a signal sequence, or a variant thereof with at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO:7.

[0054] Nucleic acids encoding the disclosed polypeptides and proteins including fusion proteins are also provided. In some forms the nucleic acid is encoded by and / or packaged in a viral vector such as a retroviral vector, a lenti viral vector such as BIV, HIV, EIAV, SIV or FIV, an adenoviral vector, a Herpes viral vector, a Hepatitis viral vector, an SV40 viral vector, an AAV vector, an EBV vector and an NDV vector. In some forms, the viral vector includes a decay accelerating factor. In some forms the nucleic acid is packaged in lipid nanoparticles (LNPs). In some forms, the LNPs include a decay accelerating factor. An exemplary vector sequence encoding PC 139 (SEQ ID NO:3) is SEQ ID NO:36. In other forms, the PCI 39 (SEQ ID NO:3) coding sequence (SEQ ID NO:4): 1321-3615 of SEQ ID NO:36 is substituted with a coding sequence for a different complement factor B analog or 45845704.1 8ATTORNEY DOCKET NO. MSD PC 139 PCT

[0055] fusion protein thereof, optionally wherein the complement factor B analog or fusion protein includes the amino acid sequence of any one of SEQ ID NOS:1, 2, 5, 12, 16, 29, 30, or 31, or a variant thereof such as those described herein. In some forms, the variant has at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% sequence identity thereto.

[0056] Pharmaceutical composition including the disclosed polypeptides, fusion proteins, dimeric, heterodimeric or the multimeric proteins, nucleic acids, viral vectors, and combinations thereof are also provided. In some forms, the pharmaceutical compositions include at least one ingredient selected from the group consisting of histidine, trehalose, a polysorbate, polysorbate 20, sucrose, arginine and praline.

[0057] Cells including, but not limited to, mammalian cells such as 293 cells, CHO cells, PerC6 cells and Vero cells, and prokaryotic cells such as E. coli cells, including the disclosed nucleic acids and optionally expressing the disclosed polypeptides and fusions proteins are also provided.

[0058] Also provided are methods of using the disclosed compositions. In some forms, the methods are directed to inhibiting complement activity by introducing or administering to a subject in need thereof an effective amount of a disclosed composition to inhibit the complement activity. Typically the polypeptide of the composition inhibits the complement activity, optionally wherein the polypeptide does not include an aspartic acid substitution at the position corresponding to the arginine at position 259 of SEQ ID NO: 1, optionally wherein the polypeptide includes the substitutions Lysine to Asparagine at position 258, Arginine to Alanine, Leucine, or Glycine at position 259, and Lysine to Threonine or Serine at position 260 relative to SEQ ID NO:1.

[0059] In some forms, the method includes administering to a subject the polypeptide, the fusion protein, the dimeric protein, the heterodimeric protein, the multimeric protein, the nucleic acid, the viral vector, the LNP, the pharmaceutical composition or any combination thereof. In some forms, the polypeptide, the fusion protein, the dimeric protein, the heterodimeric protein, or the multimeric protein can compete with binding of a native complement factor B. Thus also provided are methods of treating a complement mediated disease in a subject that include the foregoing methods. In some forms, the complement-mediated disease is a disease of the eye, optionally wherein the pharmaceutical composition is administered to the eye. In some such forms, the pharmaceutical composition is administered by intravitreal injection, subretinal injection, injection to intraanterior chamber of the eye, injection or application locally to cornea, subconjunctival injection, subtenon injection, or by eye drops. Exemplary complement-mediated diseases treatable according to 45845704.1 9ATTORNEY DOCKET NO. MSD PC 139 PCT

[0060] the disclosed methods include, but are not limited to, macular degeneration, age-related macular degeneration (AMD), geographic atrophy, wet AMD, myocardial infarction, dry AMD, drusen formation, arthritis (rheumatoid arthritis and osteoarthritis), stroke, ischemic reperfusion injury, diabetic retinopathy, vitrcorctinopathy, traumatic organ injury, corneal inflammation, comeal neovascularization, uveitis, ocular hypertension, glaucoma, atherosclerosis, airway hyperresponsiveness, immune related diseases, autoimmune related diseases, lupus nephritis, systemic lupus erythematosus (SLE), rheumatologic diseases, antiphospholipid antibody syndrome, intestinal and renal I / R injury, asthma, atypical hemolytic-uremic syndrome, Type II membranoproliferative glomerulonephritis, non-proliferative glomerulonephritis, IgA nephropathy, fetal loss, brain injury, post-traumatic organ damage, post infarction organ damage, vasculitis, hereditary angioedema, paroxysmal nocturnal hemoglobinuria, cerebrovascular accident, Alzheimer's disease, Parkinson’s disease, transplant rejection, infections, sepsis, septic shock, Sjogren's syndrome, myasthenia gravis, antibody-mediated skin diseases, Type I and Type II diabetes mellitus, insulin resistance syndrome, gestational diabetes, thyroiditis, idiopathic thrombocytopenic purpura and hemolytic anemia, neuropathies, multiple sclerosis, cardiopulmonary bypass injury, polyarteritis nodosa, Henoch Schonlcin purpura, scrum sickness, Goodpasture's disease, systemic necrotizing vasculitis, post streptococcal glomerulonephritis, idiopathic pulmonary fibrosis, membranous glomerulonephritis, acute shock lung syndrome, adult respiratory distress syndrome, and reperfusion. In particular examples, the complement-mediated disease is rheumatoid arthritis, refractory rheumatoid arthritis, lupus nephritis, paroxysmal nocturnal hemoglobinuria, or geographic atrophy.

[0061] In some forms, the subject, prior to, concurrently with, or after the administration of the pharmaceutical composition, is administered a complement inhibiting factor such as Factor H, a Factor H-like 1, a MCP, a DAF, or a soluble form of a MCP and / or an anti-angiogenic factor such as endostatin, a VEGF binding molecule, PEDF, T2-TrpRS, sFLT, aflibercept or kininostatin. In forms, an anti-inflammatory is administered prior to, concurrently with, or after the administration of the pharmaceutical composition. The antiinflammatory can be, for example, administered concurrently with the pharmaceutical composition or included in the pharmaceutical composition. In some forms, the antiinflammatory is administered to the eye. Anti-inflammatories include, but are not limited to, dexamethasone, dexamethasone sodium metasulfobenzoate, dexamethasone sodium phosphate, fluorometholone, bromfenac, pranoprofen, a cyclosporine ophthalmic emulsion, naproxen, glucocorticoids, ketorolac, ibuprofen, tolmetin, non-steroidal anti-inflammatory 45845704.1 10ATTORNEY DOCKET NO. MSD PC 139 PCT

[0062] drugs, steroidal anti-inflammatory drugs, diclofenac, flurbiprofen, indomethacin, and suprofen.

[0063] In some forms, a compound that inhibits complement activity, T-cell activation, B-cclls, tumor necrosis factor (TNF), estrogen, intcrlcukin-I or intcrfcron-gamma is administered prior to, concurrently with, or after the administration of the pharmaceutical composition. The compound can be, for example, infliximab, adalimumab, golimumab, etanercept, abatacept or rituximab.

[0064] Also provided are methods of enhancing a complement activity. The methods typically include introducing or administering an effective amount of a disclosed composition to enhance the complement activity. In some forms, the polypeptide of the composition enhances the complement activity, optionally wherein the polypeptide does not include the substitutions Lysine to Asparagine at position 258, Arginine to Alanine, Leucine, or Glycine at position 259, and Lysine to Threonine or Serine at position 260 relative to SEQ ID NO:1, optionally wherein the polypeptide includes an aspartic acid substitution at the position corresponding to the arginine at position 259 of SEQ ID NO:1.

[0065] Thus, also provided are methods of treating diseases and conditions where complement activation is compromised or where further complement activation is beneficial as a therapy. Exemplary diseases and syndromes include, but are not limited to, deficiency syndromes (e.g., C3, Factor D, and Properdin deficiencies), recurrent bacterial infections (e.g., Neisseria meningitidis, Gram-negative infections), chronic fungal infections (e.g., Cryptococcus, Candida), cancer (e.g., by enhancing complement-mediated tumor clearance), neurodegenerative diseases (e.g., Alzheimer's and Parkinson’s with impaired complement function), chronic non-healing wounds, post-surgical tissue regeneration, viral infections, and improving immune responses after organ transplantation. In some forms, the viral infection is COVID-19, a flu such as pandemic flu, or Ebola.

[0066] In some forms of any of the disclosed methods the pharmaceutical composition optionally including the viral vector is administered only once to the subject. In some forms, the pharmaceutical composition, optionally including the viral vector, is administered about once every week, month, 2 months, 3 months, 6 months, 9 months, a year, 18 months, 2 years, 30 months, 3 years, 5 years, or 10 years. In some forms, the pharmaceutical composition is administered systemically to the subject. In some forms, the pharmaceutical composition is administered to the subject locally, optionally to a site of a complement activity.

[0067] 45845704.1 11ATTORNEY DOCKET NO. MSD PC 139 PCT

[0068] Also provided are methods of producing a polypeptide including a complement factor B protein analog, the method including expressing a disclosed polypeptide or fusion protein and purifying the polypeptide.

[0069] Proteins including or consisting of the amino acid sequence of SEQ ID NO:3, 5, 11, 12, 17, 26, 28, 30, and 31 each with or without a signal sequence, and variants thereof with at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% sequence identity thereto are also expressly provided.

[0070] This summary of the present disclosure does not necessarily describe all features or necessary features. The present disclosure may also reside in a sub-combination of the described features.

[0071] BRIEF DESCRIPTION OF THE DRAWINGS

[0072] For the purpose of illustrating the present disclosure, there are depicted in the drawings certain embodiments of the present disclosure. However, the present disclosure is not limited to the precise arrangements and instrumentalities of embodiments depicted in the drawings.

[0073] Figure 1 is an alignment of amino acid sequence from amino acid 241 to 300 between the human wildtypc complement factor B (SEQ ID NO:32), human complement factor B analog PCI 13(SEQ ID NO:33), (also known as fB3-292S), human complement factor B analog PC-113-G (SEQ ID NO:34), and human complement factor B analog PCI 13-D (SEQ ID NO:35). The full-length of human complement factor B has 764 amino acids including 25 amino acid signal sequence at the N-terminus. Figure 1 only shows the stretch of 60 amino acids from 241 to 300 to show the difference between the wildtype factor B and the analogs. The amino acid changes in factor D cleavage site, C3b binding site, and the free Cysteine are indicated.

[0074] Figure 2 is an image of a Coomassie blue staining of an electrophoretic gel of purified human complement factor B analogs PCI 13, PCI 13-G, and PCI 13-D proteins after SDS-PAGE.

[0075] Figure 3 is a Western blot showing C3b-dependent cleavage of wildtype human complement factor B, human complement factor B analogs PCI 13, PCI 13-D, and PCI 13-G proteins by factor D. The data showed factor D cleaved the wildtype factor B and factor B analog PCI 13-D, but factor B analogs PCI 13 and PC-113-G were resistant to cleavage by factor D in the presence or absence of C3b under the same experimental conditions.

[0076] Figure 4 is a bar graph showing the results of a hemolytic assay to measure human alternative complement pathway activity. These results demonstrate inhibition of human 45845704.1 12ATTORNEY DOCKET NO. MSD PC 139 PCT

[0077] alternative complement pathway hemolytic activity by human factor B analog PCI 13-G but not PCI 13-D protein. The relative hemolytic activity was scored by hemoglobin released after hemolysis of rabbit red blood cells (rRBCs) by human alternative complement pathway activity. X-axis from left to right: factor B-depleted human serum supplemented with 0 pg of purified human factor B protein (control, without wildtype human complement factor B (wt hfB), no lysis of rRBCs); factor B-depleted human serum supplemented in each reaction with a mixture of 0.5 pg of purified human factor B protein and 1.0, 0.5, 0.25 or 0.125 pg of PCI 13-G protein or PCI 13-D protein. Note: 100% inhibition represented no lysis of rRBCs. The Y-axis represents percentage of inhibition of hemolysis as compared to no lysis of rRBCs. PCI 13-G effectively inhibited human alternative complement activity. PCI 13-D did not inhibit human alternative complement activity.

[0078] Figure 5 is a line graph showing human complement factor B analog PCI 13-G has higher affinity for C3b binding as compared to wildtype human complement factor B in a competitive ELISA assay. Biotin-labeled PCI 13-G incubated with immobilized C3b in the presence of increasing amounts of either unlabeled PCI 1G (Filled Triangles) or unlabeled wildtype human complement factor B protein (hfB) (Filled Circles). The results demonstrate that PCI 13-G protein displayed significantly higher binding affinity with C3b protein as compared to human factor B protein.

[0079] Figure 6 is a bar graph showing the stability of PCI 13-G after up to seven cycles of freeze and thaw. After seven cycles of freeze and thaw, PCI 13-G effectively inhibits human alternative complement pathway hemolytic activity as compared to the fresh PCI 13-G. The relative hemolytic activity was scored by hemoglobin released after hemolysis of rabbit red blood cells (rRBCs) by human alternative complement pathway activity. X-axis from left to right: factor B protein-depleted human serum supplemented with 0 pg of purified wildtype human factor B protein (Wt hfB) (control, no lysis of rRBCs); factor B protein-depleted human serum supplemented in each reaction with a mixture of 0.5 pg of purified wildtype human factor B protein and 1.0, 0.5, 0.25, 0.125 pg of PCI 13-G as indicated. 100% inhibition represents no lysis of rRBCs. The Y-axis represents percentage of inhibition of hemolysis as compared to no lysis of rRBCs.

[0080] Figure 7 is a bar graph showing the thermo-stability of PCI 13-G at 40°C. After incubation at 40°C for different time points, PCI 13-G effectively inhibits human alternative complement pathway hemolytic activity. The relative hemolytic activity was scored by hemoglobin released after hemolysis of rabbit red blood cells (rRBCs) by human alternative complement pathway activity. X-axis from left to right: factor B protein-depleted human 45845704.1 13ATTORNEY DOCKET NO. MSD PC 139 PCT

[0081] serum supplemented with 0 pg of purified wildtype human factor B protein (wt hfB) (control, no lysis of rRBCs); factor B protein-depleted human serum supplemented in each reaction with a mixture of 0.5 pg of purified wildtype human factor B protein and 1.0, 0.5, 0.25, 0.125 pg of PCI 13-G as indicated. 100% inhibition represents no lysis of rRBCs. The Y-axis represents percentage of inhibition of hemolysis as compared to no lysis of rRBCs.

[0082] Figure 8 is bar graph showing the results of a hemolytic assay. These results demonstrated PCI 13-D enhanced human alternative complement pathway hemolytic activity. The relative hemolytic activity was scored by hemoglobin released after hemolysis of rabbit red blood cells (rRBCs) by human alternative complement pathway activity. X-axis from left to right: factor B-depleted human serum supplemented with 0.5 pg of purified human factor B protein, or 0.5 pg of PCI 13-G, or 0.5 pg of PCI 13-D protein. The Y-axis represents mean OD405 and Standard Deviation (SD). The higher OD405, the more lysis of rRBCs, the more hemoglobin released. PCI 13-D enhanced human alternative complement activity.

[0083] Figure 9 depicts the alignment of amino acid sequence from amino acid 241 to 300 between the human wild type complement factor B (SEQ ID NO:9), human complement factor B analog PCI 13 (SEQ ID NO: 10), and human complement factor B analog PC-139 (SEQ ID NO: 11). The full-length of human complement factor B has 764 amino acids including 25 amino acid signal sequence at the N-terminus. Figure 9 shows the stretch of 60 amino acids from 241 to 300 and illustrates the difference between the wild type factor B and the analogs. The amino acid changes in factor D cleavage site, C3b binding site, and the free Cysteine are indicated.

[0084] Figure 10 is a diagram of PC139 / Fc dimer. From N- to C-terminus: Signal sequence (the first 25 amino acids in SED ID NO:5) (which is cleaved before PC139 / Fc dimer is secreted from the PC139 / Fc dimer-producing cells), modified human IgG4 Fc, PCI 39 without signal sequence (the first 25 amino acids). The diagram shows the dimer form of PC139 / Fc. The dimer is linked by two disulfide bonds in the hinge region of Fc.

[0085] Figure 11 depicts Coomassie blue staining of purified PC139 / Fc dimer.

[0086] Figure 12 is a bar graph showing the results of a hemolytic assay to measure human alternative complement pathway activity as a potency assay for PC139 / Fc dimer. These results demonstrated inhibition of human alternative complement pathway hemolytic activity by human factor B analog PC139 / Fc dimer. The relative hemolytic activity was scored by hemoglobin released after hemolysis of rabbit red blood cells (rRBCs) by human alternative complement pathway activity. X-axis from left to right: factor B-depleted human serum supplemented with 0 |Lig of purified human factor B protein (control, without wild type 45845704.1 14ATTORNEY DOCKET NO. MSD PC 139 PCT

[0087] human complement factor B ((wt hfB), no lysis of rRBCs as 100% inhibition); rRBCs incubated in water to create 100% lysis as a control; factor B-depleted human serum supplemented in each reaction with a mixture of PC139 / Fc dimer and purified human factor B protein at a molar ratio of 2:1, 1:1, 0.5:1, and 0.25:1. Note: 100% inhibition represented no lysis of rRBCs. 100% lysis represented no inhibition of AP. The Y-axis represents percentage of inhibition of hemolysis as compared to no lysis of rRBCs. PC139 / Fc dimer effectively inhibited human alternative complement activity.

[0088] Figure 13 is Western blot showing C3b-dependent cleavage of wild type human complement factor B, human complement factor B analogs PCI 13, and PC139 / Fc dimer by factor D. The data shows factor D cleaved the wild type factor B, but factor B analogs PCI 13 and PC139 / Fc dimer were resistant to cleavage by factor D in the presence or absence of C3b under the same experimental conditions. “PC139 / Fc” refers to PC139 / Fc dimer in this experiment and figure. The SDS-PAGE was run under reducing condition.

[0089] Figure 14 is a line graph showing that human complement factor B analog PC139 / Fc dimer had a higher affinity for C3b binding as compared to wild type human complement factor B in a competitive ELISA assay. Biotin-labeled PC139 / Fc dimer incubated with immobilized C3b in the presence of increasing amount of cither unlabclcd PC139 / Fc dimer (Filled Diamonds) or unlabeled wild type human complement factor B protein (hfB) (Filled Circles). The results demonstrated that PC139 / Fc dimer protein displayed notably higher binding affinity with C3b protein as compared to wild type human factor B protein.

[0090] Figure 15 is a bar graph showing that PC139 / Fc dimer had a higher affinity to human factor D than the wild type human factor B in C3b-dependent binding assay. Wild type factor B (fB) and PC139 / Fc dimer were used at the same molar concentration. The left two bars show wild type factor B or PC139 / Fc dimer at a concentration of 22.7 nM, and the right bars shows wild type factor B or PC139 / Fc dimer at a concentration of 45.4 nM.

[0091] Figure 16 is a bar graph showing stability of PC139 / Fc dimer after seven days at -80°C, 4°C, or 37°C. After seven days, the protein biological activity was measured by AP-specific assay. The relative hemolytic activity was scored by hemoglobin released after hemolysis of rabbit red blood cells (rRBCs) by human alternative complement pathway activity. X-axis from left to right: factor B protein-depleted human serum supplemented with 0 pg of purified wild type human factor B protein (Wt hfB) (control, no lysis of rRBCs); factor B protein-depleted human serum supplemented in each reaction with a mixture of PCI 39 / Fc dimer and purified wild type human factor B protein at a molar ratio of 2: 1, 1:1,

[0092] 45845704.1 15ATTORNEY DOCKET NO. MSD PC 139 PCT

[0093] 0.5:1, and 0.25:1. 100% inhibition represented no lysis of rRBCs. The Y-axis represents percentage of inhibition of hemolysis as compared to no lysis of rRBCs.

[0094] Figure 17 is a diagram of an Fc heterodimer with PC139 / Fc linked with sIL17RA / Fc by disulfide bonds. From N- to C-tcrminus for PC139 / Fc: Signal sequence (the first 25 amino acids in SED ID NO:5) (which is cleaved before the heterodimer is secreted from the heterodimer-producing cells), modified human IgG4 Fc, PC 139 without signal sequence (the first 25 amino acids). From N- to C-terminus for sIL17RA / Fc: Signal sequence (the first 25 amino acids in SED ID NO:7) (which is cleaved before the heterodimer is secreted from the heterodimer-producing cells), modified human IgG4 Fc, sIL17RA. The heterodimer is linked by two disulfide bonds in the hinge region of Fc.

[0095] Figure 18 is a bar graph showing the results of a hemolytic assay to measure human alternative complement pathway activity as a potency assay for PC139 / Fc dimer and PC147 / Fc dimer after the protein was stored in PBS at 4°C, 37°C, or -80°C for seven days. These results demonstrated inhibition of human alternative complement pathway hemolytic activity by human factor B analog PC139 / Fc dimer after incubation for 7 days at all tested temperatures. PC147 / Fc dimer performed well but with slightly lower activity as compared to PC139 / Fc dimer at 4°C and -80°C. However, PC147 / Fc dimer completely lost its alternative complement pathway inhibitory activity after incubation at 37°C for 7 days. The relative hemolytic activity was scored by hemoglobin released after hemolysis of rabbit red blood cells (rRBCs) by human alternative complement pathway activity. X-axis from left to right: factor B-depleted human serum supplemented with 0 pg of purified human factor B protein (control, without wild type human complement factor B ((wt hfB), no lysis of rRBCs as 100% inhibition); factor B-depleted human serum supplemented in each reaction with a mixture of PC139 / Fc dimer or PC147 / Fc dimer and purified wild type human factor B protein at a molar ratio of 2:1, 1:1, 0.5:1, and 0.25:1. Note: 100% inhibition represented no lysis of rRBCs. The Y-axis represents percentage of inhibition of hemolysis as compared to no lysis of rRBCs.

[0096] Figure 19 is an image of a Western blot showing analysis of PC 139 expression and secretion by AAV vector in human cells.

[0097] DETAILED DESCRIPTION OF THE INVENTION

[0098] The practice of the present disclosure will employ, unless otherwise indicated, conventional techniques of cell biology, molecular biology, cell culture, virology and the like which are in the skill of one in the art. These techniques are fully disclosed herein and / or in literature, for example, Sambrook, Fritsch and Maniatis eds., " Molecular Cloning, A 45845704.1 16ATTORNEY DOCKET NO. MSD PC 139 PCT

[0099] Laboratory Manual", 4th Ed., Cold Spring Harbor Laboratory Press (2012); Celis J. E. " Cell Biology, A Laboratory Handbook" 2nd Ed. Academic Press, Inc. (1998) and Bahnson et al., J. of Virol. Methods, 54:131-143 (1995).

[0100] It is contemplated that any method, preparation or composition described herein can be implemented with respect to any other method, preparation or composition described herein.

[0101] A. Definition

[0102] The use of the word “a” or “an” when used in conjunction with the term “comprising” in the claims and / or the specification may mean “one,” but it is also consistent with the meaning of “one or more,” “at least one,” and “one or more than one.” The use of the term / phrase “and / or” when used with a list means one or more of the listed items may be utilized, e.g., it is not limited to one or all of the elements.

[0103] The term “complement-mediated” refers to a process or disease that involves complement. Typically, a “complement-mediated” disease or condition is one wherein complement activity is one of the underlying causes of the disease or condition and wherein inhibition or blocking of the complement activity lessens the extent of the disease or condition. Examples of numerous complement-mediated diseases or conditions arc described herein.

[0104] The term “wildtype” (or wild-type, or wild type, or wt), which is used interchangeably with “native”, relates to a naturally occurring protein encoded by a mammalian genome, a naturally occurring nucleic acid, and so on. In some cases, there may be actually more than one protein corresponding to the wild-type version, e.g., due to allelic differences; different isoforms; and / or genetic variation among different individuals of a species.

[0105] The term “analog” refers to a structural derivative of a protein (parent protein). An analog does not necessarily retain all of the properties of the parent protein and in some cases has at least one altered property as compared to the corresponding native parent protein. In some forms, a parent protein is a native (naturally-occurring) protein. An analog or variant protein is produced by replacing, substituting, deleting, and / or adding amino acids with regard to the corresponding native amino acid sequence of the protein. The substitutions or insertions typically involve naturally occurring amino acids, but may also include synthetic or unconventional amino acids as well. In some forms, an analog or variant is produced by mutating a protein, e.g., mutating a nucleic acid encoding it. An analog will typically retain at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5% of the corresponding native parent 45845704.1 17ATTORNEY DOCKET NO. MSD PC 139 PCT

[0106] protein’s amino acid sequence (e.g., have that percent amino acid sequence identity with respect to the naturally occurring parent protein as determined over the length of the entire parent protein or, in certain forms, over a specific domain or portion of the parent protein). Analogs also include fragments of full-length analogs that include a portion of the amino acid sequence and either retain one or more biological activities of the parent protein or of a full-length analog or inhibit one or more of these biological activities.

[0107] The term "corresponds" or “corresponding” when referring to an amino acid in a particular protein refers to the particular amino acid in that particular protein and also to an amino acid in a related or similar protein and may provide a similar function to the protein. For example, an amino acid in a human complement factor B may be found to correspond with an amino acid in a murine complement factor B or in a human allelic variant of factor B, usually determined by aligning the two amino acid sequences. For example, one skilled in the art can align two or more related sequences, such as SEQ ID NOs:l and 3 to determine corresponding amino acids, e.g., using a BLAST program or Clone Manager software. Also, corresponding amino acids can be determined, e.g., by aligning motifs (e.g., a protease cleavage motif) within related or unrelated proteins. Such an alignment may also be used to derive consensus sequences of target protein or domains thereof.

[0108] As used herein, the term “gene” typically refers to a coding region for a protein. However, in some contexts herein it will be clear that the term “gene” is also referring to elements (e.g., regulatory elements) operatively linked to a coding region such as promoters, enhancers, splice sites (acceptors and / or donors), polyadenylation signals, introns, 5’ untranslated regions, 3’ untranslated regions, etc.

[0109] The term "pharmaceutically acceptable" means approved by a regulatory agency of the Federal or a state government or listed in the U. S. Pharmacopeia or other generally recognized pharmacopeia for use in humans.

[0110] A “therapeutic benefit” is not necessarily a cure for a particular disease or condition (including any disease or condition described herein), but rather, encompasses a result which most typically includes alleviation of the disease or condition, elimination of the disease or condition, reduction of one or more symptoms associated with the disease or condition, prevention or alleviation of a secondary disease or condition resulting from the occurrence of a primary disease or condition, diminishing the likelihood of developing a condition or disease, diminishing the severity of a disease or condition, changing the character of a disease or condition, shortening the course of a disease or condition, slowing or preventing the

[0111] 45845704.1 18ATTORNEY DOCKET NO. MSD PC 139 PCT

[0112] progression or worsening of a disease or condition, and / or prevention of the disease or condition.

[0113] Use of the term “about” is intended to describe values either above or below the stated value in a range of approx. + / - 10%; in other forms the values may range in value cither above or below the stated value in a range of approx. + / - 5%; in other forms the values may range in value either above or below the stated value in a range of approx. + / - 2%; in other forms the values may range in value either above or below the stated value in a range of approx. + / - 1%. The preceding ranges are intended to be made clear by context, and no further limitation is implied. All methods described herein can be performed in any suitable order unless otherwise indicated herein or otherwise clearly contradicted by context. The use of any and all examples, or exemplary language (e.g., "such as") provided herein, is intended merely to better illuminate the disclosure and does not pose a limitation on the scope of the disclosure unless otherwise claimed. No language in the specification should be construed as indicating any non-claimed element as important to the practice of the disclosure.

[0114] As used herein, the term “peptide” refers to a class of compounds composed of amino acids chemically bound together. In general, the amino acids are chemically bound together via amide linkages (CONH); however, the amino acids may be bound together by other chemical bonds known in the art. For example, the amino acids may be bound by amine linkages. Peptide as used herein includes oligomers of amino acids and small and large peptides, including polypeptides.

[0115] “Polypeptide,” “peptide,” and “protein” are used interchangeably herein to refer to a polymer of amino acid residues. All three terms apply to amino acid polymers in which one or more amino acid residue is an artificial chemical mimetic of a corresponding naturally occurring amino acid, as well as to naturally occurring amino acid polymers and non-naturally occurring amino acid polymers. As used herein, the terms encompass amino acid chains of any length, including full-length proteins, wherein the amino acid residues are linked by covalent peptide bonds. The term “polypeptides” includes proteins and functional fragments thereof. Polypeptides are disclosed herein as amino acid residue sequences. Those sequences are written left to right in the direction from the amino to the carboxy terminus. In accordance with standard nomenclature, amino acid residue sequences are denominated by either a three letter or a single letter code as indicated as follows: Alanine (Ala, A), Arginine (Arg, R), Asparagine (Asn, N), Aspartic Acid (Asp, D), Cysteine (Cys, C), Glutamine (Gin, Q), Glutamic Acid (Glu, E), Glycine (Gly, G), Histidine (His, H), Tsoleucine (Tie, I), Eeucine (Leu, L), Lysine (Lys, K), Methionine (Met, M), Phenylalanine (Phe, F), Proline (Pro, P), 45845704.1 19ATTORNEY DOCKET NO. MSD PC 139 PCT

[0116] Serine (Ser, S), Threonine (Thr, T), Tryptophan (Trp, W), Tyrosine (Tyr, Y), and Valine (Vai, V).

[0117] “Encoding” or “encode” refers to the property of specific sequences of nucleotides in a polynucleotide, such as a gene, a cDNA, or an mRNA, to serve as templates for synthesis of other polymers and macromolecules in biological processes having either a defined sequence of nucleotides (i.e., rRNA, tRNA and mRNA) or a defined sequence of amino acids and the biological properties resulting therefrom. Thus, a gene encodes a protein if transcription and translation of mRNA corresponding to that gene produces the protein in a cell or other biological system. Both the coding strand, the nucleotide sequence of which is identical to the mRNA sequence and is usually provided in sequence listings, and the non-coding strand, used as the template for transcription of a gene or cDNA, can be referred to as encoding the protein or other product of that gene or cDNA.

[0118] A “vector” is a composition of matter which includes an isolated nucleic acid and which can be used to deliver the isolated nucleic acid to the interior of a cell. Examples of vectors include but are not limited to, linear polynucleotides, polynucleotides associated with ionic or amphiphilic compounds, plasmids, and viruses. Thus, the term “vector” encompasses an autonomously replicating plasmid or a vims. The term is also construed to include non plasmid and non- viral compounds which facilitate transfer of nucleic acid into cells, such as, for example, polylysine compounds, liposomes, and the like. Examples of viral vectors include, but are not limited to, adenoviral vectors, adeno-associated vims (AAV) vectors, retroviral vectors, and the like.

[0119] As used herein, “subject” includes, but is not limited to, animals, plants, parasites and any other organism or entity. The subject can be a vertebrate, more specifically a mammal (e.g., a human, horse, pig, rabbit, dog, sheep, goat, non-human primate, cow, cat, guinea pig or rodent), a fish, a bird or a reptile or an amphibian. The subject can be an invertebrate, more specifically an arthropod (e.g., insects and crustaceans). The term does not denote a particular age or sex. Thus, adult and newborn subjects, as well as fetuses, whether male or female, are intended to be covered. A patient refers to a subject afflicted with a disease or disorder. The term “patient” includes human and veterinary subjects. In some forms, the subject can be any organism in which the disclosed method can be used to genetically modify the organism or cells of the organism.

[0120] The temr “inhibit” or other forms of the word such as “inhibiting” or “inhibition” means to decrease, hinder or restrain a particular characteristic such as an activity, response, condition, disease, or other biological parameter. It is understood that this is typically in 45845704.1 20ATTORNEY DOCKET NO. MSD PC 139 PCT

[0121] relation to some standard or expected value, i.e., it is relative, but that it is not always necessary for the standard or relative value to be referred to. “Inhibits” can also mean to hinder or restrain the synthesis, expression or function of a protein relative to a standard or control. Inhibition can include, but is not limited to, the complete ablation of the activity, response, condition, or disease. “Inhibits” can also include, for example, a 10% reduction in the activity, response, condition, disease, or other biological parameter as compared to the native or control level. Thus, the reduction can be about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64,65, 66, 67, 68, 69, 70. 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86. 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100%, or any amount of reduction in between as compared to native or control levels. For example, “inhibits expression” means hindering, interfering with or restraining the expression and / or activity of the gene / gene product pathway relative to a standard or a control.

[0122] “Treatment” or “treating” means to administer a composition to a subject or a system with an undesired condition (e.g., cancer). The condition can include one or more symptoms of a disease, pathological state, or disorder. Treatment includes medical management of a subject with the intent to cure, ameliorate, stabilize, or prevent a disease, pathological condition, or disorder. This includes active treatment, that is, treatment directed specifically toward the improvement of a disease, pathological state, or disorder, and also includes causal treatment, that is, treatment directed toward removal of the cause of the associated disease, pathological state, or disorder. In addition, this term includes palliative treatment, that is, treatment designed for the relief of symptoms rather than the curing of the disease, pathological state, or disorder; preventative treatment, that is, treatment directed to minimizing or partially or completely inhibiting the development of the associated disease, pathological state, or disorder; and supportive treatment, that is, treatment employed to supplement another specific therapy directed toward the improvement of the associated disease, pathological state, or disorder. It is understood that treatment, while intended to cure, ameliorate, stabilize, or prevent a disease, pathological condition, or disorder, need not actually result in the cure, amelioration, stabilization or prevention. The effects of treatment can be measured or assessed as described herein and as known in the art as is suitable for the disease, pathological condition, or disorder involved. Such measurements and assessments can be made in qualitative and / or quantitative terms. Thus, for example, characteristics or features of a disease, pathological condition, or disorder and / or symptoms of a disease, 45845704.1 21ATTORNEY DOCKET NO. MSD PC 139 PCT

[0123] pathological condition, or disorder can be reduced to any effect or to any amount.

[0124] “Prevention” or “preventing” means to administer a composition to a subject or a system at risk for an undesired condition. The condition can include one or more symptoms of a disease, pathological state, or disorder. The condition can also be a predisposition to the disease, pathological state, or disorder. The effect of the administration of the composition to the subject can be the cessation of a particular symptom of a condition, a reduction or prevention of the symptoms of a condition, a reduction in the severity of the condition, the complete ablation of the condition, a stabilization or delay of the development or progression of a particular event or characteristic, or reduction of the chances that a particular event or characteristic will occur.

[0125] The term “functional fragment” or “functional variant” means a fragment or variant of a polypeptide, such as a full-length or native polypeptide, that retains one or more functional properties of the full-length or native polypeptide.

[0126] As used herein, the terms “variant” or “active variant” refers to a polypeptide or polynucleotide that differs from a reference polypeptide or polynucleotide, but retains one or more functional properties (e.g., functional or biological activity). A typical variant of a polypeptide differs in amino acid sequence from another, reference polypeptide. Generally, differences are limited so that the sequences of the reference polypeptide and the variant are closely similar overall and, in many regions, identical. A variant and reference polypeptide may differ in amino acid sequence by one or more modifications (e.g., substitutions, additions, and / or deletions). A substituted or inserted amino acid residue may or may not be one encoded by the genetic code. A variant of a polypeptide may be naturally occurring such as an allelic variant, or it may be a variant that is not known to occur naturally. Modifications and changes can be made in the structure of the polypeptides of the disclosure and still obtain a molecule having similar characteristics as the polypeptide (e.g., a conservative amino acid substitution). For example, certain amino acids can be substituted for other amino acids in a sequence without appreciable loss of activity. Because it is the interactive capacity and nature of a polypeptide that defines that polypeptide’s biological or functional activity, certain amino acid sequence substitutions can be made in a polypeptide sequence and nevertheless obtain a polypeptide with like properties (e.g., functional or biological activity).

[0127] Modifications and changes can be made in the structure of the polypeptides of in disclosure and still obtain a molecule having similar characteristics as the polypeptide (e.g., a conservative amino acid substitution). For example, certain amino acids can be substituted for other amino acids in a sequence without appreciable loss of activity. Because it is the 45845704.1 22ATTORNEY DOCKET NO. MSD PC 139 PCT

[0128] interactive capacity and nature of a polypeptide that defines that polypeptide’s biological functional activity, certain amino acid sequence substitutions can be made in a polypeptide sequence and nevertheless obtain a polypeptide with like properties.

[0129] In making such changes, the hydropathic index of amino acids can be considered. The importance of the hydropathic amino acid index in conferring interactive biologic function on a polypeptide is generally understood in the art. It is known that certain amino acids can be substituted for other amino acids having a similar hydropathic index or score and still result in a polypeptide with similar biological activity. Each amino acid has been assigned a hydropathic index on the basis of its hydrophobicity and charge characteristics. Those indices are: isoleucine (+4.5); valine (+4.2); leucine (+3.8); phenylalanine (+2.8): cysteine / cysteine (+2.5); methionine (+1.9); alanine (+1.8); glycine (-0.4); threonine (-0.7); serine (-0.8); tryptophan (-0.9); tyrosine (-1.3); proline (-1.6); histidine (-3.2); glutamate (-3.5); glutamine (-3.5); aspartate (-3.5); asparagine (-3.5); lysine (-3.9); and arginine (-4.5).

[0130] It is believed that the relative hydropathic character of the amino acid determines the secondary structure of the resultant polypeptide, which in turn defines the interaction of the polypeptide with other molecules, such as enzymes, substrates, receptors, antibodies, antigens, and the like. It is known in the art that an amino acid can be substituted by another amino acid having a similar hydropathic index and still obtain a functionally equivalent polypeptide. In such changes, the substitution of amino acids whose hydropathic indices are within + 2 is preferred, those within + 1 are particularly preferred, and those within + 0.5 are even more particularly preferred.

[0131] Substitution of like amino acids can also be made on the basis of hydrophilicity, particularly, where the biological functional equivalent polypeptide or peptide thereby created is intended for use in immunological forms. The following hydrophilicity values have been assigned to amino acid residues: arginine (+3.0); lysine (+3.0); aspartate (+3.0 + 1); glutamate (+3.0 ± 1); serine (+0.3); asparagine (+0.2); glutamine (+0.2); glycine (0); proline (-0.5 ± 1); threonine (-0.4); alanine (-0.5); histidine (-0.5); cysteine (-1.0); methionine (-1.3); valine (-1.5); leucine (-1.8); isoleucine (-1.8); tyrosine (-2.3); phenylalanine (-2.5); tryptophan (-3.4). It is understood that an amino acid can be substituted for another having a similar hydrophilicity value and still obtain a biologically equivalent, and in particular, an immunologically equivalent polypeptide. In such changes, the substitution of amino acids whose hydrophilicity values are within + 2 is preferred, those within + 1 are particularly preferred, and those within + 0.5 are even more particularly preferred.

[0132] 45845704.1 23ATTORNEY DOCKET NO. MSD PC 139 PCT

[0133] As outlined above, amino acid substitutions are generally based on the relative similarity of the amino acid side-chain substituents, for example, their hydrophobicity, hydrophilicity, charge, size, and the like. Exemplary substitutions that take various of the foregoing characteristics into consideration are well known to those of skill in the art and include (original residue: exemplary substitution): (Ala: Gly, Ser), (Arg: Lys), (Asn: Gin, His), (Asp: Glu, Cys, Ser), (Gin: Asn), (Glu: Asp), (Gly: Ala), (His: Asn, Gin), (Ile: Leu, Val), (Leu: Ile, Val), (Lys: Arg), (Met: Leu, Tyr), (Ser: Thr), (Thr: Ser), (Tip: Tyr), (Tyr: Trp, Phe), and (Vai: He, Leu). Embodiments of this disclosure thus contemplate functional or biological equivalents of a polypeptide as set forth above. In particular, embodiments of the polypeptides can include variants having about 50%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99%sequence identity to the polypeptide of interest.

[0134] The term “effective amount,” as used herein, refers to an amount that is sufficient to produces an intended effect for which a substance is administered. The effect may include a desirable change in a biological process as well as the prevention, correction, or inhibition of progression of the symptoms of a disease / condition and related complications to any detectable extent. The exact amount “effective” for achieving a desired effect will depend on the nature of the therapeutic agent, the manner of administration, and 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); and Pickar, Dosage Calculations (1999)).

[0135] Disclosed are materials, compositions, and components that can be used for, can be used in conjunction with, can be used in preparation for, or are products of the disclosed method and compositions. These and other materials are disclosed herein, and it is understood that when combinations, subsets, interactions, groups, etc. of these materials are disclosed that while specific reference of each various individual and collective combinations and permutation of these compounds may not be explicitly disclosed, each is specifically contemplated and described herein. For example, if a ligand is disclosed and discussed and a number of modifications that can be made to a number of molecules including the ligand are discussed, each and every combination and permutation of ligand and the modifications that are possible are specifically contemplated unless specifically indicated to the contrary. Thus, if a class of molecules A, B, and C are disclosed as well as a class of molecules D, E, and F and an example of a combination molecule, A-D is disclosed, then even if each is not individually recited, each is individually and collectively contemplated. Thus, in this 45845704.1 24ATTORNEY DOCKET NO. MSD PC 139 PCT

[0136] example, each of the combinations A-E, A-F, B-D, B-E, B-F, C-D, C-E, and C-F are specifically contemplated and should be considered disclosed from disclosure of A, B, and C; D, E, and F; and the example combination A-D. Likewise, any subset or combination of these is also specifically contemplated and disclosed. Thus, for example, the sub-group of A-E, B-F, and C-E are specifically contemplated and should be considered disclosed from disclosure of A, B, and C; D, E, and F; and the example combination A-D. Further, each of the materials, compositions, components, etc. contemplated and disclosed as above can also be specifically and independently included or excluded from any group, subgroup, list, set, etc. of such materials.

[0137] These concepts apply to all aspects of this application including, but not limited to, steps in methods of making and using the disclosed compositions. Thus, if there are a variety of additional steps that can be performed it is understood that each of these additional steps can be performed with any specific embodiment or combination of embodiments of the disclosed methods, and that each such combination is specifically contemplated and should be considered disclosed.

[0138] All methods described herein can be performed in any suitable order unless otherwise indicated or otherwise clearly contradicted by context. The use of any and all examples, or exemplary language (e.g., “such as”) provided herein, is intended merely to better illuminate the embodiments and does not pose a limitation on the scope of the embodiments unless otherwise claimed. No language in the specification should be construed as indicating any non-claimed element as important to the practice of the disclosure.

[0139] Recitation of ranges of values herein are merely intended to serve as a shorthand method of referring individually to each separate value falling within the range, unless otherwise indicated herein, and each separate value is incorporated into the specification as if it were individually recited herein.

[0140] “Introduce” in the context of genome modification refers to bringing in to contact. For example, to introduce a gene editing composition to a cell is to provide contact between the cell and the composition. The term encompasses penetration of the contacted composition to the interior of the cell by any suitable means, e.g., via transfection, electroporation, transduction, gene gun, nanoparticle delivery, etc.

[0141] B. Compositions

[0142] 1. Complement Factor B Analogs

[0143] Provided herein are complement factor B, protein analogs and polypeptides including complement factor analogs and their uses.

[0144] 45845704.1 25ATTORNEY DOCKET NO. MSD PC 139 PCT

[0145] Nucleotide sequences for genes and coding regions encoding human factor B, as well as the amino acid sequences are known in the art. For example, a gene encoding human factor B is found in NCBI Database Accession No. NG_000013. A coding sequence for a human factor B is found in NCBI Database Accession No. NM_001710 and an amino acid sequence for a human complement factor B preproprotein is found in NCBI Database Accession No. NP_001701 or P00751.

[0146] Typically, a human factor B preprotein is a 764 amino acid protein (e.g., see SEQ ID NO:1) with a signal peptide spanning amino acid positions 1-25. The mature chain of factor B corresponds to positions 26-764 (e.g., see SEQ ID NO:1). The three SCR regions of human factor B are SCR1, also known as Sushi I, spanning from about position 35 to about position 100, SCR2, also known as Sushi 2, spanning from about position 101 to about position 160 and SCR3, also known as Sushi 3, spanning from about position 163 to about position 220.

[0147] All of the factor B analogs and polypeptides provided herein are expressly provided with and without the signal sequence. For example, in some forms and preparations, such as protein therapy, the signal sequence is absent or removed.

[0148] The amino acid sequence of wildtype factor B is known in the art, and can be MGSNLSPQLCLMPFILGLLSGGVTTTPWSLARPQGSCSLEGVEIKGGSFRLLQEGQALEYVC PSGFYPYPVQTRTCRSTGSWSTLKTQDQKTVRKAECRAIHCPRPHDFENGEYWPRSPYYNVS DEISFHCYDGYTLRGSANRTCQVNGRWSGQTAICDNGAGYCSNPGIPIGTRKVGSQYRLEDS VTYHCSRGLTLRGSQRRTCQEGGSWSGTEPSCQDSFMYDTPQEVAEAFLSSLTETIEGVDAE DGHGPGEQQKRKIVLDPSGSMNIYLVLDGSDSIGASNFTGAKKCLVNLIEKVASYGVKPRYG LVTYATYPKIWVKVSEADSSNADWVTKQLNEINYEDHKLKSGTNTKKALQAVYSMMSWPDDV PPEGWNRTRHVIILMTDGLHNMGGDPITVIDEIRDLLYIGKDRKNPREDYLDVYVFGVGPLV NQVNINALASKKDNEQHVFKVKDMENLEDVFYQMIDESQSLSLCGMVWEHRKGTDYHKQPWQ AKISVIRPSKGHESCMGAWSEYFVLTAAHCFTVDDKEHSIKVSVGGEKRDLEIEWLFHPN YNINGKKEAGIPEFYDYDVALIKLKNKLKYGQTIRP ICLPCTEGTTRALRLPPTTTCQQQKE ELLPAQDIKALFVSEEEKKLTRKEVYIKNGDKKGSCERDAQYAPGYDKVKDISEWTPRFLC TGGVSPYADPNTCRGDSGGPLIVHKRSRFIQVGVISWGWDVCKNQKRQKQVPAHARDFHIN LFQVLPWLKEKLQDEDLGFL (SEQ ID NO:1 ).

[0149] In some forms, the disclosed analogs are provided relative to the wildtype of SEQ ID NO:1.

[0150] The instant disclosure includes complement factor B protein analogs, e.g., that can be delivered as proteins and / or via gene transfer to attenuate the alternative pathway of 45845704.1 26ATTORNEY DOCKET NO. MSD PC 139 PCT

[0151] complement activation. These analogs may overcome hurdles that impede the development of some complement inhibitors including, for example: 1) avoiding long term systemic immune suppression; 2) achieving efficacy in the face of otherwise prohibitively high levels of complement factors in the blood; 3) achieving sufficient levels and distribution of the therapeutic complement factor B protein analog in the proximity of the retina and Bruch’s membrane for efficacy; 4) achieving activity of the therapeutic complement factor B protein analog within drusen; 5) achieving sufficient duration of therapeutic delivery to treat a chronic disease; 6) achieving efficacy without detrimentally interfering with the classical complement pathway or lectin complement pathway activities in the back of the eye or in the blood circulation; 7) avoiding or diminishing an immune reaction (e.g., a local immune reaction) to the therapeutic; 8) achieving sufficient levels of the therapeutic complement factor B protein analog at the site of a diseased tissue, e.g., arthritis joints, retina, kidney, or inflamed vessels; and / or 9) achieving sufficient levels of the therapeutic complement factor B protein analog at the site of diseased cells, e.g., red blood cell surface of paroxysmal nocturnal hemoglobinuria patients.

[0152] Attenuating the positive feedback loop in the alternative pathway is a means of down-regulating the entire alternative pathway. One suitable means for attenuating the alternative pathway feedback loop is to interfere with complement factor B (fB) protein function or levels. Some forms use a complement factor B analog for attenuating complement activity.

[0153] Attenuating the positive feedback loop in the alternative pathway is a means of down-regulating the entire alternative pathway. One suitable means for attenuating the alternative pathway feedback loop is to attenuating C3b and / or factor D function. Some forms use a complement factor B analog for attenuating complement factor C3b and / or factor D activity.

[0154] Analogs can include various mutation(s) relative to the naturally-occurring amino acid sequence. For example, single or multiple amino acid substitutions (e.g., conservative or non-conservative amino acid substitutions) may be made in the naturally-occurring sequence. A conservative amino acid substitution generally should not substantially change the structural characteristics of the parent sequence (e.g., a replacement amino acid should not tend to break a helix that occurs in the parent sequence, or disrupt other types of secondary structure that characterizes the parent sequence). Examples of art-recognized polypeptide secondary and tertiary structures are described in Proteins, Structures and Molecular Principles (Creighton, Ed., W. H. Freeman and Company, New York (1984)); Introduction to 45845704.1 27ATTORNEY DOCKET NO. MSD PC 139 PCT

[0155] Protein Structure (C. Branden and J. Tooze, eds., Garland Publishing, New York, N. Y.

[0156] (1991)); and Thornton et al. Nature 354:105 (1991). Conservative substitutions include, but are not limited to, those from the following groupings: Acidic Residues Asp (D) and Glu (E); Basic Residues Lys (K), Arg (R), and His (H); Hydrophilic Uncharged Residues Ser (S), Thr (T), Asn (N), and Gin (Q); Aliphatic Uncharged Residues Gly (G), Ala (A), Vai (V), Leu (L), and Ile (I); Non-polar Uncharged Residues Cys (C), Met (M), and Pro (P); Aromatic Residues Phe (F), Tyr (Y), and Trp (W); Alcohol group-containing residues S and T;

[0157] Aliphatic residues I, L, V and M; Cycloalkenyl-associated residues F, H, W and Y;

[0158] Hydrophobic residues A, C, F, G, H, I, L, M, R, T, V, W and Y; Negatively charged residues D and E; Polar residues C, D, E, H, K, N, Q, R, S and T; Positively charged residues H, K and R; Small residues A, C, D, G, N, P, S, T and V; Very small residues A, G and S;

[0159] Residues involved in turn formation A, C, D, E, G, H, K, N, Q, R, S, P and T; and Flexible residues Q, T, K, S, G, P, D, E and R.

[0160] In some forms, a non-conservative substitution is used, e.g., substitution of Arg with Gly or Asp.

[0161] In some forms, mutations include, but are not limited to, substitutions of one or more amino acids, deletions of one or more amino acids or insertions of one or more amino acids. Mutations include, but are not limited to, those which: (1) reduce susceptibility of the complement factor B analog to proteolysis, (2) reduce susceptibility of the complement factor B analog to oxidation, (3) alter binding affinity of the complement factor B analog for forming protein complexes, (4) alter (e.g., increase or decrease) binding affinities of the complement factor B analog, (5) reduce immunogenicity of the complement factor B analog; (6) increase stability e.g., thermostability ) of the complement factor B analog; (7) reduce aggregation of the complement factor B protein analog; (8) addition of glycosylation; (9) increase half-life of the complement factor B analog in vivo (e.g., in human serum) or any combinations of 1-9.

[0162] In some forms, a human complement factor B analog of the present disclosure competes with binding of native complement factor B. For example, native complement factor B can bind with complement factor C3b to form C3bB. Factor B that is part of the C3bB complex can bind factor D. Therefore, in some forms, a complement factor B analog of the present disclosure can compete with the binding of a native factor B for (i) binding to C3b, (ii) binding to factor D or (iii) both.

[0163] In some forms, a complement factor B protein analog has increased C3b binding affinity as compared to a corresponding native complement factor B protein and the 45845704.1 28ATTORNEY DOCKET NO. MSD PC 139 PCT

[0164] complement factor B protein analog includes (i) diminished protease activity as compared to a corresponding native complement factor B protein; (ii) diminished ability to be cleaved by factor D protein as compared to a corresponding native complement factor B protein; (iii) diminished protease activity as compared to a corresponding native complement factor B protein and diminished ability to be cleaved by a factor D protein as compared to a corresponding native complement factor B protein; (iv) increased binding affinity to factor D as compared to the binding affinity of a corresponding native complement factor B protein to factor D; or (v) increased N-Glycosylation sites.

[0165] In some forms, increased binding is increased by about 1.5 to about 10,000, about 10 to about 10,000, about 100 to about 10,000, about 1,000 to about 10,000, about 1.5 to about 1,000, about 1.5 to about 100, about 1.5 to about 10, about 2 to about 5, about 2 to about 10, about 5 to about 10, about 5 to about 20, about 10 to about 20, about 10 to about 30, about 20 to about 30, about 30 to about 50, about 50 to about 100, about 100 to about 500, about 500 to about 1,000, about 1,000 to about 5,000, or about 5,000 to about 10,000 fold. In some forms, increased binding is increased by greater than 1.5, 2, 3, 4, 5, 10, 50, 100, 500, 1000, 5000 or 10,000-fold. In some forms, increased binding can be measured by immunoprecipitation, ELISA or using a Biacore (GE Healthcare, Piscataway, NJ), e.g., as compared to the wild type protein.

[0166] Some factor B protein analogs of the instant disclosure may have increased binding to C3b protein and / or factor D protein by a factor of 2-fold, 4-fold, 5 -fold, 10-fold, 20-fold, 50-fold, 100-fold, 500-fold, 1000-fold as compared to binding of wild type factor B to C3b and / or factor D. In some forms, increased binding can be measured by immunoprecipitation, ELISA or using a Biacore (GE Healthcare, Piscataway, NJ).

[0167] The instant disclosure includes complement factor B protein analogs, e.g., that can be delivered as proteins and / or via gene transfer to attenuate the alternative pathway of complement activation. These analogs may overcome hurdles that impede the development of some complement inhibitors including, for example: 1) avoiding long term systemic immune suppression; 2) achieving efficacy in the face of otherwise prohibitively high levels of complement factors in the blood; 3) achieving sufficient levels and distribution of the therapeutic complement factor B protein analog in the proximity of the retina and Bruch’s membrane for efficacy; 4) achieving activity of the therapeutic complement factor B protein analog within drusen; 5) achieving sufficient duration of therapeutic delivery to treat a chronic disease; 6) achieving efficacy without detrimentally interfering with the classical complement pathway or lectin complement pathway activities in the back of the eye or in the 45845704.1 29ATTORNEY DOCKET NO. MSD PC 139 PCT

[0168] blood circulation; 7) avoiding or diminishing an immune reaction (e.g., a local immune reaction) to the therapeutic; 8) achieving sufficient levels of the therapeutic complement factor B protein analog at the site of a diseased tissue, e.g., arthritis joints, retina, kidney, or inflamed vessels; and / or 9) achieving sufficient levels of the therapeutic complement factor B protein analog at the site of diseased cells, e.g., red blood cell surface of paroxysmal nocturnal hemoglobinuria patients.

[0169] Attenuating the positive feedback loop in the alternative pathway is a means of down-regulating the entire alternative pathway. One suitable means for attenuating the alternative pathway feedback loop is to interfere with complement factor B (fB) protein function or levels. Some forms of the instant disclosure use a complement factor B analog for attenuating complement activity.

[0170] Attenuating the positive feedback loop in the alternative pathway is a means of down-regulating the entire alternative pathway. One suitable means for attenuating the alternative pathway feedback loop is to attenuating C3b and / or factor D function. Some forms of the instant disclosure use a complement factor B analog for attenuating complement factor C3b and / or factor D activity.

[0171] For exemplary purposes, specific analogs of complement factor B protein arc described herein. Factor B protein can be manipulated in a number of ways, e.g., to inhibit or reduce activation of the alternative pathway. In some forms, particular sites in factor B can be altered, for example, by site directed mutagenesis, so that the molecule no longer fully functions properly like the wild type factor B.

[0172] Some modified factor B protein analogs of the instant disclosure include one or more of the amino acid alterations discussed herein and additionally have one or more additional amino acid substitutions, insertions or alterations (e.g., at least or no more than 1, 2, 5, 8, 10, 15 20, 50, 100, or 200 alterations), which analogs retain the increased binding to C3b or other biological activity of the factor B protein analogs discussed herein, which mediates inhibition of the complement pathway. Such analogs may have at least 99.9%, 99%, 98%, 95%, 90%, 85%, 80%, 75% or 70% amino acid sequence identity with a wild type factor B protein, for example, the amino acid sequence of SEQ ID NO:1 and retain the increased binding to C3b.

[0173] In some forms, the complement factor B analog is not SEQ ID NO:2, which represents amino acid sequence of human complement factor B protein analog PCI 13 (also referred to as hfB3-292S):

[0174] MGSNLSPQLCLMPFILGLLSGGVTTTPWSLARPQGSCSLEGVEIKGGSFRLLQEGQALEYVC PSGFYPYPVQTRTCRSTGSWSTLKTQDQKTVRKAECRAIHCPRPHDFENGEYWPRSPYYNVS

[0175] 45845704.1 30ATTORNEY DOCKET NO. MSD PC 139 PCT

[0176] DEISFHCYDGYTLRGSANRTCQVNGRWSGQTAICDNGAGYCSNPGIPIGTRKVGSQYRLEDS VTYHCSRGLTLRGSQRRTCQEGGSWSGTEPSCQDSFMYDTPQEVAEAFLSSLTETIEGVDAE DGHGPGEQQAAAIVLDPSGSMNIYLVLDGSGSIGASDFTGAKKSLVNLIEKVASYGVKPRYG LVTYATYPKIWVKVSEADSSNADWVTKQLNEINYEDHKLKSGTNTKKALQAVYSMMSWPDDV PPEGWNRTRHVIILMTDGLHNMGGDPITVIDEIRDLLYIGKDRKNPREDYLDVYVFGVGPLV NQVNINALASKKDNEQHVFKVKDMENLEDVFYQMIDESQSLSLCGMVWEHRKGTDYHKQPWQ AKISVIRPSKGHESCMGAWSEYFVLTAAHCFTVDDKEHSIKVSVGGEKRDLEIEWLFHPN YNINGKKEAGIPEFYDYDVALIKLKNKLKYGQTIRPICLPCTEGTTRALRLPPTTTCQQQKE ELLPAQDIKALFVSEEEKKLTRKEVYIKNGDKKGSCERDAQYAPGYDKVKDISEWTPRFLC TGGVSPYADPNTCRGDSGGPLIVHKRSRFIQVGVISWGWDVCKNQKRQKQVPAHARDFHIN LFQVLPWLKEKLQDEDLGFL (SEQ ID NO:2).

[0177] In the context of gene therapy and expression of complement factor B protein analogs, the alterations / mutations will be reflected at the level of the encoding nucleic acid. Thus, modifications also can be made to the nucleic acid to enhance expression. For example, certain codons may be preferred by a particular host cell. Thus, recoding can be performed where certain codons are preferred in, for example, a particular mammalian expression system or cell.

[0178] Some forms of the instant disclosure arc directed to polynucleotides and host cells (or host multicellular organisms) useful in the production of a complement factor B protein analog and directed to the analogs. Methods of isolating and testing complement-mediated activity of these complement factor B protein analogs are also provided. Some aspects of the instant disclosure are directed to pharmaceutical compositions / preparations wherein a complement factor B protein analog is an active ingredient in a therapeutic and / or a prophylactic context. Some forms of the instant disclosure are also directed to methods of treating complement-mediated disorders using a therapeutically effective amount of a complement factor B protein analog.

[0179] Glycosylation and other modifications

[0180] In some forms of the instant disclosure, a complement factor B analog may include glycosylation patterns which are distinct from glycosylation patterns on a naturally-occurring complement factor B, or may have more glycosylation, or may have less glycosylation altogether. Carbohydrates may be added to and / or removed from factor B analogs including glycosylation site sequences for N- and / or O-linked glycosylation in vitro, such as with a canine pancreatic microsome system (e.g., see Mueckler and Lodish (1986) Cell 44:629 and Walter, P. (1983) Meth. Enzymol. 96:84) or the like. A complement factor B analog of the 45845704.1 31ATTORNEY DOCKET NO. MSD PC 139 PCT

[0181] instant disclosure may be produced including adding or deleting / mutating an amino acid sequence corresponding to a glycosylation site, e.g., changing the glycosylation pattem / status of a protein can change functional characteristics of a protein. A complement factor B analog of the instant disclosure may be produced including adding amino acid sequence corresponding to a glycosylation site. Changing the glycosylation pattem / status of a complement factor B analog can change functional characteristics of the protein, e.g., increasing its half-life in human serum, increasing its stability in vitro and in vivo, increasing its solubility, increasing its affinity to factor D.

[0182] In some forms, a complement factor B protein analog is PEGylated, e.g., see Roberts et al.. Advanced Drug Delivery Reviews 54(4):459-476 (2002): Veronese, Biomaterials 22(5):405-417 (2001); Fee and Alstine, Chemical Engineering Science 61(3):924-939 (2006); Kodera et al., Progress in Polymer Science 23(7): 1233-1271 (1998); Morar, Biopharm International 19(4);34 (2006); and Veronese and Pasut, Drug Discovery Today 10(21); 1451-1458 (2005). Polyethylene glycol (PEG) can be attached to a complement factor B protein analog of the instant disclosure. In some forms, PEG is attached with or without a multifunctional linker either through site-specific conjugation of the PEG e.g., to the N-terminus or to the C terminus of a complement factor B analog) or via epsilon amino groups present on lysine residues. In some forms, linear or branched polymer derivatization that results in minimal loss of biological activity can be used. The degree of conjugation can be closely monitored by SDS-PAGE and mass spectrometry to ensure proper conjugation of PEG molecules to a complement factor B analog. In some forms, unreacted PEG can be separated from PEG conjugates by size-exclusion and / or by ion exchange chromatography.

[0183] In some forms, the carboxy-terminus, the amino-terminus or both of a complement factor B analog, are chemically modified. Amino-terminal modifications such as acylation (e.g., acetylation) or alkylation (e.g., methylation) and carboxy-terminal modifications such as amidation, as well as other terminal modifications, including cyclization, may be incorporated into various forms of the instant disclosure. Certain aminoterminal and / or carboxy-terminal modifications and / or peptide extensions (such as fused to a heterologous polypeptide, such as albumin, immunoglobulin or portion thereof, such as an immunoglobulin Fc domain) to the core sequence can provide advantageous physical, chemical, biochemical, and pharmacological properties, such as: enhanced stability, increased potency and / or efficacy, resistance to serum proteases, desirable pharmacokinetic properties, and others.

[0184] 45845704.1 32ATTORNEY DOCKET NO. MSD PC 139 PCT

[0185] Analogs of the instant disclosure can be prepared by various techniques, including but not limited to, chemical synthesis or by expression of the recombinant analog.

[0186] a. Exemplary PC 113 analogs

[0187] The factor D cleavage site was studied and two human complement factor B analogs, PCI 13-G and PCI 13-D, were engineered. The difference between the PCI 13-G (SEQ ID NO:26) and PCI 13-D (SEQ ID NO:28) tested in the experiments below is only one amino acid in the factor D cleavage site out of the entire 764 amino acids (Figure 1).

[0188] PCI 13-G and PCI 13-D have an opposite biological activity: PCI 13-G is a potent inhibitor of human alternative complement pathway, whereas PCI 13-D is an enhancer of human alternative complement pathway.

[0189] Thus, provided are factor B analogs including a substitution of the arginine at position 259 relative to the wildtype protein.

[0190] Thus, in some forms, the provided factor B analogs are described or characterized with reference to wildtype (e.g., SEQ ID NO:1), and thus the Arg259 (also referred to as R259) corresponds to the arginine at position 259 in SEQ ID NO:1. Typically, the disclosed factor B analogs have a mutation at the amino acid position relative to arginine at position 259 of SEQ ID NO:1, and optionally one or more additional mutations. Preferably, the mutation at position 259 is not an alanine. In some forms, the mutation at position 259 is a glycine or an aspartic acid.

[0191] In some forms, the factor B analog is a variant of SEQ ID NO:1 including a substitution R259 that is not alanine, valine, leucine, or isoleucine, and optionally has at least 70, 75, 80, 85, 90, 95, 96, 97, 98, or 99 percent sequence identity thereto.

[0192] In some forms, the factor B analog has the amino acid sequence MGSNLSPQLCLMPFILGLLSGGVTTTPWSLARPQGSCSLEGVEIKGGSFRLLQEGQALEYVC PSGFYPYPVQTRTCRSTGSWSTLKTQDQKTVRKAECRAIHCPRPHDFENGEYWPRSPYYNVS DEISFHCYDGYTLRGSANRTCQVNGRWSGQTAICDNGAGYCSNPGIPIGTRKVGSQYRLEDS VTYHCSRGLTLRGSQRRTCQEGGSWSGTEPSCQDSFMYDTPQEVAEAFLSSLTETIEGVDAE DGHGPGEQQKGKIVLDPSGSMNIYLVLDGSDSIGASNFTGAKKCLVNLIEKVASYGVKPRYG LVTYATYPKIWVKVSEADSSNADWVTKQLNEINYEDHKLKSGTNTKKALQAVYSMMSWPDDV PPEGWNRTRHVIILMTDGLHNMGGDPITVIDEIRDLLYIGKDRKNPREDYLDVYVFGVGPLV NQVNINALASKKDNEQHVFKVKDMENLEDVFYQMIDESQSLSLCGMVWEHRKGTDYHKQPWQ AKISVIRPSKGHESCMGAWSEYFVLTAAHCFTVDDKEHSIKVSVGGEKRDLEIEWLFHPN YNINGKKEAGIPEFYDYDVALIKLKNKLKYGQTIRP ICLPCTEGTTRALRLPPTTTCQQQKE ELLPAQDIKALFVSEEEKKLTRKEVYIKNGDKKGSCERDAQYAPGYDKVKDISEWTPRFLC

[0193] 45845704.1 33ATTORNEY DOCKET NO. MSD PC 139 PCT

[0194] TGGVSPYADPNTCRGDSGGPLIVHKRSRFIQVGVISWGWDVCKNQKRQKQVPAHARDFHIN LFQVLPWLKEKLQDEDLGFL (SEQ ID NO:30) or is a fragment or variant thereof including G259, and optionally at least 70, 75, 80, 85, 90, 95, 96, 97, 98, or 99 percent sequence identity thereto.

[0195] In some forms, the factor B analog has the amino acid sequence MGSNLSPQLCLMPFILGLLSGGVTTTPWSLARPQGSCSLEGVEIKGGSFRLLQEGQALEYVC PSGFYPYPVQTRTCRSTGSWSTLKTQDQKTVRKAECRAIHCPRPHDFENGEYWPRSPYYNVS DEISFHCYDGYTLRGSANRTCQVNGRWSGQTAICDNGAGYCSNPGIPIGTRKVGSQYRLEDS VTYHCSRGLTLRGSQRRTCQEGGSWSGTEPSCQDSFMYDTPQEVAEAFLSSLTETIEGVDAE DGHGPGEQQKDKIVLDPSGSMNIYLVLDGSDSIGASNFTGAKKCLVNLIEKVASYGVKPRYG LVTYATYPKIWVKVSEADSSNADWVTKQLNEINYEDHKLKSGTNTKKALQAVYSMMSWPDDV PPEGWNRTRHVIILMTDGLHNMGGDPITVIDEIRDLLYIGKDRKNPREDYLDVYVFGVGPLV NQVNINALASKKDNEQHVFKVKDMENLEDVFYQMIDESQSLSLCGMVWEHRKGTDYHKQPWQ AKISVIRPSKGHESCMGAWSEYFVLTAAHCFTVDDKEHSIKVSVGGEKRDLEIEWLFHPN YNINGKKEAGIPEFYDYDVALIKLKNKLKYGQTIRP ICLPCTEGTTRALRLPPTTTCQQQKE ELLPAQDIKALFVSEEEKKLTRKEVYIKNGDKKGSCERDAQYAPGYDKVKDISEWTPRFLC TGGVSPYADPNTCRGDSGGPLIVHKRSRFIQVGVISWGWDVCKNQKRQKQVPAHARDFHIN LFQVLPWLKEKLQDEDLGFL (SEQ ID NO:31) or is a fragment or variant thereof including D259, and optionally at least 70, 75, 80, 85, 90, 95, 96, 97, 98, or 99 percent sequence identity thereto.

[0196] Thus, the complement factor B protein analogs that do not include an arginine at position 259. Mutation of arginine at position 259 can be combined with other mutations of a complement factor B protein.

[0197] In some forms, a complement factor B protein analog is an analog of SEQ ID NO: 1 having the factor D cleavage site, Lys258-Arg259-Lys260, substituted with more than one amino acid, or deleted by one or more than one amino acid.

[0198] Some forms include a substitution of an amino acid corresponding to amino acid 279 of SEQ ID NO:1, e.g., with an amino acid selected from the group including glycine, alanine and asparagine. Some forms contain a substitution of an amino acid corresponding to amino acid 279 of SEQ ID NO: 1 with an amino acid selected from the group including glycine, alanine, valine, leucine and isolcucinc. Some forms include a substitution of an amino acid corresponding to amino acid 279 of SEQ ID NO:1 with an amino acid selected from the group including asparagine, glutamic acid and glutamine. Some forms include a deletion of an amino acid corresponding to amino acid 279 of SEQ ID NO: 1. Some forms include the 45845704.1 34ATTORNEY DOCKET NO. MSD PC 139 PCT

[0199] insertion or substitution of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more amino acids immediately next to or in place of an amino acid corresponding to amino acid 279 of SEQ ID NO: 1.

[0200] Some forms include a substitution of an amino acid corresponding to amino acid 285 of SEQ ID NO:1, e.g., with an amino acid selected from the group including alanine and aspartic acid. Some forms include a substitution of an amino acid corresponding to amino acid 285 of SEQ ID NO: 1 with an amino acid selected from the group including glycine, alanine, valine, leucine and isoleucine. Some forms include a substitution of an amino acid corresponding to amino acid 285 of SEQ ID NO:1 with an amino acid selected from the group including aspartic acid, glutamic acid and glutamine. Some forms include a deletion of an amino acid corresponding to amino acid 285 of SEQ ID NO:1. Some forms include the insertion or substitution of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more amino acids immediately next to or in place of an amino acid corresponding to amino acid 285 of SEQ ID NO:1.

[0201] Some forms include mutations of the amino acids corresponding to 258, 259, 260, 279, 285, and 292 of SEQ ID NO: 1 as described herein.

[0202] The disclosure includes complement factor B protein analogs that include a combination of the mutations (substitutions, deletions and additions) discussed herein. In some forms, these complement factor B analogs retain one or more of the attributes of any other complement factor B analog discussed herein. The disclosure further provides analogs that are fragments (for example including one or more domains of a complement factor B protein having one or more of the amino acid mutations set forth herein) of these analogs that have one or more of the attributes of the analogs discussed above. In addition, the analogs may include additional amino acid substitutions, deletions or insertions (for example, conservative amino acid substitutions, truncations of the N-terminus or C-terminus, etc.) such that the analog has at least 99.5%, 99%, 98%, 95%, 90%, 85%, 80%, 75% or 75% identity with the corresponding wild-type complement factor B or, in the case of an analog including a fragment of complement factor B, the analog has at least 99.5%, 99%, 98%, 95%, 90%, 85%, 80%, 75% or 70% identity between the corresponding parts of the analog and wild-type complement factor B.

[0203] In some forms disclosed herein, a human complement factor B protein analog is at least 90%, at least 95%, at least 98% or at least 99% identical to SEQ ID NOs:l, 2, 26, 28, 30, or 31. In some forms, a human complement factor B protein analog includes SEQ ID NO:26, 28, 30, or 31.

[0204] In some forms, a complement factor B analog includes a mutation in the C3b binding domain and the complement factor B protein analog exhibits increased binding affinity to 45845704.1 35ATTORNEY DOCKET NO. MSD PC 139 PCT

[0205] C3b as compared to the binding affinity of a corresponding native complement factor B protein to C3b. In some forms, a mutation in the C3b binding domain includes (i) a substitution or deletion of an aspartic acid corresponding to amino acid 279 of SEQ ID NO: 1, a substitution or deletion of an asparagine corresponding to amino acid 285 of SEQ ID NO: 1 or both; or (ii) an insertion of at least one amino acid next to the aspartic acid or the asparagine. In some forms, this aspartic acid, asparagine or both are substituted with one or more amino acids. In some forms, an aspartic acid corresponding to amino acid 279 of SEQ ID NO:1 is substituted with glycine, alanine or asparagine. In some forms, an asparagine corresponding to amino acid 285 of SEQ ID NO:1 is substituted with glycine, alanine, or aspartic acid. In some forms, an aspartic acid corresponding to amino acid 279 of SEQ ID NO:1 is substituted with glycine and an asparagine corresponding to amino acid 285 of SEQ ID NO:1 is substituted with aspartic acid.

[0206] In some forms, a complement factor B protein analog is a human complement factor B protein analog, based on a human complement factor protein.

[0207] Human complement factor B analog PC113-G has a higher affinity to C3b as compared to wildtype human complement factor B and is resistant to C3b-dependent factor D cleavage and creates an inactive C3 convertase after binding to C3b.

[0208] Some forms include a complement factor B protein analog wherein the factor D cleavage site has been mutated. In some forms, this mutation of the factor D cleavage site can include a deletion of Lys258 and / or Lys260 or substitution of one or both of the amino acids with another amino acid(s). These two amino acids can be substituted with essentially any amino acid(s), that still allows for the complement factor B protein analog to retain at least some of the desired characteristic(s), such as the ability to resist C3b-dependent cleavage by factor D, to downregulate, to diminish or to ablate alternative complement activity. A substitution may be with one or more amino acids. In some forms, the mutation(s) create a complement factor B analog that is resistant to C3b-dependent cleavage by factor D, binds C3b with higher affinity, forms inactive C3 convertase with C3b, and inhibits human alternative complement pathway activity.

[0209] Thus in some forms, mutation of arginine at position 259 is combined with other mutations at the factor D cleavage site of the WT version, Lys258-Arg259-Lys260. A complement factor B protein analog may include R259G or R259D and at least one mutation corresponding to a mutation of SEQ ID NO: 1 selected from the group including K258A, K260A, D279G, N285D and C292S. In some forms, it contains mutations corresponding to K258A, R259G, K260A, D279G, N285D and C292S of SEQ ID NO:1.

[0210] 45845704.1 36ATTORNEY DOCKET NO. MSD PC 139 PCT

[0211] Thus, for example, in some forms, the factor D cleavage site of a complement factor B analog is mutated from Lys258-Arg259-Lys260 to Ala258-Gly259-Ala260. Other mutations in the same complement factor B analog can include D279G and N285D mutations in the C3b binding site, and C292S mutation in the free cysteine site.

[0212] For exemplary purposes, specific analogs of complement factor B protein are described herein. Factor B protein can be further manipulated in a number of ways, e.g.. to inhibit or reduce activation of the alternative pathway. In some forms, particular sites in factor B can be altered, for example, by site directed mutagenesis, so that the molecule no longer fully functions properly like the wildtype factor B. In some forms, the factor D cleavage site, Lys258-Arg259-Lys260, can be altered so the molecule can no longer be cleaved by factor D. In some forms, the factor D cleavage site, Lys258-Arg259-Lys260, can be altered so that the molecule exhibits high binding affinity to factor D as compared to the binding affinity of a corresponding native complement factor B protein to factor D. In some forms, the enzyme portion or domain, (e.g., the protease domain, which is a serine protease) of the molecule can be altered so that the molecule no longer has enzymatic activity or has reduced enzymatic activity (e.g., reduced by at least 2 fold, 5 fold, 10 fold, 50 fold or 100 fold). In some forms, a complement factor B protein analog contains a mutation in the active site of the serine protease domain, wherein the mutation decreases or ablates the complement factor B protein analog’s ability to cleave complement factor C3 as compared to a corresponding native complement factor B protein.

[0213] Other sites in factor B that can be altered include: 1) the binding site for properdin (the properdin binding domain) such that binding occurs with lower affinity (for example, such as 2 fold, 5 fold, 10 fold, 50 fold or 100 fold reduced affinity as compared to the wildtype factor B protein) or with greater affinity (such as at least 2 fold, 5 fold, 10 fold, 50 fold or 100 fold increased affinity as compared to the wildtype factor B); 2) the binding site for C3b protein (the C3b binding domain) such that binding occurs with lower affinity (such as at least 2 fold, 5 fold, 10 fold, 50 fold or 100 fold reduced affinity as compared to the wildtype factor B protein) or with greater affinity (such as at least 2 fold, 5 fold, 10 fold, 50 fold or 100 fold increased affinity as compared to wildtype factor B protein, for example, this may be achieved by substituting the amino acid corresponding to position 279 and / or position 285 of SEQ ID NO: 1 with other amino acids, for example, wherein the amino acid at the position corresponding to position 279 is substituted with asparagine (N), alanine (A) or glycine (G) and / or the amino acid at the position corresponding to position 285 is substituted with aspartic acid (D) or alanine (A)); 3) the site acted on by factor D such that factor D has 45845704.1 37ATTORNEY DOCKET NO. MSD PC 139 PCT

[0214] reduced ability to cleave or no longer cleaves factor B analog to form Bb (for example, at the factor D cleavage site, -Arg259- and least one of the amino acids at the positions corresponding to position Lys258 and Lys260 of SEQ ID NO:1, for example, can be altered to Ala258-Gly259-Ala260 or; a combination of any of 1, 2, and / or 3 above).

[0215] In some forms, a complement factor B protein analog contains an alteration in the complement factor D cleavage site wherein the alteration decreases or ablates cleavage of the complement factor B protein analog by factor D protein. In some forms, an alteration in the factor D cleavage site includes (i) a substitution or deletion of an arginine corresponding to amino acid 259 of SEQ ID NO:1, a substitution or deletion of one or both lysines corresponding to amino acid 258 or 260 of SEQ ID NO:1 or a substitution or deletion of the arginine and both lysines; or (ii) an insertion next to the arginine, next to the one or both lysines, or next to the arginine and one or both of the lysines. In some forms, a complement factor B protein analog has amino acids corresponding to amino acids 258-260 of SEQ ID NO:1 each replaced with different amino acids.

[0216] In one form, a complement factor B protein analog comprises an amino acid sequence having at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least 99.5% identity to the amino acid sequence of SEQ ID NO:1, wherein the complement factor B analog comprises a glycine or aspartic acid substitution at the position corresponding to the arginine at position 259 of SEQ ID NO:1, and optionally further comprises (a) a mutation of a free cysteine amino acid, (b) a mutation in a C3b binding site, (c) an additional mutation in a complement factor D cleavage site, or any combination thereof. In one form, a complement factor B protein analog comprises an amino acid sequence having at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least 99.5% identity to the amino acid sequence of SEQ ID NO: 1, wherein the complement factor B analog comprises a glycine or aspartic acid substitution at the position corresponding to the arginine at position 259 of SEQ ID NO:1, a glycine substitution at the position corresponding to the aspartic acid at position 279 of SEQ ID NO:1, an aspartic acid substitution at the position corresponding to the asparagine at position 285 of SEQ ID NO: 1, and a serine substitution at the position corresponding to the cysteine at position 292 of SEQ ID NO:1.

[0217] In some forms, the factor B analog is PCI 13-G or a variant thereof. PCI 13-G includes a change in the factor D cleavage site wherein Lys258-Arg259-Lys260 from wildtype (WT) is substituted with Ala258-Gly259-Ala260. In addition, two amino acids at the C3b binding site, Asp279 and Asn285 (WT), are substituted with Gly279 and Asp285, respectively. The free cysteine at position 292 in wildtype factor B is substituted with a 45845704.1 38ATTORNEY DOCKET NO. MSD PC 139 PCT

[0218] serine. PCI 13-G is a dominant negative analog of human factor B and a potent inhibitor of the human alternative complement pathway.

[0219] Thus, in some forms, the complement factor B analog is SEQ ID NO:26, which represents amino acid sequence of human complement factor B protein analog PC113-G: MGSNLSPQLCLMPFILGLLSGGVTTTPWSLARPQGSCSLEGVEIKGGSFRLLQEGQALEYVC P SGFYPYP VQTRTCRSTGSWSTLKTQDQKTVRKAECRAIHCPRPHDFENGEYWPRSPYYNVS DEISFHCYDGYTLRGSANRTCQVNGRWSGQTAICDNGAGYCSNPGIPIGTRKVGSQYRLEDS VTYHCSRGLTLRGSQRRTCQEGGSWSGTEPSCQDSFMYDTPQEVAEAFLSSLTETIEGVDAE DGHGPGEQQAGAIVLDPSGSMNIYLVLDGSGSIGASDFTGAKKSLVNLIEKVASYGVKPRYG LVTYATYPKIWVKVSEADSSNADWVTKQLNEINYEDHKLKSGTNTKKALQAVYSMMSWPDDV PPEGWNRTRHVIILMTDGLHNMGGDPITVIDEIRDLLYIGKDRKNPREDYLDVYVFGVGPLV NQVNINALASKKDNEQHVFKVKDMENLEDVFYQMIDESQSLSLCGMVWEHRKGTDYHKQPWQ AKISVIRPSKGHESCMGAWSEYFVLTAAHCFTVDDKEHSIKVSVGGEKRDLEIEWLFHPN YNINGKKEAGIPEFYDYDVALIKLKNKLKYGQTIRP ICLPCTEGTTRALRLPPTTTCQQQKE ELLPAQDIKALFVSEEEKKLTRKEVYIKNGDKKGSCERDAQYAPGYDKVKDISEWTPRFLC TGGVSPYADPNTCRGDSGGPLIVHKRSRFIQVGVISWGWDVCKNQKRQKQVPAHARDFHIN LFQVLPWLKEKLQDEDLGFL (SEQ ID NO:26) or is a fragment or variant thereof including Ala258-Gly259-Ala260, Gly279, and Asp285, respectively and optionally at least 70, 75, 80, 85, 90, 95, 96, 97, 98, or 99 percent sequence identity thereto.

[0220] SEQ ID NO:27 is a nucleotide sequence encoding human complement factor B protein analog PCI 13-G:

[0221] ATGGGCTCCAACCTGTCCCCCCAGCTGTGCCTGATGCCTTTCATCCTGGGCCTGCTGTCTGG CGGCGTGACCACCACCCCTTGGTCCCTGGCCAGGCCTCAGGGCTCCTGCTCCCTGGAGGGCG TGGAGATCAAGGGCGGCTCCTTCCGGCTGCTGCAGGAAGGCCAGGCTCTGGAGTACGTGTGC CCTTCCGGCTTCTACCCTTACCCTGTGCAGACAAGGACCTGTAGGTCCACCGGCTCTTGGTC CACACTGAAAACCCAGGACCAGAAAACCGTCCGGAAGGCCGAGTGCCGGGCCATCCACTGCC CTCGGCCTCACGACTTCGAGAACGGCGAGTACTGGCCTCGGTCCCCTTACTACAACGTGTCC GACGAGATCTCCTTCCACTGCTACGACGGCTACACCCTGCGGGGCTCCGCCAACAGGACCTG CCAGGTCAACGGCCGGTGGTCCGGCCAGACCGCCATCTGCGACAACGGCGCTGGCTACTGCT CCAACCCTGGCATCCCTATCGGCACCCGGAAGGTCGGCTCCCAGTACCGGCTGGAGGACTCC GTGACCTACCACTGCTCCAGAGGCCTGACCCTGAGAGGCTCCCAGCGGCGCACCTGTCAGGA AGGTGGCAGCTGGTCTGGCACCGAACCATCTTGCCAGGACTCCTTCATGTACGACACCCCTC AGGAAGTGGCCGAGGCCTTCCTGTCCTCCCTGACCGAGACAATCGAGGGCGTGGACGCCGAG GATGGCCACGGCCCTGGCGAGCAGCAGGCCGGTGCCATCGTGCTGGACCCCTCCGGCTCCAT

[0222] 45845704.1 39ATTORNEY DOCKET NO. MSD PC 139 PCT

[0223] GAACATCTACCTGGTGCTGGACGGCTCCGGCAGCATCGGCGCCTCCGACTTCACCGGCGCCA AGAAGAGCCTGGTCAACCTGATCGAGAAGGTGGCCTCCTACGGCGTGAAGCCTAGATACGGC CTGGTGACCTACGCCACCTACCCTAAGATCTGGGTGAAGGTGTCCGAGGCCGACTCCTCCAA CGCCGACTGGGTGACCAAGCAGCTGAACGAGATCAACTACGAGGACCACAAGCTGAAGTCCG GCACCAACACCAAGAAGGCCCTGCAGGCCGTCTACTCCATGATGTCCTGGCCTGACGACGTG CCTCCTGAGGGCTGGAACCGGACCCGGCACGTGATTATCCTGATGACCGACGGCCTGCACAA CATGGGCGGCGACCCTATCACCGTGATCGACGAGATCCGGGACCTGCTGTACATCGGCAAGG ACCGGAAGAACCCTCGGGAGGACTACCTGGACGTGTACGTGTTCGGCGTGGGCCCTCTGGTG AACCAGGTCAACATCAACGCCCTGGCCTCCAAGAAGGACAACGAGCAGCACGTGTTCAAGGT CAAGGACATGGAGAACCTGGAGGACGTGTTCTACCAGATGATCGATGAGTCCCAGTCCCTGA GCCTGTGCGGCATGGTCTGGGAGCACCGCAAGGGAACCGACTACCACAAGCAGCCTTGGCAG GCCAAGATCTCCGTGATCCGGCCTTCCAAGGGCCACGAGTCCTGCATGGGCGCCGTGGTGTC CGAGTACTTCGTGCTGACCGCCGCTCACTGCTTCACCGTGGACGACAAGGAACACTCCATCA AAGTCTCCGTGGGCGGCGAGAAGCGGGACCTGGAGATCGAGGTGGTGCTGTTCCACCCTAAC TACAACATCAACGGCAAGAAGGAAGCCGGCATCCCTGAGTTCTACGACTACGACGTGGCCCT GATCAAGCTGAAGAATAAGCTGAAGTATGGCCAGACCATCCGGCCTATCTGCCTGCCTTGCA CCGAGGGCACCACCAGGGCCCTGCGGCTGCCTCCTACCACCACCTGCCAGCAGCAGAAGGAA GAGCTGCTGCCTGCCCAGGACATCAAGGCCCTGTTCGTGTCCGAGGAAGAGAAGAAGCTGAC CCGGAAGGAAGTGTACATCAAGAACGGCGACAAGAAGGGCAGCTGCGAGCGGGACGCCCAGT ACGCCCCTGGCTACGATAAGGTCAAGGATATCTCCGAGGTGGTGACCCCTCGGTTCCTGTGC ACCGGCGGAGTGTCCCCCTACGCCGACCCTAACACCTGCAGAGGCGACTCTGGCGGCCCTCT GATCGTGCACAAGCGGTCCCGGTTCATCCAGGTCGGCGTGATCTCCTGGGGCGTGGTGGACG TGTGCAAGAACCAGAAGCGGCAGAAGCAGGTCCCCGCCCACGCCCGGGACTTCCACATCAAC CTGTTCCAGGTGCTGCCTTGGCTGAAGGAAAAGCTGCAGGATGAGGACCTGGGCTTCCTGTG

[0224] A (SEQ ID NO:27).

[0225] PCI 13-D includes a change in the factor D cleavage site, Lys258-Arg259-Lys260 from WT is substituted with Ala258-Asp259-Ala260. In addition, two amino acids at the C3b binding site, Asp279 and Asn285, are substituted with Gly279 and Asp285, respectively. The free cysteine at position 292 in wildtype factor B was substituted with a serine. PCI 13-D is a dominant positive analog of human factor B and an enhancer of the human alternative complement pathway.

[0226] Thus, in some forms, the factor B analog is PCI 13-D or a variant thereof.

[0227] In some forms, the complement factor B analog is SEQ ID NO:28, which represents amino acid sequence of human complement factor B protein analog PC113-D:

[0228] 45845704.1 40ATTORNEY DOCKET NO. MSD PC 139 PCT

[0229] MGSNLSPQLCLMPFILGLLSGGVTTTPWSLARPQGSCSLEGVEIKGGSFRLLQEGQALEYVC PSGFYPYPVQTRTCRSTGSWSTLKTQDQKTVRKAECRAIHCPRPHDFENGEYWPRSPYYNVS DEISFHCYDGYTLRGSANRTCQVNGRWSGQTAICDNGAGYCSNPGIPIGTRKVGSQYRLEDS VTYHCSRGLTLRGSQRRTCQEGGSWSGTEPSCQDSFMYDTPQEVAEAFLSSLTETIEGVDAE DGHGPGEQQADAIVLDPSGSMNIYLVLDGSGSIGASDFTGAKKSLVNLIEKVASYGVKPRYG LVTYATYPKIWVKVSEADSSNADWVTKQLNEINYEDHKLKSGTNTKKALQAVYSMMSWPDDV PPEGWNRTRHVIILMTDGLHNMGGDPITVIDEIRDLLYIGKDRKNPREDYLDVYVFGVGPLV NQVNINALASKKDNEQHVFKVKDMENLEDVFYQMIDESQSLSLCGMVWEHRKGTDYHKQPWQ AKISVIRPSKGHESCMGAWSEYFVLTAAHCFTVDDKEHSIKVSVGGEKRDLEIEWLFHPN YNINGKKEAGIPEFYDYDVALIKLKNKLKYGQTIRP ICLPCTEGTTRALRLPPTTTCQQQKE ELLPAQDIKALFVSEEEKKLTRKEVYIKNGDKKGSCERDAQYAPGYDKVKDISEWTPRFLC TGGVSPYADPNTCRGDSGGPLIVHKRSRFIQVGVISWGWDVCKNQKRQKQVPAHARDFHIN LFQVLPWLKEKLQDEDLGFL (SEQ ID NO:28) or is a fragment or variant thereof including Ala258-Asp259-Ala260, Gly279, and Asp285, respectively and optionally at least 70, 75, 80, 85, 90, 95, 96, 97, 98, or 99 percent sequence identity thereto.

[0230] SEQ ID NO: 29 is a nucleotide sequence encoding human complement factor B protein analog PCI 13-D:

[0231] ATGGGCTCCAACCTGTCCCCCCAGCTGTGCCTGATGCCTTTCATCCTGGGCCTGCTGTCTGG CGGCGTGACCACCACCCCTTGGTCCCTGGCCAGGCCTCAGGGCTCCTGCTCCCTGGAGGGCG TGGAGATCAAGGGCGGCTCCTTCCGGCTGCTGCAGGAAGGCCAGGCTCTGGAGTACGTGTGC CCTTCCGGCTTCTACCCTTACCCTGTGCAGACAAGGACCTGTAGGTCCACCGGCTCTTGGTC CACACTGAAAACCCAGGACCAGAAAACCGTCCGGAAGGCCGAGTGCCGGGCCATCCACTGCC CTCGGCCTCACGACTTCGAGAACGGCGAGTACTGGCCTCGGTCCCCTTACTACAACGTGTCC GACGAGATCTCCTTCCACTGCTACGACGGCTACACCCTGCGGGGCTCCGCCAACAGGACCTG CCAGGTCAACGGCCGGTGGTCCGGCCAGACCGCCATCTGCGACAACGGCGCTGGCTACTGCT CCAACCCTGGCATCCCTATCGGCACCCGGAAGGTCGGCTCCCAGTACCGGCTGGAGGACTCC GTGACCTACCACTGCTCCAGAGGCCTGACCCTGAGAGGCTCCCAGCGGCGCACCTGTCAGGA AGGTGGCAGCTGGTCTGGCACCGAACCATCTTGCCAGGACTCCTTCATGTACGACACCCCTC AGGAAGTGGCCGAGGCCTTCCTGTCCTCCCTGACCGAGACAATCGAGGGCGTGGACGCCGAG GATGGCCACGGCCCTGGCGAGCAGCAGGCCGATGCCATCGTGCTGGACCCCTCCGGCTCCAT GAACATCTACCTGGTGCTGGACGGCTCCGGCAGCATCGGCGCCTCCGACTTCACCGGCGCCA AGAAGAGCCTGGTCAACCTGATCGAGAAGGTGGCCTCCTACGGCGTGAAGCCTAGATACGGC CTGGTGACCTACGCCACCTACCCTAAGATCTGGGTGAAGGTGTCCGAGGCCGACTCCTCCAA CGCCGACTGGGTGACCAAGCAGCTGAACGAGATCAACTACGAGGACCACAAGCTGAAGTCCG

[0232] 45845704.1 41ATTORNEY DOCKET NO. MSD PC 139 PCT

[0233] GCACC ACACCAAGT AGGCCCTGCAGGCCGTCTACTCCATGATGTCCTGGCCTGACGACGTG CCTCCTGAGGGCTGGAACCGGACCCGGCACGTGATTATCCTGATGACCGACGGCCTGCACAA CATGGGCGGCGACCCTATCACCGTGATCGACGAGATCCGGGACCTGCTGTACATCGGCAAGG ACCGGAAGAACCCTCGGGAGGACTACCTGGACGTGTACGTGTTCGGCGTGGGCCCTCTGGTG AACCAGGTCAACATCAACGCCCTGGCCTCCAAGAAGGACAACGAGCAGCACGTGTTCAAGGT CAAGGACATGGAGAACCTGGAGGACGTGTTCTACCAGATGATCGATGAGTCCCAGTCCCTGA GCCTGTGCGGCATGGTCTGGGAGCACCGCAAGGGAACCGACTACCACAAGCAGCCTTGGCAG GCCAAGATCTCCGTGATCCGGCCTTCCAAGGGCCACGAGTCCTGCATGGGCGCCGTGGTGTC CGAGTACTTCGTGCTGACCGCCGCTCACTGCTTCACCGTGGACGACAAGGAACACTCCATCA AAGTCTCCGTGGGCGGCGAGAAGCGGGACCTGGAGATCGAGGTGGTGCTGTTCCACCCTAAC TACAACATCAACGGCAAGAAGGAAGCCGGCATCCCTGAGTTCTACGACTACGACGTGGCCCT GATCAAGCTGAAGAATAAGCTGAAGTATGGCCAGACCATCCGGCCTATCTGCCTGCCTTGCA CCGAGGGCACCACCAGGGCCCTGCGGCTGCCTCCTACCACCACCTGCCAGCAGCAGAAGGAA GAGCTGCTGCCTGCCCAGGACATCAAGGCCCTGTTCGTGTCCGAGGAAGAGAAGAAGCTGAC CCGGAAGGAAGTGTACATCAAGAACGGCGACAAGAAGGGCAGCTGCGAGCGGGACGCCCAGT ACGCCCCTGGCTACGATAAGGTCAAGGATATCTCCGAGGTGGTGACCCCTCGGTTCCTGTGC ACCGGCGGAGTGTCCCCCTACGCCGACCCTAACACCTGCAGAGGCGACTCTGGCGGCCCTCT GATCGTGCACAAGCGGTCCCGGTTCATCCAGGTCGGCGTGATCTCCTGGGGCGTGGTGGACG TGTGCAAGAACCAGAAGCGGCAGAAGCAGGTCCCCGCCCACGCCCGGGACTTCCACATCAAC CTGTTCCAGGTGCTGCCTTGGCTGAAGGAAAAGCTGCAGGATGAGGACCTGGGCTTCCTGTG

[0234] A (SEQ ID NO:29).

[0235] b. Exemplary PC139 analogs

[0236] The factor D cleavage site was studied and a complement factor B analog PC 139 was engineered (Figure 9). PC 139 is a potent inhibitor of human alternative complement pathway.

[0237] Thus, provided is factor B analog including the substitutions Lysine to Asparagine at position 258, Arginine to Alanine, Leucine, or Glycine at position 259, and Lysine to Threonine or Serine at position 260 of SEQ ID NO: 1. In a particular form, the substitution at 259 is Leucine, and the substitution at 260 is Threonine. Such polypeptides typically inhibit complement activity.

[0238] In a specific example, factor B analog has Asparagine, Leucine, and Threonine substitutions at the positions corresponding to the Lysine at position 258, Arginine at position 259 and Lysine at position 260 respectively relative to the wildtype protein (SEQ ID NO:1).

[0239] 45845704.1 42ATTORNEY DOCKET NO. MSD PC 139 PCT

[0240] In some forms, the factor B analog is a variant of SEQ ID NO:1 and optionally has at least 70, 75, 80, 85, 90, 95, 96, 97, 98, or 99 percent sequence identity thereto.

[0241] In some forms, the factor B analog has the amino acid sequence:

[0242] MGSNLSPQLCLMPFILGLLSGGVTTTPWSLARPQGSCSLEGVEIKGGSFRLLQEGQALEYVC PSGFYPYPVQTRTCRSTGSWSTLKTQDQKTVRKAECRAIHCPRPHDFENGEYWPRSPYYNVS DEISFHCYDGYTLRGSANRTCQVNGRWSGQTAICDNGAGYCSNPGIPIGTRKVGSQYRLEDS VTYHCSRGLTLRGSQRRTCQEGGSWSGTEPSCQDSFMYDTPQEVAEAFLSSLTETIEGVDAE DGHGPGEQQNLTIVLDPSGSMNIYLVLDGSDSIGASNFTGAKKCLVNLIEKVASYGVKPRYG LVTYATYPKIWVKVSEADSSNADWVTKQLNEINYEDHKLKSGTNTKKALQAVYSMMSWPDDV PPEGWNRTRHVIILMTDGLHNMGGDPITVIDEIRDLLYIGKDRKNPREDYLDVYVFGVGPLV NQVNINALASKKDNEQHVFKVKDMENLEDVFYQMIDESQSLSLCGMVWEHRKGTDYHKQPWQ AKISVIRPSKGHESCMGAWSEYFVLTAAHCFTVDDKEHSIKVSVGGEKRDLEIEWLFHPN YNINGKKEAGIPEFYDYDVALIKLKNKLKYGQTIRP ICLPCTEGTTRALRLPPTTTCQQQKE ELLPAQDIKALFVSEEEKKLTRKEVYIKNGDKKGSCERDAQYAPGYDKVKDISEWTPRFLC TGGVSPYADPNTCRGDSGGPLIVHKRSRFIQVGVISWGWDVCKNQKRQKQVPAHARDFHIN LFQVLPWLKEKLQDEDLGFL (SEQ ID NO: 12)

[0243] or is a fragment or variant thereof including N258, L259, and T260, and optionally at least 70, 75, 80, 85, 90, 95, 96, 97, 98, or 99 percent sequence identity thereto.

[0244] Thus, the complement factor B protein analogs that do not include a Lysine at position 258, Arginine at position 259 and Lysine at position 260. Mutation of Lysine at position 258, Arginine at position 259 and Lysine at position 260 can be combined with other mutations of a complement factor B protein.

[0245] Some forms of the present disclosure include a complement factor B protein analog wherein the factor D cleavage site has been mutated. In some forms, this mutation of the factor D cleavage site can include a deletion of the Lys258-Arg259-Lys260 or substitution of any of the amino acids with another amino acid(s). In some forms, these three amino acids can be substituted with any amino acid(s), that still allows for the complement factor B protein analog to retain at least some of the desired characteristic(s), such as the ability to resist C3b-dependent cleavage by factor D, to downregulate, to diminish or to ablate alternative complement activity. A substitution may be with one or more amino acids. In some forms, Lys258-Arg259-Lys260 is substituted with Asn258-Leu259-Thr260. In some forms, arginine at position 259 at the factor D cleavage site is substituted with one or more of any amino acid(s) to create a complement factor B analog that is resistant to C3b-dependent cleavage by factor D, binds C3b with higher affinity, forms inactive C3 convertase with C3b, 45845704.1 43ATTORNEY DOCKET NO. MSD PC 139 PCT

[0246] and inhibits human alternative complement pathway activity. In some forms, the Arg259 corresponds to the arginine at position 259 in SEQ ID NO:1. In some forms, Lys258-Arg259-Lys260 is substituted with Asn258-Leu259-Thr260 where Asn258 is glycosylated. In some forms, arginine at position 259 at the factor D cleavage site is substituted with Leu to create a complement factor B analog that is resistant to C3b-dependent cleavage by factor D, and blocks human alternative complement pathway activity. In some forms, substitution of Lys258-Arg259-Lys260 with Asn258-Leu259-Thr260 sequesters factor D in an inactive C3 convertase.

[0247] In some forms, the present disclosure provides complement factor B protein analogs that do not include an arginine at position 259. The present disclosure also provides methods of making or producing a complement factor B protein analog including mutating arginine at position 259.

[0248] Mutation of arginine at position 259 can be combined with other mutations of a complement factor B protein, e.g., other mutations as described herein. In some forms, mutation of arginine at position 259 can be combined with other mutations at the factor D cleavage site, Lys258-Arg259-Lys260.

[0249] In some forms, the factor D cleavage site of a complement factor B analog is mutated from Lys258-Arg259-Lys260 to Asn258-Leu259-Thr260. Other mutations in the same complement factor B analog include D279G and N285D mutations in the C3b binding site, and C292S mutation in the free cysteine site. Mutation of Lys at position 258 with Asn258 and mutation at Lys at position 260 with Thr260 creates a glycosylation site where Asn258 is glycosylated.

[0250] In some forms, the complement factor B analog is SEQ ID NO:3.

[0251] In some forms, a complement factor B protein analog of the present disclosure (SEQ ID NO:3), is an analog of SEQ ID NO:1 having the factor D cleavage site, Lys258-Arg259-Lys260, substituted with one amino acid, more than one amino acid, or deleted by one or more than one amino acid with no substitution.

[0252] Some forms of the instant disclosure include a substitution of an amino acid corresponding to amino acid 279 of SEQ ID NO:1, e.g., with an amino acid selected from the group including of glycine, alanine and asparagine. Some forms of the instant disclosure include a substitution of an amino acid corresponding to amino acid 279 of SEQ ID NO: 1 with an amino acid selected from the group including of glycine, alanine, valine, leucine and isoleucine. Some forms of the instant disclosure include a substitution of an amino acid corresponding to amino acid 279 of SEQ ID NO:1 with an amino acid selected from the 45845704.1 44ATTORNEY DOCKET NO. MSD PC 139 PCT

[0253] group including of asparagine, glutamic acid and glutamine. Some forms of the instant disclosure include a deletion of an amino acid corresponding to amino acid 279 of SEQ ID NO:1. Some forms of the instant disclosure include the insertion or substitution of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more amino acids immediately next to or in place of an amino acid corresponding to amino acid 279 of SEQ ID NO:1.

[0254] Some forms of the instant disclosure include a substitution of an amino acid corresponding to amino acid 285 of SEQ ID NO:1, e.g., with an amino acid selected from the group including of alanine and aspartic acid. Some forms of the instant disclosure include a substitution of an amino acid corresponding to amino acid 285 of SEQ ID NO: 1 with an amino acid selected from the group including of glycine, alanine, valine, leucine and isoleucine. Some forms of the instant disclosure include a substitution of an amino acid corresponding to amino acid 285 of SEQ ID NO:1 with an amino acid selected from the group including of aspartic acid, glutamic acid and glutamine. Some forms of the instant disclosure include a deletion of an amino acid corresponding to amino acid 285 of SEQ ID NO:1. Some forms of the instant disclosure include the insertion or substitution of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more amino acids immediately next to or in place of an amino acid corresponding to amino acid 285 of SEQ ID NO:1.

[0255] Some forms of the instant disclosure include mutations of the amino acids corresponding to 258, 259, 260, 279, 285, and 292 of SEQ ID NO:1 as described herein. The instant disclosure includes complement factor B protein analogs that include a combination of the mutations (substitutions, deletions and additions) discussed herein. In some forms, these complement factor B analogs retain one or more of the attributes of any other complement factor B analog discussed herein. The instant disclosure further provides analogs that are fragments (for example including one or more domains of a complement factor B protein having one or more of the amino acid mutations set forth herein) of these analogs that have one or more of the attributes of the analogs discussed above. In addition, the analogs may include additional amino acid substitutions, deletions or insertions (for example, conservative amino acid substitutions, truncations of the N-terminus or C-terminus, etc.) such that the analog has at least 99.5%, 99%, 98%, 95%, 90%, 85%, 80%, 75% or 75% identity with the corresponding wild-type complement factor B or, in the case of an analog including a fragment of complement factor B, the analog has at least 99.5%, 99%, 98%, 95%, 90%, 85%, 80%, 75% or 70% identity between the corresponding parts of the analog and wild-type complement factor B.

[0256] 45845704.1 45ATTORNEY DOCKET NO. MSD PC 139 PCT

[0257] In some forms, a complement factor B analog includes a mutation in the C3b binding domain and the complement factor B protein analog exhibits increased binding affinity to C3b as compared to the binding affinity of a corresponding native complement factor B protein to C3b. In some forms, a mutation in the C3b binding domain includes (i) a substitution or deletion of an aspartic acid corresponding to amino acid 279 of SEQ ID NO:1, a substitution or deletion of an asparagine corresponding to amino acid 285 of SEQ ID NO: 1 or both; or (ii) an insertion of at least one amino acid next to said aspartic acid or said asparagine. In some forms, this aspartic acid, asparagine or both are substituted with one or more amino acids. In some forms, an aspartic acid corresponding to amino acid 279 of SEQ ID NO:1 is substituted with glycine, alanine or asparagine. In some forms, an asparagine corresponding to amino acid 285 of SEQ ID NO:1 is substituted with glycine, alanine, or aspartic acid. In some forms, an aspartic acid corresponding to amino acid 279 of SEQ ID NO:1 is substituted with glycine and an asparagine corresponding to amino acid 285 of SEQ ID NO:1 is substituted with aspartic acid.

[0258] Thus, in some forms, the complement factor B analog is SEQ ID NO:3, which represents amino acid sequence of human complement factor B protein analog PCI 39:

[0259] Amino acid sequence of human complement factor B protein analog PCI 39:

[0260] MGSNLSPQLCLMPFILGLLSGGVTTTPWSLARPQGSCSLEGVEIKGGSFRLLQEGQALEYVC PSGFYPYPVQTRTCRSTGSWSTLKTQDQKTVRKAECRAIHCPRPHDFENGEYWPRSPYYNVS DEISFHCYDGYTLRGSANRTCQVNGRWSGQTAICDNGAGYCSNPGIPIGTRKVGSQYRLEDS VTYHCSRGLTLRGSQRRTCQEGGSWSGTEPSCQDSFMYDTPQEVAEAFLSSLTETIEGVDAE DGHGPGEQQNLTIVLDPSGSMNIYLVLDGSGSIGASDFTGAKKSLVNLIEKVASYGVKPRYG LVTYATYPKIWVKVSEADSSNADWVTKQLNEINYEDHKLKSGTNTKKALQAVYSMMSWPDDV PPEGWNRTRHVIILMTDGLHNMGGDPITVIDEIRDLLYIGKDRKNPREDYLDVYVFGVGPLV NQVNINALASKKDNEQHVFKVKDMENLEDVFYQMIDESQSLSLCGMVWEHRKGTDYHKQPWQ AKISVIRPSKGHESCMGAWSEYFVLTAAHCFTVDDKEHSIKVSVGGEKRDLEIEWLFHPN YNINGKKEAGIPEFYDYDVALIKLKNKLKYGQTIRP ICLPCTEGTTRALRLPPTTTCQQQKE ELLPAQDIKALFVSEEEKKLTRKEVYIKNGDKKGSCERDAQYAPGYDKVKDISEWTPRFLC TGGVSPYADPNTCRGDSGGPLIVHKRSRFIQVGVISWGWDVCKNQKRQKQVPAHARDFHIN LFQVLPWLKEKLQDEDLGFL (SEQ ID NO:3 ) or is a fragment or variant thereof including Asn258-Leu259-Thr260, Gly279, and Asp285, respectively and optionally at least 70, 75, 80, 85, 90, 95, 96, 97, 98, or 99 percent sequence identity thereto.

[0261] SEQ ID NO:4 is a nucleotide sequence encoding human complement factor B analog PCI 39:

[0262] 45845704.1 46ATTORNEY DOCKET NO. MSD PC 139 PCT

[0263] ATGGGCTCCAACCTGTCCCCCCAGCTGTGCCTGATGCCTTTCATCCTGGGCCTGCTGTCTGG CGGCGTGACCACCACCCCTTGGTCCCTGGCCAGGCCTCAGGGCTCCTGCTCCCTGGAGGGCG TGGAGATCAAGGGCGGCTCCTTCCGGCTGCTGCAGGAAGGCCAGGCTCTGGAGTACGTGTGC CCTTCCGGCTTCTACCCTTACCCTGTGCAGACAAGGACCTGTAGGTCCACCGGCTCTTGGTC CACACTGAAAACCCAGGACCAGAAAACCGTCCGGAAGGCCGAGTGCCGGGCCATCCACTGCC CTCGGCCTCACGACTTCGAGAACGGCGAGTACTGGCCTCGGTCCCCTTACTACAACGTGTCC GACGAGATCTCCTTCCACTGCTACGACGGCTACACCCTGCGGGGCTCCGCCAACAGGACCTG CCAGGTCAACGGCCGGTGGTCCGGCCAGACCGCCATCTGCGACAACGGCGCTGGCTACTGCT CCAACCCTGGCATCCCTATCGGCACCCGGAAGGTCGGCTCCCAGTACCGGCTGGAGGACTCC GTGACCTACCACTGCTCCAGAGGCCTGACCCTGAGAGGCTCCCAGCGGCGCACCTGTCAGGA AGGTGGCAGCTGGTCTGGCACCGAACCATCTTGCCAGGACTCCTTCATGTACGACACCCCTC AGGAAGTGGCCGAGGCCTTCCTGTCCTCCCTGACCGAGACAATCGAGGGCGTGGACGCCGAG GATGGCCACGGCCCTGGCGAGCAGCAGAACCTTACCATCGTGCTGGACCCCTCCGGCTCCAT GAACATCTACCTGGTGCTGGACGGCTCCGGCAGCATCGGCGCCTCCGACTTCACCGGCGCCA AGAAGAGCCTGGTCAACCTGATCGAGAAGGTGGCCTCCTACGGCGTGAAGCCTAGATACGGC CTGGTGACCTACGCCACCTACCCTAAGATCTGGGTGAAGGTGTCCGAGGCCGACTCCTCCAA CGCCGACTGGGTGACCAAGCAGCTGAACGAGATCAACTACGAGGACCACAAGCTGAAGTCCG GCACCAACACCAAGAAGGCCCTGCAGGCCGTCTACTCCATGATGTCCTGGCCTGACGACGTG CCTCCTGAGGGCTGGAACCGGACCCGGCACGTGATTATCCTGATGACCGACGGCCTGCACAA CATGGGCGGCGACCCTATCACCGTGATCGACGAGATCCGGGACCTGCTGTACATCGGCAAGG ACCGGAAGAACCCTCGGGAGGACTACCTGGACGTGTACGTGTTCGGCGTGGGCCCTCTGGTG AACCAGGTCAACATCAACGCCCTGGCCTCCAAGAAGGACAACGAGCAGCACGTGTTCAAGGT CAAGGACATGGAGAACCTGGAGGACGTGTTCTACCAGATGATCGATGAGTCCCAGTCCCTGA GCCTGTGCGGCATGGTCTGGGAGCACCGCAAGGGAACCGACTACCACAAGCAGCCTTGGCAG GCCAAGATCTCCGTGATCCGGCCTTCCAAGGGCCACGAGTCCTGCATGGGCGCCGTGGTGTC CGAGTACTTCGTGCTGACCGCCGCTCACTGCTTCACCGTGGACGACAAGGAACACTCCATCA AAGTCTCCGTGGGCGGCGAGAAGCGGGACCTGGAGATCGAGGTGGTGCTGTTCCACCCTAAC TACAACATCAACGGCAAGAAGGAAGCCGGCATCCCTGAGTTCTACGACTACGACGTGGCCCT GATCAAGCTGAAGAATAAGCTGAAGTATGGCCAGACCATCCGGCCTATCTGCCTGCCTTGCA CCGAGGGCACCACCAGGGCCCTGCGGCTGCCTCCTACCACCACCTGCCAGCAGCAGAAGGAA GAGCTGCTGCCTGCCCAGGACATCAAGGCCCTGTTCGTGTCCGAGGAAGAGAAGAAGCTGAC CCGGAAGGAAGTGTACATCAAGAACGGCGACAAGAAGGGCAGCTGCGAGCGGGACGCCCAGT ACGCCCCTGGCTACGATAAGGTCAAGGATATCTCCGAGGTGGTGACCCCTCGGTTCCTGTGC ACCGGCGGAGTGTCCCCCTACGCCGACCCTAACACCTGCAGAGGCGACTCTGGCGGCCCTCT

[0264] 45845704.1 47ATTORNEY DOCKET NO. MSD PC 139 PCT

[0265] GATCGTGCACAAGCGGTCCCGGTTCATCCAGGTCGGCGTGATCTCCTGGGGCGTGGTGGACG TGTGCAAGAACCAGAAGCGGCAGAAGCAGGTCCCCGCCCACGCCCGGGACTTCCACATCAAC CTGTTCCAGGTGCTGCCTTGGCTGAAGGAAAAGCTGCAGGATGAGGACCTGGGCTTCCTGTG

[0266] A (SEQ ID NO: 4).

[0267] In some forms, a complement factor B protein analog is a human complement factor B protein analog, based on a human complement factor protein.

[0268] A complement factor B protein analog of the instant disclosure may include at least one mutation corresponding to a mutation of SEQ ID NO:1 selected from the group including of K258N, R259L, K260T, D279G, N285D and C292S. In some forms, it includes mutations corresponding to K258N, R259L, K260T, D279G, N285D and C292S of SEQ ID NO: 1. In some forms, a complement factor B protein analog includes a mutation corresponding to K258N of SEQ ID NO: 1.

[0269] In some forms, the factor D cleavage site, Lys258-Arg259-Lys260, can be altered so the molecule can no longer be cleaved by factor D. In some forms, the factor D cleavage site, Lys258-Arg259-Lys260, can be altered so that the molecule exhibits high binding affinity to factor D as compared to the binding affinity of a corresponding native complement factor B protein to factor D. In some forms, the enzyme portion or domain, (e.g., the protease domain, which is a serine protease) of the molecule can be altered so that the molecule no longer has enzymatic activity or has reduced enzymatic activity (e.g., reduced by at least 2-fold, 5-fold, 10-fold, 50-fold or 100-fold). In some forms, a complement factor B protein analog includes a mutation in the active site of the serine protease domain, wherein the mutation decreases or ablates the complement factor B protein analog’s ability to cleave complement factor C3 as compared to a corresponding native complement factor B protein. In some forms, the factor D cleavage site, Lys258-Arg259-Lys260, can be altered so that the molecule can have a N-Glycosylation site at this site.

[0270] Other sites in factor B that can be altered include: 1) the binding site for properdin (the properdin binding domain) such that binding occurs with lower affinity (for example, such as 2 fold, 5 fold, 10 fold, 50 fold or 100 fold reduced affinity as compared to the wild type factor B protein) or with greater affinity (such as at least 2 fold, 5 fold, 10 fold, 50 fold or 100 fold increased affinity as compared to the wild type factor B); 2) the binding site for C3b protein (the C3b binding domain) such that binding occurs with lower affinity (such as at least 2 fold, 5 fold, 10 fold, 50 fold or 100 fold reduced affinity as compared to the wild type factor B protein) or with greater affinity (such as at least 2 fold, 5 fold, 10 fold, 50 fold or 100 fold increased affinity as compared to wild type factor B protein, for example, this may be 45845704.1 48ATTORNEY DOCKET NO. MSD PC 139 PCT

[0271] achieved by substituting the amino acid corresponding to position 279 and / or position 285 of SEQ ID NO:1 with other amino acids, for example, wherein the amino acid at the position corresponding to position 279 is substituted with asparagine (N), alanine (A) or glycine (G) and / or the amino acid at the position corresponding to position 285 is substituted with aspartic acid (D) or alanine (A)); 3) the site acted on by factor D such that factor D has reduced ability to cleave or no longer cleaves factor B analog to form Bb (for example, at the factor D cleavage site, at least one of the amino acids at the positions corresponding to position Lys258-Arg259-Lys260 of SEQ ID NO:1, for example, can be altered to Asn258-Leu259-Thr260 or; a combination of any of 1, 2, and / or 3 above).

[0272] In some forms, a complement factor B protein analog includes an alteration in the complement factor D cleavage site wherein the alteration decreases or ablates cleavage of the complement factor B protein analog by factor D protein. In some forms, an alteration in the factor D cleavage site includes (i) a substitution or deletion of an arginine corresponding to amino acid 259 of SEQ ID NO: 1, a substitution or deletion of one or both lysines corresponding to amino acid 258 or 260 of SEQ ID NO: 1 or a substitution or deletion of the arginine and both lysine; or (ii) an insertion next to the arginine, next to the one or both lysine, or next to the arginine and one or both of the lysine. In some forms, a complement factor B protein analog has amino acids corresponding to amino acids 258-260 of SEQ ID NO:1 each replaced with different amino acids.

[0273] In some forms of a human complement factor B protein analog is at least 90%, at least 95%, at least 98% or at least 99% identical to SEQ ID NOs:l, 2, 3, or 12. In some forms, a human complement factor B protein analog of the instant disclosure includes SEQ ID NO: 3 or 12.

[0274] 2. Fusion Proteins

[0275] Also disclosed herein are fusion proteins that includes a complement factor B analog or an anti-inflammatory molecule / Fc and dimers and multimers formed therefrom.

[0276] In some forms, fusion proteins disclosed herein are of formula I:

[0277] N-R1-R2-R3-C

[0278] wherein “N” represents the N-terminus of the fusion protein, “C” represents the C-terminus of the fusion protein, “Rl” is a second polypeptide such as an Fc protein, “R2” is an optional peptide / polypeptide linker domain, and “R3” is a first polypeptide such as a complement factor B analog or anti-inflammatory molecule. Alternatively, R3 can be the second polypeptide such as an Fc protein and Rl can be the first polypeptide such as a complement factor B analog or anti-inflammatory molecule. In some forms, the terms “first 45845704.1 49ATTORNEY DOCKET NO. MSD PC 139 PCT

[0279] polypeptide” and “first fusion partner” are used interchangeably unless otherwise indicated. In some form, the terms “second polypeptide” and “second fusion partner” are used interchangeably unless otherwise indicated.

[0280] The fusion proteins optionally contain a domain that functions to dimerize or multimerize two or more fusion proteins. The peptide / polypeptide linker domain can either be a separate domain or alternatively can be contained within one of one of the other domains of the fusion protein. Similarly, the domain that functions to dimerize or multimerize the fusion proteins can either be a separate domain or alternatively can be contained within one of the other domains of the fusion protein. In one form, the dimerization / multimerization domain and the peptide / polypeptide linker domain are the same.

[0281] For example, disclosed herein are fusion proteins containing a first polypeptide (e.g. complement factor B analog or anti-inflammatory molecule) coupled to a second polypeptide (e.g. Fc protein) to form fusion proteins. In some forms, complement factor B analog such as PC 139 is a first polypeptide including all or a part of the PC 139 protein fused (i) directly to a second polypeptide such as Fc protein or, (ii) optionally, fused to a linker peptide sequence that is fused to the second polypeptide. In some forms, a complement factor B analog such as PCI 39 is a second polypeptide and Fc is a first polypeptide optionally, fused to a linker peptide sequence. In some forms, an anti-inflammatory molecule is a first polypeptide including all or a part of the anti-inflammatory molecule protein fused (i) directly to a second polypeptide such as Fc protein or, (ii) optionally, fused to a linker peptide sequence that is fused to the second polypeptide.

[0282] Linker Domains

[0283] The disclosed fusion proteins optionally contain a peptide or polypeptide linker domain that separates the first polypeptide from the second polypeptide.

[0284] In some forms, suitable peptide / polypeptide linker domains include naturally occurring or non-naturally occurring peptides or polypeptides. Peptide linker sequences are at least 2 amino acids in length. Preferably the peptide or polypeptide domains are flexible peptides or polypeptides. A “flexible linker” herein refers to a peptide or polypeptide containing two or more amino acid residues joined by peptide bond(s) that provides increased rotational freedom for two polypeptides linked thereby than the two linked polypeptides would have in the absence of the flexible linker. Such rotational freedom allows two or more antigen binding sites joined by the flexible linker to each access target antigen(s) more efficiently. In some forms, flexible peptides / polypeptides include, but are not limited to, the amino acid sequences Gly-Ser, Gly-Ser-Gly-Ser (SEQ ID NO: 13), Ala-Ser, Gly-Gly-Gly-Ser 45845704.1 50ATTORNEY DOCKET NO. MSD PC 139 PCT

[0285] (SEQ ID NO: 14), (Gly4-Ser)3(SEQ ID NO: 15) and (Gly4-Ser)4(SEQ ID NO: 16). Additional flexible peptide / polypeptide sequences are well known in the art.

[0286] In some forms, the linker domain contains the hinge region of an immunoglobulin. In a preferred form, the hinge region is derived from a human immunoglobulin. Suitable human immunoglobulins that the hinge can be derived from include IgG, IgD and IgA. In a preferred form, the hinge region is derived from human IgG. Amino acid sequences of immunoglobulin hinge regions and other domains are well known in the art.

[0287] Dimerization and Multimerization Domains

[0288] The fusion proteins disclosed herein optionally contain a dimerization or multimerization domain that functions to dimerize or multimerize two or more fusion proteins. The domain that functions to dimerize or multimerize the fusion proteins can either be a separate domain, or alternatively can be contained within one of the other domains (the first polypeptide, second polypeptide, or peptide / polypeptide linker domain) of the fusion protein.

[0289] Autoimmune diseases are characterized by complex pathophysiological features and in some cases more than one inflammatory pathway is involved in the onset and pathogenesis of an autoimmune disease. Bispccific biologies that simultaneously target two disease modulators have improved efficacy and benefits for the treatment of autoimmune diseases (Spiess et al., I. Biol. Chem. (2013) 288:26583-26593; Alvarenga et al.. Drugs (2024) 84:1379-1394; Choi et al., Bimol. Ther. (2024) 32:708-722).

[0290] The current disclosure further provides Fc-fusion protein that is monospecific (e.g., homodimer) or bispecific (e.g., heterodimer).

[0291] In some forms, Fc fusion protein forms a homodimer of PC139 / Fc. In some forms, Fc fusion proteins form a multimer of PC139 / Fc. The human complement factor B analogs PCI 39 and PC139 / Fc have a higher affinity to C3b as compared to wild type human complement factor B and is resistant to C3b-dependent factor D cleavage, creating an inactive C3 convertase after binding to C3b. The PC 139 and PC139 / Fc also have a higher affinity to human factor D, sequestering factor D, the rate-limiting catalyst of AP in an inactive C3 convertase.

[0292] In some forms, a bispecific Fc fusion protein is not a homodimer of PC139-Fc, rather a Fc heterodimer with PC 139 on one arm and other anti-inflammatory molecule on the other arm. For example, as shown in Figure 17, the other molecule in the heterodimer is a soluble IE-17 receptor A (sIE-17RA) fused with TgG4 Fc (SEQ ID NO: 7 and 8). The partner for PC139-Fc heterodimer include but not limited to molecules that block various inflammatory 45845704.1 51ATTORNEY DOCKET NO. MSD PC 139 PCT

[0293] pathways, these inflammatory pathways include but not limited to IL4, IL6, IL13, IL17, IL22, IL23, and IL31 pathways, and Thymic Stromal lymphopoietin (TSLP), and 0X40-OX40L axis. The heterodimer Fc-fusion proteins could potentially be more effective in treating autoimmune diseases where more than one inflammatory pathway is involved.

[0294] A “dimerization domain” is formed by the association of at least two amino acid residues or of at least two peptides or polypeptides (which may have the same, or different, amino acid sequences). The peptides or polypeptides may interact with each other through covalent and / or non-covalent association(s). Preferred dimerization domains contain at least one cysteine that is capable of forming an intermolecular disulfide bond with a cysteine on the partner fusion protein. The dimerization domain can contain one or more cysteine residues such that disulfide bond(s) can form between the partner fusion proteins. In one form, dimerization domains contain one, two or three to about ten cysteine residues. In a preferred form, the dimerization domain is the hinge region of an immunoglobulin.

[0295] In one form, PC139 / Fc is a monomer. It is well known in the art to create a monomer Fc fusion protein instead of dimer Fc fusion protein, e.g., by mutating the Cysteines in the immunoglobin hinge region.

[0296] Additional exemplary dimerization domain can be any known in the art and include, but not limited to, coiled coils, acid patches, zinc fingers, calcium hands, a CHI -CL pair, an “interface” with an engineered “knob” and / or “protruberance” as described in U. S. Patent No.

[0297] 5,821,333, leucine zippers (e.g., from jun and / or fos) (U. S. Patent No. 5,932,448), SH2 (sre homology 2), SH3 (sre Homology 3) (Vidal, et al., Biochemistry, 43, 7336-44 ((2004)), phosphotyrosine binding (PTB) (Zhou, et al., Nature, 378:584-592 (1995)), WW (Sudol, Prog. Biochys. Mol. Bio., 65:113-132 (1996)), PDZ (Kim, et al., Nature, 378: 85-88 (1995); Komau, et al., Science, 269:1737-1740 (1995)) 14-3-3, WD40 (Hu, et al., J Biol Chem., 273, 33489-33494 (1998)) EH, Lim, an isoleucine zipper, a receptor dimer pair (e.g., interleukin-8 receptor (IL-8R); and integrin heterodimers such as LFA-1 and GPIIIb / IIIa), or the dimerization region(s) thereof, dimeric ligand polypeptides (e.g. nerve growth factor (NGF), neurotrophin-3 (NT-3), interleukin-8 (IL-8), vascular endothelial growth factor (VEGF), VEGF-C, VEGF-D, PDGF members, and brain-derived neurotrophic factor (BDNF) (Arakawa, et al., J. Biol. Chem., 269(45): 27833-27839 (1994) and Radziejewski, et al., Biochem., 32(48): 1350 (1993)) and can also be variants of these domains in which the affinity is altered. The polypeptide pairs can be identified by methods known in the art, including yeast two hybrid screens. Yeast two hybrid screens are described in U. S. Pat. Nos.

[0298] 5,283,173 and 6,562,576. Affinities between a pair of interacting domains can be determined 45845704.1 52ATTORNEY DOCKET NO. MSD PC 139 PCT

[0299] using methods known in the art, including as described in Katahira, et al., J. Biol. Chem., 277, 9242-9246 (2002)). Alternatively, a library of peptide sequences can be screened for heterodimerization, for example, using the methods described in WO 01 / 00814. Useful methods for protein-protein interactions arc also described in U. S. Patent No. 6,790,624.

[0300] A “multimerization domain” is a domain that causes three or more peptides or polypeptides to interact with each other through covalent and / or non-covalent association(s). Suitable multimerization domains include, but are not limited to, coiled-coil domains. A coiled-coil is a peptide sequence with a contiguous pattern of mainly hydrophobic residues spaced 3 and 4 residues apart, usually in a sequence of seven amino acids (heptad repeat) or eleven amino acids (undecad repeat), which assembles (folds) to form a multimeric bundle of helices. Coiled-coils with sequences including some irregular distribution of the 3 and 4 residues spacing are also contemplated. Hydrophobic residues are in particular the hydrophobic amino acids Vai, He, Eeu, Met, Tyr, Phe and Trp. “Mainly hydrophobic” means that at least 50% of the residues must be selected from the mentioned hydrophobic amino acids.

[0301] The coiled coil domain may be derived from laminin. In the extracellular space, the hctcrotrimcric coiled coil protein laminin plays an important role in the formation of basement membranes. Apparently, the multifunctional oligomeric structure is required for laminin function. Coiled coil domains may also be derived from the thrombospondins in which three (TSP-1 and TSP-2) or five (TSP-3, TSP-4 and TSP-5) chains are connected, or from COMP (COMPcc) (Guo, et at., EMBO J., 1998, 17: 5265-5272) which folds into a parallel five-stranded coiled coil (Malashkevich, et al., Science, 274: 761-765 (1996)).

[0302] Additional coiled-coil domains derived from other proteins, and other domains that mediate polypeptide multimerization are known in the art and are suitable for use in the disclosed fusion proteins.

[0303] In some forms, the disclosed polypeptides such as complement factor B analogs, antiinflammatory molecues, fusion proteins, or fragments thereof can be induced to form multimers by binding to a second multivalent polypeptide, such as an antibody. Antibodies suitable for use to multimerize the disclosed polypeptides, fusion proteins, or fragments thereof include, but are not limited to, IgM antibodies and cross-linked, multivalent IgG, IgA, IgD, or IgE complexes.

[0304] 45845704.1 53ATTORNEY DOCKET NO. MSD PC 139 PCT

[0305] i. First Polypeptide

[0306] a. Complement factor B analog

[0307] In some forms, the first polypeptide or the first fusion partner includes a complement factor B analog.

[0308] Exemplary analogs are introduced above, and any such analogs can be a first polypeptide of the disclosed fusion proteins.

[0309] Additional complement factor B analogs are disclosed in U. S. Patent No. 9,228,003, the entire contents of which is specifically incorporated by reference herein in its entirety, and can be used as the first polypeptide in the disclosed fusion proteins.

[0310] In specific forms, the first polypeptide is SEQ ID NO:2, 3, 12, 28, 28, 30, or 31 or a fragment or variant thereof with at least 65, 70, 75, 80, 85, 90, 95, 96, 97, 98, or 99 percent sequence identity thereto.

[0311] b. Anti-inflammatory Molecules

[0312] In some forms, the first polypeptide or the first fusion partner includes an antiinflammatory molecule such as a cytokine, metalloprotease, or other molecule including, but not limited to IL-10, TNF-a, TGF-beta, IFN-y, IL-17, IL-6, IL-23, IL-22, IL-21, and MMPs.

[0313] In some forms the anti-inflammatory molecule includes a soluble IL- 17 receptor A (slL-17RA). Amino acid sequences for IL-17 receptor A is known in the art and include, for example, splQ96F46II17RA_HUMAN Interleukin- 17 receptor A OS=Homo sapiens OX=9606 GN=IL17RA PE=1 SV=2, GenBank: AAH11624.1, which is specifically incorporated by reference herein in its entirety. The first polypeptide is typically a soluble portion of the receptor or fragment or variant thereof, e.g., with at least 65, 70, 75, 80, 85, 90, 95, 96, 97, 98, or 99 percent sequence identity thereto.

[0314] An exemplary sequence for a soluble IL- 17 receptor A is LRLLDHRALVCSQPGLNCTVKNSTCLDDSWIHPRNLTPSSPKDLQIQLHFAHTQQGD LFPVAHIEWTLQTDAS ILYLEGAELSVLQLNTNERLCVRFEFLSKLRHHHRRWRFTFSHFW DPDQEYEVTVHHLPKP IPDGDPNHQSKNFLVPDCEHARMKVTTPCMSSGSLWDPNITVETLE AHQLRVSFTLWNESTHYQILLTSFPHMENHSCFEHMHHIPAPRPEEFHQRSNVTLTLRNLKG CCRHQVQIQPFFSSCLNDCLRHSATVSCPEMPD (SEQ ID NO:25).

[0315] Thus, in some forms, the first polypeptide is (SEQ ID NO:25) or a fragment or variant thereof, e.g., with at least 65, 70, 75, 80, 85, 90, 95, 96, 97, 98, or 99 percent sequence identity thereto.

[0316] In some forms the anti-inflammatory molecule includes but are not limited to molecules that block inflammatory pathways, these inflammatory pathways include, but are 45845704.1 54ATTORNEY DOCKET NO. MSD PC 139 PCT

[0317] not limited to, the pathways initiated by IL4, IL6, IL13, IL17, IL22, IL23, IL31, Thymic Stromal lymphopoietin (TSLP), and OX40-OX40L axis. The anti-inflammatory molecules against these pathways include, but are not limited to, antibody fragments (e.g., scFv, Fab) against these inflammatory molecules that include, but arc not limited to, IL4, IL6, IL13, IL17, IL22, IL23, IL31, TSLP, and 0X40. The anti-inflammatory molecules against these pathways include, but are not limited to, soluble receptors that can bind these inflammatory molecules that include, but are not limited to, IL4, IL6, IL13, IL17, IL22, IL23, IL31, TSLP, and 0X40.

[0318] ii. Second Polypeptide

[0319] The presence of the second polypeptide can alter the solubility, stability, affinity and / or valency of the first fusion polypeptide. As used herein, “valency” refers to the number of binding sites available per molecule. In one form the second polypeptide is a polypeptide from a different source or different protein (e.g., such as a heterologous polypeptide such as albumin, immunoglobulin or portion thereof, such as an immunoglobulin Fc domain).

[0320] Thus, in some forms, the second polypeptide is an immunoglobulin Fc domain.

[0321] In some forms, a second polypeptide or a second fusion partner includes human immunoglobulin Fc. In some forms, the second polypeptide or the second fusion partner is an IgG Fc or variant thereof. In some forms, the second polypeptide or the second fusion partner is an IgG4 Fc or variant thereof.

[0322] In some forms, the immunoglobulin constant domain may contain one or more amino acid insertions, deletions or substitutions that enhance binding to specific cell types, increase the bioavailablity, or increase the stability of the first polypeptides, fusion proteins, or fragments thereof. Suitable amino acid substitutions include conservative and nonconservative substitutions.

[0323] The Fc portion of the fusion protein may be varied by isotype or subclass, may be a chimeric or hybrid, and / or may be modified, for example to improve effector functions, control of half-life, tissue accessibility, augment biophysical characteristics such as stability, and improve efficiency of production (and less costly). Many modifications useful in construction of disclosed fusion proteins and methods for making them are known in the art, see for example Mueller, et al., Mol. Immun., 34(6):441-452 (1997), Swann, et al., Cur. Opin. Inimun., 20:493-499 (2008), and Presta, Cur. Opin. Immun. 20:460-470 (2008). In some forms the Fc region is the native IgGL IgG2, or IgG4 Fc region. In some forms the Fc region is a hybrid, for example a chimeric including of IgG2 / IgG4 Fc constant regions.

[0324] Modifications to the Fc region include, but are not limited to, IgG4 modified to prevent 45845704.1 55ATTORNEY DOCKET NO. MSD PC 139 PCT

[0325] binding to Fc gamma receptors and complement, IgGl modified to improve binding to one or more Fc gamma receptors, IgG 1 modified to minimize effector function (amino acid changes), IgGl with altered / no glycan (typically by changing expression host), and IgGl with altered pH-dcpcndcnt binding to FcRn. The Fc region may include the entire hinge region, or less than the entire hinge region.

[0326] Another form includes IgG2-4 hybrids and lgG4 mutants that have reduced binding to FcR which increase their half life. Representative IgG2-4 hybrids and IgG4 mutants are described in Angal, S. et al., Molecular Immunology, 30(1): 105- 108 (1993); Mueller, J. et al., Molecular Immonology, 34(6): 441-452 (1997); and U. S. Patent No. 6,982,323 to Wang et al. In some forms the IgGl and / or IgG2 domain is deleted for example, Angal et al. describe IgGl and IgG2 having serine 241 replaced with a proline.

[0327] In some forms, the second polypeptide or the second fusion partner is selected from the group including one or more immunoglobulin Fc region, an albumin-binding domain, a transferrin or transferrin-binding domain, an antibody mimetic protein, a cytokine, a growth factor, a cell-penetrating peptide, an antimicrobial peptide, a stability-enhancing polypeptide, or a combination thereof.

[0328] In some forms, the first polypeptide may be fused to a second polypeptide. In some forms, the factor B analogs such as but not limited to PC 139 may be fused to a second polypeptide. In some forms, an anti-inflammatory described herein may be fused to a second polypeptide.

[0329] The fusion proteins can be dimerized or multimerized. Dimerization or multimerization can occur between or among two or more fusion proteins through dimerization or multimerization domains. Alternatively, dimerization or multimerization of fusion proteins can occur by chemical crosslinking. The dimers or multimers that are formed can be homodimeric / homomultimeric or heterodimeric / heteromultimeric.

[0330] Thus, in some forms, an Fc domain is capable of forming a dimer with another Fc domain. In some forms, a complement factor B analog is capable of forming dimers (e.g., homologous dimers), such as, but not limited to, through interactions of Fc domains. In some forms, a complement factor B analog does not form dimers or the majority of a complement factor B analog population / preparation is in the form of monomers. In some forms, a complement factor B analog including an Fc domain does not form dimers or the majority of this complement factor B analog population / preparation is in the form of monomers. In some forms, a complement factor B analog includes an Fc domain that has one or mutations of a cysteine(s) in the Fc domain sequence, e.g., a cysteine involved in dimerization of the Fc 45845704.1 56ATTORNEY DOCKET NO. MSD PC 139 PCT

[0331] domain. In some forms, a complement factor B analog includes an Fc domain that has one or mutations of a free cysteine(s) in the Fc domain sequence. In some forms, a cysteine(s) is substituted with an amino acid selected from the group consisting of histidine, isoleucine, leucine, methionine, phenylalanine, serine, threonine, tyrosine, and valine. In some forms, a cysteine is deleted. In some forms, an amino acid sequence linker is used between amino acid sequences for a complement factor B analog and an Fc region. In some forms, this linker is one amino acid, e.g., arginine.

[0332] Fc domains can include one, two, or all three of an immunoglobulin hinge domain, CH2 domain, and CH3 domain. Fc domains are known in the art. See, for example, Fc domains that can be used in the disclosed fusion proteins include, but are not limited to, DBA13400.1 TPA: IGHG4*09, partial [Homo sapiens] 326, GenBank:

[0333] DBA13400.1; and splP01861IIGHG4_HUMAN Immunoglobulin heavy constant gamma 4 OS=Homo sapiens OX=9606 GN=IGHG4 PE=1 SV=2, each of which is specifically incorporated by reference herein in its entirety, and fragments and variants thereof with at least 65, 70, 75, 80, 85, 90, 95, 96, 97, 98, or 99 percent sequence identity thereto.

[0334] Exemplary Fc domains include, but are not limited to, ESKYGPPCPPCPAPEFLGGPSVFLFPPKPKDTLMISRTPEVTCVWDVSQEDPEVQFNWYVD GVEVHNAKTKPREEQFNSTYRWSVLTVLHQDWLNGKEYKCKVSNKGLPSSIEKTISKAKGQ PREPQVYTLPPSQEEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSF FLYSKLTVDKSRWQEGNVFSCSVMHEALHNHYTQKSLSLSLGK (SEQ ID NO: 19), ESKYGPPCPSCP APEFLGGP SVFLFPPKPKDTLM SRTPEVTCVWDVSQEDPEVQFNWYVD GVEVHNAKTKPREEQFNSTYRWSVLTVLHQDWLNGKEYKCKVSNKGLPSSIEKTISKAKGQ PREPQVYTLPPSQEEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSF FLYSRLTVDKSRWQEGNVFSCSVMHEALHNHYTQKSLSLSLEL (SEQ ID NO:20), ESKYGPPCPSCP APEFLGGP SVFLFPPKPKDTLM SRTPEVTCVWDVSQEDPEVQFNWYVD GVEVHNAKTKPREEQFNSTYRWSVLTVLHQDWLNGKEYKCKVSNKGLPSSIEKTISKAKGQ PREPQVYTLPPSQEEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSF FLYSKLTVDKSRWQEGNVFSCSVMHEALHNHYTQKSLSLSLGK (SEQ ID NO:21), FPPKPKDTLMISRTPEVTCVWDVSQEDPEVQFNWYVDGVEVHNAKTKPREEQFNSTYRWS VLTVLHQDWLNGKEYKCKVSNKGLPSSIEKTISKAKGQPREPQVYTLPPSQEEMTKNQVSLT CLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSRLTVDKSRWQEGNVFSCSVM HEALHNHYTQKSLSLSPGK (SEQ ID NO:22),

[0335] SPPCPSCP APEFLGGP SVFLFPPKPKDTLMISRTPEVTCVWDVSQEDPEVQFNWYVDGVEV HNAKTKPREEQFNSTYRWSVLTVLHQDWLNGKEYKCKVSNKGLPSSIEKTISKAKGQPREP

[0336] 45845704.1 57ATTORNEY DOCKET NO. MSD PC 139 PCT

[0337] QVYTLPPSQEEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYS RLTVDKSRWQEGNVFSCSVMHEALHNHYTQKSLSLSPGK (SEQ ID NO:23), and SNTKVDKRVESKYGPPCPSCPAPEFLGGPSVFLFPPKPKDTLMISRTPEVTCWVDVSQEDP EVQFNWYVDGVEVHNAKTKPREEQFNSTYRWSVLTVLHQDWLNGKEYKCKVSNKGLPSSIE KTISKAKGQPREPQVYTLPPSQEEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTP PVLDSDGSFFLYSRLTVDKSRWQEGNVFSCSVMHEALHNHYTQKSLSLSLGK (SEQ ID NO: 24).

[0338] In some forms, the second polypeptide is any one of SEQ ID NOS: 19-24 with or without the hinge domain and / or any linker sequence, or a fragment or variant of the foregoing, e.g., having least 65, 70, 75, 80, 85, 90, 95, 96, 97, 98, or 99 percent sequence identity thereto.

[0339] 3. Exemplary Fusion Proteins

[0340] a. Complement Factor B Fusion / FC Proteins

[0341] In some forms, compositions include a fusion protein including complement factor B analogs and Fc proteins. In some forms, the Fc is a human IgG Fc. In some forms, the human IgG Fc is IgG4 Fc. The Fc could be placed at the N-terminus or C-terminus of the disclosed complement factor B analogs. In some forms, the disclosed complement factor B analog is PC139 (SEQ ID NO:3). PC139 / Fc represents fusion protein where Fc is in N-terminus and PC139 is on the C-terminus (SEQ ID NOS: 5 and 6). PC147 / Fc represents fusion protein where Fc is in C-terminus and PC139 is on the N-terminus (SEQ ID NOS:17 and 18).

[0342] The PC139 / Fc has the signal sequence of PC139 at the N-terminus of the fusion protein (the first 25 amino acids in SEQ ID NO:5), followed by IgG4 Fc, followed by PC139 without a signal peptide sequence (SEQ ID NO:5; SEQ ID NO: 6). Fc fusion could further increase the analog’s half-life and stability.

[0343] In some forms, the fusion protein is a PC139 / Fc fusion protein having the following amino acid sequence:

[0344] MGSNLSPQLCLMPFILGLLSGGVTTTPGSESKYGPPCPPCPAPEFLGGPSVFLFPPKPKDTL MISRTPEVTCVWDVSQEDPEVQFNWYVDGVEVHNAKTKPREEQFNSTYRWSVLTVLHQDW LNGKEYKCKVSNKGLPSSIEKTISKAKGQPREPQVYTLPPSQEEMTKNQVSLTCLVKGFYPS DIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQEGNVFSCSVMHEALHNHYT QKSLSLSLGKAAATPWSLARPQGSCSLEGVEIKGGSFRLLQEGQALEYVCPSGFYPYPVQTR TCRSTGSWSTLKTQDQKTVRKAECRAIHCPRPHDFENGEYWPRSPYYNVSDEISFHCYDGYT LRGSANRTCQVNGRWSGQTAICDNGAGYCSNPGIPIGTRKVGSQYRLEDSVTYHCSRGLTLR GSQRRTCQEGGSWSGTEPSCQDSFMYDTPQEVAEAFLSSLTETIEGVDAEDGHGPGEQQNLT

[0345] 45845704.1 58ATTORNEY DOCKET NO. MSD PC 139 PCT

[0346] IVLDPSGSMNIYLVLDGSGSIGASDFTGAKKSLVNLIEKVASYGVKPRYGLVTYATYPKIWV KVSEADSSNADWVTKQLNEINYEDHKLKSGTNTKKALQAVYSMMSWPDDVPPEGWNRTRHVI ILMTDGLHNMGGDPITVIDEIRDLLYIGKDRKNPREDYLDVYVFGVGPLVNQVNINALASKK DNEQHVFKVKDMENLEDVFYQMIDESQSLSLCGMVWEHRKGTDYHKQPWQAKISVIRPSKGH ESCMGAWSEYFVLTAAHCFTVDDKEHSIKVSVGGEKRDLEIEVVLFHPNYNINGKKEAGIP EFYDYDVALIKLKNKLKYGQTIRP ICLPCTEGTTRALRLPPTTTCQQQKEELLPAQDIKALF VSEEEKKLTRKEVYIKNGDKKGSCERDAQYAPGYDKVKDISEWTPRFLCTGGVSPYADPNT CRGDSGGPLIVHKRSRFIQVGVISWGWDVCKNQKRQKQVPAHARDFHINLFQVLPWLKEKL QDEDLGFL (SEQ ID NO:5)

[0347] or is a fragment or variant thereof including N258, L259, and T260, and optionally at least 70, 75, 80, 85, 90, 95, 96, 97, 98, or 99 percent sequence identity thereto.

[0348] SEQ ID NO:6 provides a nucleotide sequence encoding human complement factor B protein analog PC139 / Fc:

[0349] ATGGGCTCCAACCTGTCCCCCCAGCTGTGCCTGATGCCTTTCATCCTGGGCCTGCTGTCTGG CGGCGTGACCACCACCCCTGGATCCGAGTCCAAATATGGTCCCCCATGCCCACCATGCCCAG CACCTGAGTTCCTGGGGGGACCATCAGTCTTCCTGTTCCCCCCAAAACCCAAGGACACTCTC ATGATCTCCCGGACCCCTGAGGTCACGTGCGTGGTGGTGGACGTGAGCCAGGAAGACCCCGA GGTCCAGTTCAACTGGTACGTGGATGGCGTGGAGGTGCATAATGCCAAGACAAAGCCGCGGG AGGAGCAGTTCAACAGCACGTACCGTGTGGTCAGCGTCCTCACCGTCCTGCACCAGGACTGG CTGAACGGCAAGGAGTACAAGTGCAAGGTCTCCAACAAAGGCCTCCCGTCCTCCATCGAGAA AACCATCTCCAAAGCCAAAGGGCAGCCCCGAGAGCCACAGGTGTACACCCTGCCCCCATCCC AGGAGGAGATGACCAAGAACCAGGTCAGCCTGACCTGCCTGGTCAAAGGCTTCTACCCCAGC GACATCGCCGTGGAGTGGGAGAGCAATGGGCAGCCGGAGAACAACTACAAGACCACGCCTCC CGTGCTGGACTCCGACGGCTCCTTCTTCCTCTACAGCAAGCTTACCGTGGACAAGAGCAGGT GGCAGGAGGGGAATGTCTTCTCATGCTCCGTGATGCATGAGGCTCTGCACAACCACTACACA CAGAAGAGCCTCTCCCTGTCTCTGGGTAAAGCGGCCGCCACCCCTTGGTCCCTGGCCAGGCC TCAGGGCTCCTGCTCCCTGGAGGGCGTGGAGATCAAGGGCGGCTCCTTCCGGCTGCTGCAGG AAGGCCAGGCTCTGGAGTACGTGTGCCCTTCCGGCTTCTACCCTTACCCTGTGCAGACAAGG ACCTGTAGGTCCACCGGCTCTTGGTCCACACTGAAAACCCAGGACCAGAAAACCGTCCGGAA GGCCGAGTGCCGGGCCATCCACTGCCCTCGGCCTCACGACTTCGAGAACGGCGAGTACTGGC CTCGGTCCCCTTACTACAACGTGTCCGACGAGATCTCCTTCCACTGCTACGACGGCTACACC CTGCGGGGCTCCGCCAACAGGACCTGCCAGGTCAACGGCCGGTGGTCCGGCCAGACCGCCAT CTGCGACAACGGCGCTGGCTACTGCTCCAACCCTGGCATCCCTATCGGCACCCGGAAGGTCG GCTCCCAGTACCGGCTGGAGGACTCCGTGACCTACCACTGCTCCAGAGGCCTGACCCTGAGA

[0350] 45845704.1 59ATTORNEY DOCKET NO. MSD PC 139 PCT

[0351] GGCTCCCAGCGGCGCACCTGTCAGGAAGGTGGCAGCTGGTCTGGCACCGAACCATCTTGCCA GGACTCCTTCATGTACGACACCCCTCAGGAAGTGGCCGAGGCCTTCCTGTCCTCCCTGACCG AGACAATCGAGGGCGTGGACGCCGAGGATGGCCACGGCCCTGGCGAGCAGCAGAACCTTACC ATCGTGCTGGACCCCTCCGGCTCCATGAACATCTACCTGGTGCTGGACGGCTCCGGCAGCAT CGGCGCCTCCGACTTCACCGGCGCCAAGAAGAGCCTGGTCAACCTGATCGAGAAGGTGGCCT CCTACGGCGTGAAGCCTAGATACGGCCTGGTGACCTACGCCACCTACCCTAAGATCTGGGTG AAGGTGTCCGAGGCCGACTCCTCCAACGCCGACTGGGTGACCAAGCAGCTGAACGAGATCAA CTACGAGGACCACAAGCTGAAGTCCGGCACCAACACCAAGAAGGCCCTGCAGGCCGTCTACT CCATGATGTCCTGGCCTGACGACGTGCCTCCTGAGGGCTGGAACCGGACCCGGCACGTGATT ATCCTGATGACCGACGGCCTGCACAACATGGGCGGCGACCCTATCACCGTGATCGACGAGAT CCGGGACCTGCTGTACATCGGCAAGGACCGGAAGAACCCTCGGGAGGACTACCTGGACGTGT ACGTGTTCGGCGTGGGCCCTCTGGTGAACCAGGTCAACATCAACGCCCTGGCCTCCAAGAAG GACAACGAGCAGCACGTGTTCAAGGTCAAGGACATGGAGAACCTGGAGGACGTGTTCTACCA GATGATCGATGAGTCCCAGTCCCTGAGCCTGTGCGGCATGGTCTGGGAGCACCGCAAGGGAA CCGACTACCACAAGCAGCCTTGGCAGGCCAAGATCTCCGTGATCCGGCCTTCCAAGGGCCAC GAGTCCTGCATGGGCGCCGTGGTGTCCGAGTACTTCGTGCTGACCGCCGCTCACTGCTTCAC CGTGGACGACAAGGAACACTCCATCAAAGTCTCCGTGGGCGGCGAGAAGCGGGACCTGGAGA TCGAGGTGGTGCTGTTCCACCCTAACTACAACATCAACGGCAAGAAGGAAGCCGGCATCCCT GAGTTCTACGACTACGACGTGGCCCTGATCAAGCTGAAGAATAAGCTGAAGTATGGCCAGAC CATCCGGCCTATCTGCCTGCCTTGCACCGAGGGCACCACCAGGGCCCTGCGGCTGCCTCCTA CCACCACCTGCCAGCAGCAGAAGGAAGAGCTGCTGCCTGCCCAGGACATCAAGGCCCTGTTC GTGTCCGAGGAAGAGAAGAAGCTGACCCGGAAGGAAGTGTACATCAAGAACGGCGACAAGAA GGGCAGCTGCGAGCGGGACGCCCAGTACGCCCCTGGCTACGATAAGGTCAAGGATATCTCCG AGGTGGTGACCCCTCGGTTCCTGTGCACCGGCGGAGTGTCCCCCTACGCCGACCCTAACACC TGCAGAGGCGACTCTGGCGGCCCTCTGATCGTGCACAAGCGGTCCCGGTTCATCCAGGTCGG CGTGATCTCCTGGGGCGTGGTGGACGTGTGCAAGAACCAGAAGCGGCAGAAGCAGGTCCCCG CCCACGCCCGGGACTTCCACATCAACCTGTTCCAGGTGCTGCCTTGGCTGAAGGAAAAGCTG CAGGATGAGGACCTGGGCTTCCTGTGA (SEQ ID NO:6).

[0352] In some forms, the fusion protein is a PC147 / Fc fusion protein having the following amino acid sequence:

[0353] MGSNLSPQLCLMPFILGLLSGGVTTTPWSLARPQGSCSLEGVEIKGGSFRLLQEGQALEYVC PSGFYPYPVQTRTCRSTGSWSTLKTQDQKTVRKAECRAIHCPRPHDFENGEYWPRSPYYNVS DEISFHCYDGYTLRGSANRTCQVNGRWSGQTAICDNGAGYCSNPGIPIGTRKVGSQYRLEDS VTYHCSRGLTLRGSQRRTCQEGGSWSGTEPSCQDSFMYDTPQEVAEAFLSSLTETIEGVDAE

[0354] 45845704.1 60ATTORNEY DOCKET NO. MSD PC 139 PCT

[0355] DGHGPGEQQNLTIVLDPSGSMNIYLVLDGSGSIGASDFTGAKKSLVNLIEKVASYGVKPRYG LVTYATYPKIWVKVSEADSSNADWVTKQLNEINYEDHKLKSGTNTKKALQAVYSMMSWPDDV PPEGWNRTRHVIILMTDGLHNMGGDPITVIDEIRDLLYIGKDRKNPREDYLDVYVFGVGPLV NQVNINALASKKDNEQHVFKVKDMENLEDVFYQMIDESQSLSLCGMVWEHRKGTDYHKQPWQ AKISVIRPSKGHESCMGAWSEYFVLTAAHCFTVDDKEHSIKVSVGGEKRDLEIEWLFHPN YNINGKKEAGIPEFYDYDVALIKLKNKLKYGQTIRP ICLPCTEGTTRALRLPPTTTCQQQKE ELLPAQDIKALFVSEEEKKLTRKEVYIKNGDKKGSCERDAQYAPGYDKVKDISEWTPRFLC TGGVSPYADPNTCRGDSGGPLIVHKRSRFIQVGVISWGWDVCKNQKRQKQVPAHARDFHIN LFQVLPWLKEKLQDEDLGFLGSESKYGPPCPPCPAPEFLGGPSVFLFPPKPKDTLMISRTPE VTCVWDVSQEDPEVQFNWYVDGVEVHNAKTKPREEQFNSTYRVVSVLTVLHQDWLNGKEYK CKVSNKGLPSSIEKTISKAKGQPREPQVYTLPPSQEEMTKNQVSLTCLVKGFYPSDIAVEWE SNGQPENNYKTTPPVLDSDGSFFLYSRLTVDKSRWQEGNVFSCSVMHEALHNHYTQKSLSLS LGK (SEQ ID NO: 17),

[0356] or is a fragment or variant thereof including N258, L259, and T260, and optionally at least 70, 75, 80, 85, 90, 95, 96, 97, 98, or 99 percent sequence identity thereto.

[0357] In some forms, SEQ ID NO: 18 provides a nucleotide sequence encoding human complement factor B protein analog PC147 / Fc.

[0358] ATGGGCTCCAACCTGTCCCCCCAGCTGTGCCTGATGCCTTTCATCCTGGGCCTGCTGTCTGG CGGCGTGACCACCACCCCTTGGTCCCTGGCCAGGCCTCAGGGCTCCTGCTCCCTGGAGGGCG TGGAGATCAAGGGCGGCTCCTTCCGGCTGCTGCAGGAAGGCCAGGCTCTGGAGTACGTGTGC CCTTCCGGCTTCTACCCTTACCCTGTGCAGACAAGGACCTGTAGGTCCACCGGCTCTTGGTC CACACTGAAAACCCAGGACCAGAAAACCGTCCGGAAGGCCGAGTGCCGGGCCATCCACTGCC CTCGGCCTCACGACTTCGAGAACGGCGAGTACTGGCCTCGGTCCCCTTACTACAACGTGTCC GACGAGATCTCCTTCCACTGCTACGACGGCTACACCCTGCGGGGCTCCGCCAACAGGACCTG CCAGGTCAACGGCCGGTGGTCCGGCCAGACCGCCATCTGCGACAACGGCGCTGGCTACTGCT CCAACCCTGGCATCCCTATCGGCACCCGGAAGGTCGGCTCCCAGTACCGGCTGGAGGACTCC GTGACCTACCACTGCTCCAGAGGCCTGACCCTGAGAGGCTCCCAGCGGCGCACCTGTCAGGA AGGTGGCAGCTGGTCTGGCACCGAACCATCTTGCCAGGACTCCTTCATGTACGACACCCCTC AGGAAGTGGCCGAGGCCTTCCTGTCCTCCCTGACCGAGACAATCGAGGGCGTGGACGCCGAG GATGGCCACGGCCCTGGCGAGCAGCAGAACCTTACCATCGTGCTGGACCCCTCCGGCTCCAT GAACATCTACCTGGTGCTGGACGGCTCCGGCAGCATCGGCGCCTCCGACTTCACCGGCGCCA AGAAGAGCCTGGTCAACCTGATCGAGAAGGTGGCCTCCTACGGCGTGAAGCCTAGATACGGC CTGGTGACCTACGCCACCTACCCTAAGATCTGGGTGAAGGTGTCCGAGGCCGACTCCTCCAA CGCCGACTGGGTGACCAAGCAGCTGAACGAGATCAACTACGAGGACCACAAGCTGAAGTCCG

[0359] 45845704.1 61ATTORNEY DOCKET NO. MSD PC 139 PCT

[0360] GCACCAACACCAAGAAGGCCCTGCAGGCCGTCTACTCCATGATGTCCTGGCCTGACGACGTG CCTCCTGAGGGCTGGAACCGGACCCGGCACGTGATTATCCTGATGACCGACGGCCTGCACAA CATGGGCGGCGACCCTATCACCGTGATCGACGAGATCCGGGACCTGCTGTACATCGGCAAGG ACCGGAAGAACCCTCGGGAGGACTACCTGGACGTGTACGTGTTCGGCGTGGGCCCTCTGGTG AACCAGGTCAACATCAACGCCCTGGCCTCCAAGAAGGACAACGAGCAGCACGTGTTCAAGGT CAAGGACATGGAGAACCTGGAGGACGTGTTCTACCAGATGATCGATGAGTCCCAGTCCCTGA GCCTGTGCGGCATGGTCTGGGAGCACCGCAAGGGAACCGACTACCACAAGCAGCCTTGGCAG GCCAAGATCTCCGTGATCCGGCCTTCCAAGGGCCACGAGTCCTGCATGGGCGCCGTGGTGTC CGAGTACTTCGTGCTGACCGCCGCTCACTGCTTCACCGTGGACGACAAGGAACACTCCATCA AAGTCTCCGTGGGCGGCGAGAAGCGGGACCTGGAGATCGAGGTGGTGCTGTTCCACCCTAAC TACAACATCAACGGCAAGAAGGAAGCCGGCATCCCTGAGTTCTACGACTACGACGTGGCCCT GATCAAGCTGAAGAATAAGCTGAAGTATGGCCAGACCATCCGGCCTATCTGCCTGCCTTGCA CCGAGGGCACCACCAGGGCCCTGCGGCTGCCTCCTACCACCACCTGCCAGCAGCAGAAGGAA GAGCTGCTGCCTGCCCAGGACATCAAGGCCCTGTTCGTGTCCGAGGAAGAGAAGAAGCTGAC CCGGAAGGAAGTGTACATCAAGAACGGCGACAAGAAGGGCAGCTGCGAGCGGGACGCCCAGT ACGCCCCTGGCTACGATAAGGTCAAGGATATCTCCGAGGTGGTGACCCCTCGGTTCCTGTGC ACCGGCGGAGTGTCCCCCTACGCCGACCCTAACACCTGCAGAGGCGACTCTGGCGGCCCTCT GATCGTGCACAAGCGGTCCCGGTTCATCCAGGTCGGCGTGATCTCCTGGGGCGTGGTGGACG TGTGCAAGAACCAGAAGCGGCAGAAGCAGGTCCCCGCCCACGCCCGGGACTTCCACATCAAC CTGTTCCAGGTGCTGCCTTGGCTGAAGGAAAAGCTGCAGGATGAGGACCTGGGCTTCCTGGG ATCCGAGTCCAAATATGGTCCCCCATGCCCACCATGCCCAGCACCTGAGTTCCTGGGGGGAC CATCAGTCTTCCTGTTCCCCCCAAAACCCAAGGACACTCTCATGATCTCCCGGACCCCTGAG GTCACGTGCGTGGTGGTGGACGTGAGCCAGGAAGACCCCGAGGTCCAGTTCAACTGGTACGT GGATGGCGTGGAGGTGCATAATGCCAAGACAAAGCCGCGGGAGGAGCAGTTCAACAGCACGT ACCGTGTGGTCAGCGTCCTCACCGTCCTGCACCAGGACTGGCTGAACGGCAAGGAGTACAAG TGCAAGGTCTCCAACAAAGGCCTCCCGTCCTCCATCGAGAAAACCATCTCCAAAGCCAAAGG GCAGCCCCGAGAGCCACAGGTGTACACCCTGCCCCCATCCCAGGAGGAGATGACCAAGAACC AGGTCAGCCTGACCTGCCTGGTCAAAGGCTTCTACCCCAGCGACATCGCCGTGGAGTGGGAG AGCAATGGGCAGCCGGAGAACAACTACAAGACCACGCCTCCCGTGCTGGACTCCGACGGCTC CTTCTTCCTCTACAGCAGGCTAACCGTGGACAAGAGCAGGTGGCAGGAGGGGAATGTCTTCT CATGCTCCGTGATGCATGAGGCTCTGCACAACCACTACACACAGAAGAGCCTCTCCCTGTCT CTGGGTAAATGA (SEQ ID NO: 18).

[0361] 45845704.1 62ATTORNEY DOCKET NO. MSD PC 139 PCT

[0362] b. Anti-Inflammatory / Fc Fusion Proteins

[0363] In some forms, compositions include a fusion protein including an anti-inflammatory molecule and Fc proteins. In some forms, a soluble IL-17 receptor A (slL-17RA) is fused to a second polypeptide. In some forms, a soluble IL-17 receptor A (slL-17RA) is fused to Fc proteins. In some forms, a soluble IL-17 receptor A (slL-17RA) is fused to IgG4 Fc. In some forms the fusion protein includes an anti-inflammatory molecule that block inflammatory pathways such as but not limited to soluble IL- 17 receptor A (sIL-17RA), IL-4 antagonist, IL-6 antagonist, IL-13 antagonist, IL-17 antagonist, IL-22 antagonist, IL-23 antagonist, IL-31 antagonist, TSLP antagonist, or OX40-OX40L axis antagonist axis fused to Fc proteins.

[0364] The Fc can be placed at the N-terminus or C-terminus of an anti-inflammatory molecule. The anti-inflammatory molecule / Fc fusion protein has the signal sequence of an anti-inflammatory molecule at the N-terminus of the fusion protein, followed by IgG4 Fc, followed by an anti-inflammatory molecule without a signal peptide sequence. Fc fusion could further increase half-life and stability anti-inflammatory molecules.

[0365] SEQ ID NO:7 represents amino acid sequence of human IgG4-Fc fused with soluble human IL- 17 receptor A:

[0366] MGSNLSPQLCLMPFILGLLSGGVTTTPGSESKYGPPCPPCPAPEFLGGPSVFLFPPKPKDTL MISRTPEVTCVWDVSQEDPEVQFNWYVDGVEVHNAKTKPREEQFNSTYRVVSVLTVLHQDW LNGKEYKCKVSNKGLPSSIEKTISKAKGQPREPQVYTLPPSQEEMTKNQVSLTCLVKGFYPS DIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQEGNVFSCSVMHEALHNHYT QKSLSLSLGKAAAKGKLRLLDHRALVCSQPGLNCTVKNSTCLDDSWIHPRNLTP SSPKDLQI QLHFAHTQQGDLFPVAHIEWTLQTDASILYLEGAELSVLQLNTNERLCVRFEFLSKLRHHHR RWRFTFSHFVVDPDQEYEVTVHHLPKPIPDGDPNHQSKNFLVPDCEHARMKVTTPCMSSGSL WDPNITVETLEAHQLRVSFTLWNESTHYQILLTSFPHMENHSCFEHMHHIPAPRPEEFHQRS NVTLTLRNLKGCCRHQVQIQPFFSSCLNDCLRHSATVSCPEMPDTPEP IPDYMPLW (SEQ ID NO:7).

[0367] In some forms, the fusion protein includes the sequence of SEQ ID NO:7 or fragment or a variant of SEQ ID NO:7 and optionally has at least 70, 75, 80, 85, 90, 95, 96, 97, 98, or 99 percent sequence identity thereto.

[0368] SEQ ID NO:8 represents nucleotide sequence encoding soluble human IL-17 receptor A fused with human IgG4-Fc:

[0369] ATGGGCTCCAACCTGTCCCCCCAGCTGTGCCTGATGCCTTTCATCCTGGGCCTGCTGTCTGG CGGCGTGACCACCACCCCTGGATCCGAGTCCAAATATGGTCCCCCATGCCCACCATGCCCAG CACCTGAGTTCCTGGGGGGACCATCAGTCTTCCTGTTCCCCCCAAAACCCAAGGACACTCTC

[0370] 45845704.1 63ATTORNEY DOCKET NO. MSD PC 139 PCT

[0371] ATGATCTCCCGGACCCCTGAGGTCACGTGCGTGGTGGTGGACGTGAGCCAGGAAGACCCCGA GGTCCAGTTCAACTGGTACGTGGATGGCGTGGAGGTGCATAATGCCAAGACAAAGCCGCGGG AGGAGCAGTTCAACAGCACGTACCGTGTGGTCAGCGTCCTCACCGTCCTGCACCAGGACTGG CTGAACGGCAAGGAGTACAAGTGCAAGGTCTCCAACAAAGGCCTCCCGTCCTCCATCGAGAA AACCATCTCCAAAGCCAAAGGGCAGCCCCGAGAGCCACAGGTGTACACCCTGCCCCCATCCC AGGAGGAGATGACCAAGAACCAGGTCAGCCTGACCTGCCTGGTCAAAGGCTTCTACCCCAGC GACATCGCCGTGGAGTGGGAGAGCAATGGGCAGCCGGAGAACAACTACAAGACCACGCCTCC CGTGCTGGACTCCGACGGCTCCTTCTTCCTCTACAGCAAGCTTACCGTGGACAAGAGCAGGT GGCAGGAGGGGAATGTCTTCTCATGCTCCGTGATGCATGAGGCTCTGCACAACCACTACACA CAGAAGAGCCTCTCCCTGTCTCTGGGTAAAGCGGCCGCAAAAGGAAAACTGCGACTCCTGGA CCACCGGGCGCTGGTCTGCTCCCAGCCGGGGCTAAACTGCACGGTCAAGAATAGTACCTGCC TGGATGACAGCTGGATTCACCCTCGAAACCTGACCCCCTCCTCCCCAAAGGACCTGCAGATC CAGCTGCACTTTGCCCACACCCAACAAGGAGACCTGTTCCCCGTGGCTCACATCGAATGGAC ACTGCAGACAGACGCCAGCATCCTGTACCTCGAGGGTGCAGAGTTATCTGTCCTGCAGCTGA ACACCAATGAACGTTTGTGCGTCAGGTTTGAGTTTCTGTCCAAACTGAGGCATCACCACAGG CGGTGGCGTTTTACCTTCAGCCACTTTGTGGTTGACCCTGACCAGGAATATGAGGTGACCGT TCACCACCTGCCCAAGCCCATCCCTGATGGGGACCCAAACCACCAGTCCAAGAATTTCCTTG TGCCTGACTGTGAGCACGCCAGGATGAAGGTAACCACGCCATGCATGAGCTCAGGCAGCCTG TGGGACCCCAACATCACCGTGGAGACCCTGGAGGCCCACCAGCTGCGTGTGAGCTTCACCCT GTGGAACGAATCTACCCATTACCAGATCCTGCTGACCAGTTTTCCGCACATGGAGAACCACA GTTGCTTTGAGCACATGCACCACATACCTGCGCCCAGACCAGAAGAGTTCCACCAGCGATCC AACGTCACACTCACTCTACGCAACCTTAAAGGGTGCTGTCGCCACCAAGTGCAGATCCAGCC CTTCTTCAGCAGCTGCCTCAATGACTGCCTCAGACACTCCGCGACTGTTTCCTGCCCAGAAA TGCCAGACACTCCAGAACCAATTCCGGACTACATGCCCCTGTGGTAG (SEQ ID NO:8).

[0372] 4. Nucleic Acids

[0373] The present disclosure includes nucleic acids including a nucleotide sequence encoding a provided complement factor B protein analog or fusion protein and includes vectors including these nucleic acids.

[0374] To ensure local and long-term expression of a nucleic acid of interest, some forms contemplate transducing a cell with a nucleic acid or vector encoding a complement factor B analog. The instant disclosure is not to be construed as limited to any one particular nucleic delivery method, and any available nucleic acid delivery vehicle with either an in vivo or in vitro nucleic acid delivery strategy, or the use of manipulated cells (such as the technology of Neurotech, Lincoln, RI, e.g., see U. S. Patent Nos. 6,231,879; 6,262,034; 6,264,941;

[0375] 45845704.1 64ATTORNEY DOCKET NO. MSD PC 139 PCT

[0376] 6,303,136; 6,322,804; 6,436,427; 6,878,544) as well as nucleic acids encoding a complement factor B analog per se (e.g., “naked DNA”), can be used in the practice of the instant disclosure. Various delivery vehicles, such as vectors, can be used. For example, viral vectors, amphitrophic lipids, cationic polymers, such as polyethylenimine (PEI) and polylysine, dendrimers, such as combust molecules and starburst molecules, nonionic lipids, anionic lipids, vesicles, liposomes and other synthetic nucleic acid means of gene delivery (e.g., see U. S. Pat. Nos. 6,958,325 and 7,098,030; Langer, Science 249:1527-1533 (1990); Treat et al., in “Liposomes” in “The Therapy of Infectious Disease and Cancer”; and Lopez-Berestein & Fidler (eds.), Liss, New York, pp. 317-327 and 353-365 (1989); “naked” nucleic acids and so on can be used in the practice of the instant disclosure.

[0377] A vector is a means by which a nucleic acid of interest (e.g., a therapeutic nucleic acid, e.g., that can encode a therapeutic protein) is introduced into a target cell of interest. A vector is typically constructed or obtained from a starting material, such as a nucleic acid capable of carrying a foreign gene or transgene and which is capable of entering into and being expressed in a target cell. Suitable starting materials from which a vector can be obtained include transposons, plasmids, viruses, PCR products, cDNAs, mRNAs and so on, as known in the art. Methods for obtaining or constructing a vector of interest include, but are not limited to, standard gene manipulation techniques, sequencing reactions, restriction enzymes digests, polymerase reactions, PCR, PCR SOEing, ligations, recombinase reactions (e.g., Invitrogen’s GATEWAY® technology) other enzymes active on nucleic acids, bacteria and virus propagation materials and methods, chemicals and reagents, site directed mutagenesis protocols and so on, as known in the art, see, for example, the Maniatis et al. text, “Molecular Cloning.”

[0378] Nucleic acids will typically include a promoter operatively linked to a complement factor B protein analog or fusion protein coding sequence. A promoter may be a tissue specific promoter, a cell specific promoter, an inducible promoter, a repressible promoter, a constitutive promoter, a synthetic promoter or a hybrid promoter, for example. Examples of promoters useful in the constructs include, but are not limited to, a phage lambda (PL) promoter; an SV40 early promoter; a herpes simplex viral (HSV) promoter; a cytomegalovirus (CMV) promoter, such as the human CMV immediate early promoter; a tetracycline-controlled trans-activator-responsive promoter (tet) system; a long terminal repeat (LTR) promoter, such as a MoMLV LTR, BIV LTR or an HIV LTR; a U3 region promoter of Moloney murine sarcoma virus; a Granzyme A promoter; a regulatory sequence(s) of the metallothionein gene; a CD34 promoter; a CD8 promoter; a thymidine 45845704.1 65ATTORNEY DOCKET NO. MSD PC 139 PCT

[0379] kinase (TK) promoter; a B 19 parvovirus promoter; a PGK promoter; a glucocorticoid promoter; a heat shock protein (HSP) promoter, such as HSP65 and HSP70 promoters; an immunoglobulin promoter; an MMTV promoter; a Rous sarcoma virus (RSV) promoter; a lac promoter; a CaMV 35S promoter; and a nopaline synthetase promoter. In some forms, a promoter is an MND promoter (Robbins et aL, 1997, J. Virol. 71:9466-9474), or an MNC promoter, which is a derivative of the MND promoter in which the LTR enhancers are combined with a minimal CMV promoter (Haberman et al., J. Virol. 74(18):8732-8739, 2000).

[0380] In some forms, a vector includes an intron, e.g., as part of the gene coding for a complement factor B protein analog or fusion protein. Heterologous introns are known and non-limiting examples include a human |3-globin gene intron. An intron can be from a complement factor B gene or a heterologous intron.

[0381] Signal sequences or leader sequences are known and can be used in complement factor B analog and fusion protein expression constructs. Signal sequences are translated in frame as a peptide attached to the amino-terminal end of a polypeptide of choice, the secretory signal sequence will cause the secretion of the polypeptide by interacting with the machinery of the host cell. As part of the secretory process, this secretory signal sequence will be cleaved off. The human placental alkaline phosphatase secretory signal sequence is an example of a useful signal sequence. The disclosure is not limited by specific secretory signal sequences and others are known to those skilled in the art. The term “signal sequence” also refers to a nucleic acid sequence encoding the secretory peptide. If a signal sequence is included, it can either be a wildtype complement factor B sequence, a homologous sequence, or a heterologous sequence.

[0382] Vectors

[0383] The disclosure includes vectors (viral or non- viral) encoding compositions disclosed herein. The disclosure is not limited to a particular viral vector. Viral vectors include, but are not limited to, retroviral vectors, lentiviral vectors, adenoviral vectors, AAV vectors, Herpes viral vectors (HSV-1 or HSV-2 based Herpes simplex viral vector). In some forms, a lentiviral vector is an HIV, EIAV, SIV, FIV or BIV vector. In some forms, an AAV vector is AAV2, AAV5, AAV8, AAV9 vector. In some forms, an AAV vector has a modified capsid to enhance its transduction efficiency in a particular tissue / organ. The disclosure also provides a cell that produces a viral vector.

[0384] Vector virions may be administered in vivo or in vitro to cells (e.g., mammalian cells). Vectors (viral or nonviral) can be used to transduce or transform cells including, but 45845704.1 ggATTORNEY DOCKET NO. MSD PC 139 PCT

[0385] not limited to, undifferentiated cells, differentiated cells, somatic cells, primitive cells and / or stem cells.

[0386] Some of the delivery methods for non- viral vectors can include, but not limited to, electroporation, microinjection, gene gun, sonoporation, hydrodynamic injection, laser-assisted delivery, liposomes, lipid nanoparticles (LNPs), cationic polymers, dendrimers, inorganic nanoparticles, chitosan-based carriers, cyclodextrins, plasmids, exosomes, peptide-based delivery, CRISPR delivery systems, DNA origami, carbon nanotubes, or graphene.

[0387] A non- limiting exemplary vector is

[0388] SEQ ID NO: 36. Nucleotide sequence of rAAV2. PC139 transfer vector construct Left ITR: 1-130

[0389] CMV promoter: 210-716

[0390] Human beta-globin intron: 809-1301

[0391] PC139 coding sequence: 1321-3615 (SEQ ID NO:4, bold / italics below)

[0392] Poly A: 3676-4152

[0393] Right ITR: 4192-4332 CCTGCAGGCAGCTGCGCGCTCGCTCGCTCACTGAGGCCGCCCGGGCGTCGGGCGACCTTTGG TCGCCCGGCCTCAGTGAGCGAGCGAGCGCGCAGAGAGGGAGTGGCCAACTCCATCACTAGGG GTTCCTGCGGCCGCACGCGTGGAGCTAGTTATTAATAGTAATCAATTACGGGGTCATTAGTT CATAGCCCATATATGGAGTTCCGCGTTACATAACTTACGGTAAATGGCCCGCCTGGCTGACC GCCCAACGACCCCCGCCCATTGACGTCAATAATGACGTATGTTCCCATAGTAACGTCAATAG GGACTTTCCATTGACGTCAATGGGTGGAGTATTTACGGTAAACTGCCCACTTGGCAGTACAT CAAGTGTATCATATGCCAAGTACGCCCCCTATTGACGTCAATGACGGTAAATGGCCCGCCTG GCATTATGCCCAGTACATGACCTTATGGGACTTTCCTACTTGGCAGTACATCTACGTATTAG TCATCGCTATTACCATGGTGATGCGGTTTTGGCAGTACATCAATGGGCGTGGATAGCGGTTT GACTCACGGGGATTTCCAAGTCTCCACCCCATTGACGTCAATGGGAGTTTGTTTTGCACCAA AATCAACGGGACTTTCCAAAATGTCGTAACAACTCCGCCCCATTGACGCAAATGGGCGGTAG GCGTGTACGGTGGGAGGTCTATATAAGCAGAGCTCGTTTAGTGAACCGTCAGATCGCCTGGA GACGCCATCCACGCTGTTTTGACCTCCATAGAAGACACCGGGACCGATCCAGCCTCCGCGGA TTCGAATCCCGGCCGGGAACGGTGCATTGGAACGCGGATTCCCCGTGCCAAGAGTGACGTAA GTACCGCCTATAGAGTCTATAGGCCCACAAAAAATGCTTTCTTCTTTTAATATACTTTTTTG TTTATCTTATTTCTAATACTTTCCCTAATCTCTTTCTTTCAGGGCAATAATGATACAATGTA TCATGCCTCTTTGCACCATTCTAAAGAATAACAGTGATAATTTCTGGGTTAAGGCAATAGCA ATATTTCTGCATATAAATATTTCTGCATATAAATTGTAACTGATGTAAGAGGTTTCATATTG CTAATAGCAGCTACAATCCAGCTACCATTCTGCTTTTATTTTATGGTTGGGATAAGGCTGGA

[0394] 45845704.1 67ATTORNEY DOCKET NO. MSD PC 139 PCT

[0395] TTATTCTGAGTCCAAGCTAGGCCCTTTTGCTAATCATGTTCATACCTCTTATCTTCCTCCCA CAGCTCCTGGGCAACGTGCTGGTCTGTGTGCTGGCCCATCACTTTGGCAAAGAATTGGGATT C GAAC T C GAT T G AT T C ATGGGCTCCAACCTGTCCCCCCAGCTGTGCCTGATGCCTTTCAT CCTGGGCCTGCTGTCTGGCGGCGTGACCACCACCCCTTGGTCCCTGGCCAGGCCTCAGGGCT CCTGCTCCCTGGAGGGCGTGGAGATCAAGGGCGGCTCCTTCCGGCTGCTGCAGGAAGGCCAG GCTCTGGAGTACGTGTGCCCTTCCGGCTTCTACCCTTACCCTGTGCAGACAAGGACCTGTAG GTCCACCGGCTCTTGGTCCACACTGAAAACCCAGGACCAGAAAACCGTCCGGAAGGCCGAGT GCCGGGCCATCCACTGCCCTCGGCCTCACGACTTCGAGAACGGCGAGTACTGGCCTCGGTCC CCTTACTACAACGTGTCCGACGAGATCTCCTTCCACTGCTACGACGGCTACACCCTGCGGGG CTCCGCCAACAGGACCTGCCAGGTCAACGGCCGGTGGTCCGGCCAGACCGCCATCTGCGACA ACGGCGCTGGCTACTGCTCCAACCCTGGCATCCCTATCGGCACCCGGAAGGTCGGCTCCCAG TACCGGCTGGAGGACTCCGTGACCTACCACTGCTCCAGAGGCCTGACCCTGAGAGGCTCCCA GCGGCGCACCTGTCAGGAAGGTGGCAGCTGGTCTGGCACCGAACCATCTTGCCAGGACTCCT TCATGTACGACACCCCTCAGGAAGTGGCCGAGGCCTTCCTGTCCTCCCTGACCGAGACAATC GAGGGCGTGGACGCCGAGGATGGCCACGGCCCTGGCGAGCAGCAGAACCTTACCATCGTGCT GGACCCCTCCGGCTCCATGAACATCTACCTGGTGCTGGACGGCTCCGGCAGCATCGGCGCCT CCGACTTCACCGGCGCCAAGAAGAGCCTGGTCAACCTGATCGAGAAGGTGGCCTCCTACGGC GTGAAGCCTAGATACGGCCTGGTGACCTACGCCACCTACCCTAAGATCTGGGTGAAGGTGTC CGAGGCCGACTCCTCCAACGCCGACTGGGTGACCAAGCAGCTGAACGAGATCAACTACGAGG ACCACAAGCTGAAGTCCGGCACCAACACCAAGAAGGCCCTGCAGGCCGTCTACTCCATGATG TCCTGGCCTGACGACGTGCCTCCTGAGGGCTGGAACCGGACCCGGCACGTGATTATCCTGAT GACCGACGGCCTGCACAACATGGGCGGCGACCCTATCACCGTGATCGACGAGATCCGGGACC TGCTGTACATCGGCAAGGACCGGAAGAACCCTCGGGAGGACTACCTGGACGTGTACGTGTTC GGCGTGGGCCCTCTGGTGAACCAGGTCAACATCAACGCCCTGGCCTCCAAGAAGGACAACGA GCAGCACGTGTTCAAGGTCAAGGACATGGAGAACCTGGAGGACGTGTTCTACCAGATGATCG ATGAGTCCCAGTCCCTGAGCCTGTGCGGCATGGTCTGGGAGCACCGCAAGGGAACCGACTAC CACAAGCAGCCTTGGCAGGCCAAGATCTCCGTGATCCGGCCTTCCAAGGGCCACGAGTCCTG CATGGGCGCCGTGGTGTCCGAGTACTTCGTGCTGACCGCCGCTCACTGCTTCACCGTGGACG ACAAGGAACACTCCATCAAAGTCTCCGTGGGCGGCGAGAAGCGGGACCTGGAGATCGAGGTG GTGCTGTTCCACCCTAACTACAACATCAACGGCAAGAAGGAAGCCGGCATCCCTGAGTTCTA CGACTACGACGTGGCCCTGATCAAGCTGAAGAATAAGCTGAAGTATGGCCAGACCATCCGGC CTATCTGCCTGCCTTGCACCGAGGGCACCACCAGGGCCCTGCGGCTGCCTCCTACCACCACC TGCCAGCAGCAGAAGGAAGAGCTGCTGCCTGCCCAGGACATCAAGGCCCTGTTCGTGTCCGA GGAAGAGAAGAAGCTGACCCGGAAGGAAGTGTACATCAAGAACGGCGACAAGAAGGGCAGCT

[0396] 45845704.1 68ATTORNEY DOCKET NO. MSD PC 139 PCT

[0397] GCGAGCGGGACGCCCAGTACGCCCCTGGCTACGATAAGGTCAAGGATATCTCCGAGGTGGTG ACCCCTCGGTTCCTGTGCACCGGCGGAGTGTCCCCCTACGCCGACCCTAACACCTGCAGAGG CGACTCTGGCGGCCCTCTGATCGTGCACAAGCGGTCCCGGTTCATCCAGGTCGGCGTGATCT CCTGGGGCGTGGTGGACGTGTGCAAGAACCAGAAGCGGCAGAAGCAGGTCCCCGCCCACGCC CGGGACTTCCACATCAACCTGTTCCAGGTGCTGCCTTGGCTGAAGGAAAAGCTGCAGGATGA GGACCTGGGCTTCCTGTGAG G T C C T C T AG G T C G AC C T G C AG AAG C T T G C C T C G AG C AG C G CTGCTCGAGAGATCTACGGGTGGCATCCCTGTGACCCCTCCCCAGTGCCTCTCCTGGCCCTG GAAGTTGCCACTCCAGTGCCCACCAGCCTTGTCCTAATAAAATTAAGTTGCATCATTTTGTC TGACTAGGTGTCCTTCTATAATATTATGGGGTGGAGGGGGGTGGTATGGAGCAAGGGGCAAG TTGGGAAGACAACCTGTAGGGCCTGCGGGGTCTATTGGGAACCAAGCTGGAGTGCAGTGGCA CAATCTTGGCTCACTGCAATCTCCGCCTCCTGGGTTCAAGCGATTCTCCTGCCTCAGCCTCC CGAGTTGTTGGGATTCCAGGCATGCATGACCAGGCTCAGCTAATTTTTGTTTTTTTGGTAGA GACGGGGTTTCACCATATTGGCCAGGCTGGTCTCCAACTCCTAATCTCAGGTGATCTACCCA CCTTGGCCTCCCAAATTGCTGGGATTACAGGCGTGAACCACTGCTCCCTTCCCTGTCCTTCT GATTTTGTAGGTAACCACGTGCGGACCGAGCGGCCGCAGGAACCCCTAGTGATGGAGTTGGC CACTCCCTCTCTGCGCGCTCGCTCGCTCACTGAGGCCGGGCGACCAAAGGTCGCCCGACGCC CGGGCTTTGCCCGGGCGGCCTCAGTGAGCGAGCGAGCGCGCAGCTGCCTGCAGG (SEQ ID NO: 36).

[0398] In other forms, the PC139 (SEQ ID NO:3) coding sequence (SEQ ID NO:4): 1321-3615 of SEQ ID NO:36 is substituted with a coding sequence for a different complement factor B analog or fusion protein thereof, optionally wherein the complement factor B analog or fusion protein includes the amino acid sequence of any one of SEQ ID NOs: 1, 2, 5, 12, 16, 29, 30, or 31, or a variant thereof such as those described herein.

[0399] 5. Pharmaceutical Compositions

[0400] Disclosed herein are pharmaceutical compositions for therapeutic uses. In some forms, the pharmaceutical composition described herein includes a complement factor B analog or a disclosed fusion protein or dimer or multimer thereof.

[0401] In some forms, the pharmaceutical composition disclosed herein includes a nucleic acid or a vector that encodes a complement factor B analog or fusion protein, or a combination thereof.

[0402] Some forms of the instant disclosure include pharmaceutical preparations including a complement factor B protein analog or fusion protein or dimer or multimer thereof, a nucleic acid of the instant disclosure, a viral vector of the instant disclosure or any combination thereof.

[0403] 45845704.1 69ATTORNEY DOCKET NO. MSD PC 139 PCT

[0404] Formulations (e.g., for injection) are generally, but not necessarily, biocompatible solutions of the active ingredient, e.g., including Hank's solution or Ringer's solution.

[0405] Formulations for transdermal or transmucosal administration generally include, but are not limited, penetrants such as fusidic acid or bile salts in combination with detergents or surface-active agents. In some forms, formulations can be manufactured as aerosols, suppositories, or patches. In some forms, oral administration may not be favored for protein or peptide active ingredients; however, this type of composition may be suitably formulated, e.g., in an enteric coated form, in a depot, in a capsule and so on, so as to be protected from the digestive enzymes, so that oral administration can also be employed. Some formulations include balanced salt solution (Alcon Laboratories, Inc., Fort Worth, Texas) or balanced salt solution plus (Alcon Laboratories, Inc.). In some forms, a formulation includes one or more of the following: citrate, NaCl (e.g., 0.64%), potassium chloride (KC1) (e.g., 0.075%), calcium chloride dihydrate (CaC12-2H2O) (e.g., 0.048%), magnesium chloride hexahydrate (MgC12-6H2O) (e.g., 0.03%), sodium acetate trihydrate (Cl FCCLNa- 31 FO) (e.g., 0.39%), sodium citrate dihydrate (CYHsChNas^ftO) (e.g., 0.17%), sucrose and sodium hydroxide and / or hydrochloric acid (to adjust pH) and water. The preceding list includes some molecules that are listed as particular hydrates, e.g., dihydrate, trihydrate, hexahydrate, etc. It is understood that various hydrates of these compounds can be used in the disclosure and the disclosure is not limited to these particular hydrate forms of the listed molecules.

[0406] In some forms, a formulation includes one or more of the following: NaCl, monobasic phosphate monohydrate, dibasic sodium phosphate heptahydrate and hydrochloric acid and / or sodium hydroxide to adjust pH and water. In some forms, a pharmaceutical composition includes at least one ingredient selected from the group including histidine, MgCh. trehalose, a polysorbate, polysorbate 20, NaCl, sucrose, arginine and proline. In some forms, a formulation includes one or more of the following: histidine (e.g., about 10 mM); a, a-trehalose dehydrate (e.g., about 10% or about 50 mM); MgCh (e.g., about 10 mM); a polysorbate such as polysorbate 20 (e.g., about 0.01%); and NaCl (e.g., about 0.1%). In some forms, a formulation may include one or more of the following: sucrose, arginine or proline. In some forms, a formulation includes a molecule(s) of the disclosure, 10 mM histidine, lOmM MgCL, 50 mM trehalose and 0.01% polysorbate 20. In some forms, a formulation includes or includes a molecule(s) of the disclosure, 1.0% NaCl and 10 mM MgCl2. In some forms, a formulation includes a molecule(s) of the disclosure, and a balanced salt solution enriched with bicarbonate, dextrose, and glutathione, such as BSS PLUS®. In some forms, a formulation does not include trehalose.

[0407] 45845704.1 79ATTORNEY DOCKET NO. MSD PC 139 PCT

[0408] In some forms, a formulation or composition is at a pH of about 5.5. In some forms, a formulation or composition is at a pH of between from about 5.0 to 9.0, about 5.0 to 5.5, about 5.3 to 5.7, about 5.5 to 6.0, about 5.8 to 6.2, about 6.0 to 6.5, about 6.3 to 6.7, about 6.5 to 7.0, about 6.8 to 7.2, about 7.0 to 7.5, about 7.3 to 7.7, about 7.5 to 8.0, about 7.8 to 8.2, about 8.0 to 8.5, about 8.3 to 8.7 and about 8.5 to 9.0, whatever is suitable to retain the biological activity and stability of the active ingredient(s).

[0409] Some formulations can be manufactured as aerosols, suppositories, eye drops or patches. Examples of suitable formulations and formulatory methods for a desired mode of administration may be found in Remington’s Pharmaceutical Sciences, latest edition, Mack Publishing Co., Easton, PA and in U. S. Patent No. 7,208,577.

[0410] In some forms, a composition for use in vivo contains a “carrier” or a “pharmaceutically acceptable carrier”. The term “carrier” refers to a diluent, adjuvant, excipient, or vehicle with which the vector of interest is administered. The term “carrier” includes, but is not limited to, either solid or liquid material, which may be inorganic or organic and of synthetic or natural origin, with which an active component(s) of the composition is mixed or formulated to facilitate administration to a subject.

[0411] In general, a suitable oil(s), saline, aqueous dextrose (glucose), and related sugar solutions and glycols such as propylene glycol or polyethylene glycols are typically suitable carriers for parenteral solutions. In some forms, solutions for parenteral administration contain a water-soluble salt of the active ingredient, suitable stabilizing agents, and if desirable or necessary, buffer substances. Antioxidizing agents such as sodium bisulfite, sodium sulfite, or ascorbic acid, either alone or combined, can be used as stabilizing agents. Also used are citric acid and its salts and sodium EDTA. In addition, parenteral solutions can contain preservatives, such as benzalkonium chloride, methyl- or propyl-paraben, and chlorobutanol.

[0412] Carriers can include carbohydrates such as trehalose, mannitol, glutathione, xylitol, sucrose, lactose, and sorbitol. Other ingredients for use in formulations may include, for example, DPPC (l,2-Didecanoyl-sn-glycero-3-phosphocholine), DOPE (1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine), DSPC (l,2-Distearoyl-sn-glycero-3-phosphocholinez 1,2-Distearoyl-sn-glycero-3-phosphocholine) and DOPC (l,2-Dioleoyl-sn-glycero-3-phosphocholine). Natural or synthetic surfactants may be used. Polyethylene glycol may be used (even apart from its use in derivatizing a protein). Dextrans, such as cyclodextran, may be used. In some forms, cyclodextrin, tertiary amines and / or beta-cyclodextrin may be used. Bile salts and other related enhancers may be used. Cellulose and cellulose derivatives may 45845704.1 71ATTORNEY DOCKET NO. MSD PC 139 PCT

[0413] be used. Amino acids may be used, such as use in a buffer formulation. Also, the use of liposomes, microcapsules or microspheres, inclusion complexes, or other types of carriers is contemplated.

[0414] Suitable pharmaceutical excipients include, but are not limited to, starch, glucose, lactose, sucrose, gelatin, antibiotics, preservatives, malt, rice, flour, chalk, silica gel, sodium stearate, glycerol monostearate, talc, sodium chloride, dried skim milk, glycerol, propylene, glycol, water, ethanol and the like. A composition, if desired, can also contain wetting and / or emulsifying agents, and / or pH buffering agents. Where necessary, a composition may also include a solubilizing agent and / or a local anesthetic such as lignocaine to ease pain at the site of the injection.

[0415] Also contemplated herein is pulmonary delivery of an agent or protein (or derivative thereof) of the disclosure. In some forms, a complement factor B analog(s) or a disclosed fusion protein or dimer or multimer thereof is delivered to the lungs of a mammal / patient while inhaling and can mostly remain in the lungs or in some forms traverses across the lung epithelial lining to the blood stream, (e.g., see Adjei et al., Pharmaceutical Research 7:565-569 (1990); Adjei et al., International Journal of Pharmaceutics 63:135-144 (1990); Braquet et al., Journal of Cardiovascular Pharmacology 13(suppl. 5): s.143-146 (1989); Hubbard et al., Annals of Internal Medicine 3:206-212 (1989); Smith et al., J. Clin. Invest. 84:1145-1146 (1989); Oswein et al., Proceedings of Symposium on Respiratory Drug Delivery II, Keystone, Colo., March, 1990; Debs et al., The Journal of Immunology 140:3482-3488 (1988) and Platz et al., U. S. Pat. No. 5,284,656). Contemplated for use in the practice of the disclosure provided herein are a wide range of mechanical devices designed for pulmonary delivery of therapeutic products, including but not limited to nebulizers, metered dose inhalers, and powder inhalers. Some specific examples of commercially available devices suitable for the practice of some forms are the ULTRA VENT™ nebulizer, manufactured by Mallinckrodt, Inc., St. Louis, Mo.; the ACORN II® nebulizer, manufactured by Marquest Medical Products, Englewood, Colo.; the VENTOLIN metered dose inhaler, manufactured by Glaxo Inc., Research Triangle Park, N. C.; and the SPINHALER powder inhaler, manufactured by Fisons Corp., Bedford, Mass.

[0416] In some forms, a protein is prepared in particulate form. In some forms, this particulate form has an average particle size of less than 10 pm (or microns), most preferably 0.5 to 5 pm, for delivery to the distal lung.

[0417] Formulations suitable for use with a nebulizer (e.g., jet or ultrasonic) will typically include a complement factor B analog or a disclosed fusion protein or dimer or multimer 45845704.1 72ATTORNEY DOCKET NO. MSD PC 139 PCT

[0418] thereof dissolved in water, in some forms, at a concentration of about 0.1 to about 25 mg of biologically active protein per mL of solution. A formulation may also include a buffer and / or a simple sugar (e.g., for protein stabilization and regulation of osmotic pressure). A nebulizer formulation may also contain a surfactant, to reduce or prevent surface induced aggregation of a protein(s) caused by atomization of the solution in forming the aerosol.

[0419] Formulations for use with a metered-dose inhaler device will generally include a finely divided powder containing a complement factor B analog or a disclosed fusion protein or dimer or multimer thereof suspended in a propellant, e.g., with the aid of a surfactant. A propellant may be any conventional material employed for this purpose, such as a chlorofluorocarbon, a hydrochlorofluorocarbon, a hydrofluorocarbon, or a hydrocarbon, including trichlorofluoromethane, dichlorodifluoromethane, dichlorotetrafluoroethanol, and 1,1,1,2-tetrafluoroethane, or combinations thereof. Suitable surfactants include sorbitan trioleate and soya lecithin. Oleic acid may also be useful as a surfactant. In some forms, formulations for dispensing from a powder inhaler device will include a finely divided dry powder containing a complement factor B analog or a disclosed fusion protein or dimer or multimer thereof and may also include a bulking agent, such as lactose, sorbitol, sucrose, mannitol, trehalose, or xylitol in amounts which facilitate dispersal of the powder from the device, e.g., 50 to 90% by weight of the formulation.

[0420] C. Methods

[0421] 1. Producing Complement Factor B Analogs and Fusion Proteins

[0422] The complement factor B protein analogs and fusion proteins and dimers and multimers thereof disclosed herein can be produced from a cell. In some forms, the complement factor B protein analog or fusion protein is then purified from the cell and / or from cell culture medium.

[0423] The instant disclosure includes (i) cells including a nucleic acid including a nucleotide sequence encoding a complement factor B analog or fusion protein of the instant disclosure and / or (ii) cells expressing a complement factor B protein analog or fusion protein of the instant disclosure. In some forms, a mammalian cell is utilized. In some forms, a prokaryotic cell is utilized.

[0424] Host cells are typically transfected or transduced with an expression or cloning vector for protein production and cultured in conventional nutrient media modified as appropriate for inducing promoters, selecting transformants, amplifying the genes encoding the desired sequences or for downstream purification and / or concentration procedures.

[0425] 45845704.1 73ATTORNEY DOCKET NO. MSD PC 139 PCT

[0426] Suitable host cells for cloning or expressing a coding region in a vector are prokaryote, yeast, or higher eukaryote cells. Suitable prokaryotes for this purpose include, but are not limited to, eubacteria, such as Gram-negative or Gram-positive organisms, for example, Enterobacteriaceae such as Escherichia, e.g., E. coli, Enterobacter, Erwinia, Klebsiella, Proteus, Salmonella, e.g., Salmonella typhimurium, Serratia, e.g., Serratia marcescens, and Shigella, as well as Bacilli such as B. subtilis and B. licheniformis (e.g., B. licheniformis 41P), Pseudomonas such as P. aeruginosa, and Streptomyces. In some forms, an E. coli cloning host is E. coli 294 (e.g., ATCC 31,446), although other strains such as E. coli B, E. coli X1776 (e.g., ATCC 31,537), and E. coli W3110 (e.g., ATCC 27,325) may be suitable.

[0427] In addition to prokaryotes, eukaryotic microbes such as filamentous fungi or yeast are suitable cloning or expression hosts. Saccharomyces cerevisiae, or common baker's yeast, is commonly used among lower eukaryotic host microorganisms. However, a number of other genera, species, and strains are commonly available and useful herein, such as Schizosaccharomyces pombe; Kluyveromyces hosts such as, e.g., K. lactis, K. fragilis (e.g., ATCC 12,424), K. bulgaricus (e.g., ATCC 16,045), K. wickeramii (e.g., ATCC 24,178), K. waltii (e.g., ATCC 56,500), K. drosophilarum (e.g., ATCC 36,906), K. thermotolerans, and K. marxiamis; yarrowia (e.g., EP402,226); Pichia pastoris (e.g., EP183,070); Candida; Trichoderma reesia (e.g., EP244.234); Neurospora crassa; Schwanniomyces such as Schwanniomyces occidentalis; and filamentous fungi such as, e.g., Neurospora, Penicillium, Tolypocladium, and Aspergillus hosts such as A. nidulans and A. niger.

[0428] Suitable host cells, e.g., for the expression of glycosylated proteins, can be derived from multicellular organisms. Examples of invertebrate cells include plant and insect cells. Numerous baculoviral strains and variants and corresponding permissive insect host cells from hosts such as Spodoptera frugiperda (caterpillar), Aedes aegypti (mosquito), Aedes albopictus (mosquito), Drosophila melanogaster (fruit fly), and Bombyx mori have been identified and can be used for expressing proteins. A variety of viral strains for transfection can be used for protein expression and are publicly available, e.g., the L-l variant of Autographa californica NPV and the Bm-5 strain of Bombyx mori NPV, and such viruses may be used according to the present instant disclosure, for example, for transfection of Spodoptera frugiperda cells. Plant cell cultures of cotton, com, potato, soybean, petunia, tomato, and tobacco can also be utilized as hosts.

[0429] Some forms of the instant disclosure utilize vertebrate or mammalian cells, and propagation of vertebrate cells in culture (tissue culture) can be a routine procedure.

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[0431] Examples of useful mammalian host cell lines are a monkey kidney CVI cell line transformed by SV40 (e.g., COS-7, ATCC CRL 1651); human embryonic kidney line (e.g., 293 or 293T cells including either cell line subcloned for growth in suspension culture, Graham et al., J. Gen Virol. 36:59 (1977) such as 293 Freestyle (Invitrogen, Carlsbad, CA)) or 293FT; baby hamster kidney cells (e.g., BHK, ATCC CCL 10); Chinese hamster ovary cells; Chinese hamster ovary cells / -DHFR (e.g., CHO, Urlaub etal., Proc. Natl. Acad. Sci. USA 77:4216 (1980)); mouse sertoli cells (e.g., TM4, Mather, Biol. Reprod. 23:243-251 (1980)); monkey kidney cells (e.g., CVI ATCC CCL 70); African green monkey kidney cells (e.g., VERO-76, ATCC CRL- 1587); human cervical carcinoma cells (e.g., HELA, ATCC CCL 2); canine kidney cells (e.g., MOCK, ATCC CCL 34); CF2TH cells; buffalo rat liver cells (e.g., BRL 3A, ATCC CRL 1442); human lung cells (e.g., W138, ATCC CCL 75); human liver cells (e.g., Hep G2, HB 8065); mouse mammary tumor cells (e.g., MMT 060562, ATCC CCL51); TRI cells (Mather et al., Annals N. Y. Acad. Sci. 383:44-68 (1983)); MRC 5 cells; and FS4 cells.

[0432] In some instances, a host cell may be modified to decrease or eliminate expression of an endogenous protein. For example, if a complement factor B protein analog or fusion protein is to be produced in a particular host cell (e.g., a CHO cell), then the host cell could be modified so as expression of the host cell’s native factor B protein (e.g., hamster factor B) is reduced or eliminated. This may be advantageous for the downstream purification of the complement factor B protein analog or fusion protein. Therefore, the instant disclosure provides a method of producing a complement protein analog or a disclosed fusion protein or dimer or multimer thereof of the instant disclosure including reducing or eliminating the expression of the corresponding native complement protein in the host cell. Methods for reducing, eliminating or knocking out expression of a host cell protein are known in the art. For example, a protein’s expression level may be reduced or eliminated by engineering the host cell to express inhibitory RNA (e.g., RNAi) specific for the RNA coding for the protein. For example, Clontech (Mountain View, CA) sells various vectors and kits, such as those referred to as part of the KNOCKOUT™ RNAi Systems, for knocking down expression of proteins in a host cell. Other methods include gene targeting by homologous recombination which allows the introduction of specific mutations into any cloned gene, e.g., see Current Protocols in Molecular Biology, John Wiley & Sons, Inc., 1994-1998, Sections 9.16 and 9.17. This can be used to knockout the gene expressing the host cell protein.

[0433] Another method which may be utilized to reduce expression of an endogenous protein, involves using a targeted transcription factor that represses expression of the 45845704.1 75ATTORNEY DOCKET NO. MSD PC 139 PCT

[0434] endogenous protein. For example, a repressor domain from a transcription factor may be attached or fused to a DNA binding domain such as a zinc finger polypeptide. One skilled in the art can design zinc finger polypeptides that bind specific DNA sequences, e.g., see U. S. Patent Nos. 6,140,081; and 7,067,617; and U. S. Published Patent Applications 20060078880; 20040224385; and 20070213269. One skilled in the art can associate designed zinc finger polypeptides with a transcriptional repressor domain (e.g., a KRAB (Kriippel-associated box) domain). Examples of such molecules and techniques are described in Beerli et al. (Proc Natl Acad Sci U S A. 200097(4): 1495- 1500) and U. S. Published Patent Application 20070020627. In some forms of the instant disclosure, a host cell would be transduced with a vector expressing the transcriptional repressor. This approach has an advantage over knocking out the gene of interest using homologous recombination because, in most cases, a host cell will be diploid and it would be desirable to knock out both gene copies. Whereas, expression of a transcriptional repressor should repress expression of both gene copies.

[0435] A complement factor B protein analog or fusion protein containing composition prepared from cells can be purified using, for example, hydroxylapatite chromatography, gel electrophoresis, dialysis, size exclusion chromatography, affinity chromatography, immunoaffinity chromatography, tangential flow purification, diafiltration, ion exchange chromatography, hydrophobic interaction chromatography (HIC), ceramic hydoxyapatite chromatography (CHT), reverse phase chromatography, MabSelect SuRe column chromatography, Protein A column chromatography, Source 15Q column chromatography, heparin sepharose affinity chromatography and other known forms of separation and concentration. Following any purification step(s), a mixture including a complement factor B protein analog or fusion protein and contaminants, if any, may be subjected to low pH hydrophobic interaction chromatography, e.g., using an elution buffer at a pH between about 2.5-4.5, in some cases performed at low salt concentrations (e.g., from about 0-0.25M salt) or other procedures for further purification.

[0436] In some forms, a complement factor B protein analog or fusion protein of the instant disclosure is at least 90%, at least 93%, at least 95%, at least 98%, at least 99.5% or at least 99.9% pure in relation to total protein.

[0437] The instant disclosure also provides methods of producing a complement factor B protein analog or fusion protein including expressing in a cell a complement factor B protein analog of the instant disclosure and purifying the complement factor B protein analog or fusion protein.

[0438] 45845704.1 76ATTORNEY DOCKET NO. MSD PC 139 PCT

[0439] i. Tools for generating complement factor B analogs

[0440] The disclosed methods typically include the adding, deleting, and / or substituting amino acids at various locations in factor B protein or disclosed fusion proteins. Any suitable means can be used to achieve this.

[0441] a. CRISPR-Cas Expression Vector

[0442] CRISPR-Cas compounds and expression vectors thereof that can be used to introduce mutations. The CRISPR-Cas system is a defense mechanism found in bacteria and archaea that allows them to recognize, target, and destroy foreign genetic material, such as viruses and plasmids. Generally, the CRISPR-Cas expression vector contains a CRISPR-associated (Cas) endonuclease enzyme, a single guide RNA (sgRNA) molecule, and a delivery vector carrier.

[0443] The CRISPR-Cas expression compounds and vectors encoding the same can include one or more Cas (CRISPR associated) proteins to mediate processing of CRISPR loci transcripts, cleavage of the target DNA or RNA, and new spacer integration. In some forms, the Cas protein is Cas5, Cas6, Cas7, Cas8, Cas9, Casl2a, Casl2b, and Casl3, or any combination thereof. In some forms, the Cas protein is a recombinant Cas protein having from about 75% to about 100%, from about 80% to about 100%, from about 90% to about 100%, or from about 95% to about 100% sequence identity to a Cas5, Cas6, Cas7, Cas8, Cas9, Cas 12a, Cas 12b, Cas 13 protein, or any combination thereof.

[0444] In certain forms, the Cas protein is Cas9. The structure and mechanism of function of Cas9 proteins are known in the art. Briefly, the Cas9 protein is a bi-lobed structure, having an alpha helical recognition (REC) lobe and a nuclease (NUC) lobe. The REC lobe recognizes the target DNA by finding the complementary DNA region, and the NUC lobe cleaves the double stranded DNA by RNA-guided dsDNA endonuclease activity (Jiang and Doudna, Annual Review of Biophysics, 46:505-529 (2017)). Cas9 proteins generally have six domains: a REC I domain, a REC II domain, a Bridge Ilelix domain, a PAM Interacting domain, a HNH domain and a RuvC domain (Jinek, et al., Science, 343(6176): 1247997 (2014) and Nishimasu et al., Cell, 156(5):935-49 (2014)). The REC I domain, the largest domain, spans residues 94-179 and 308-713, and facilitates RNA guided DNA targeting. The arginine-rich bridge helix spans residues 60-93 and initiates cleavage activity upon binding of target DNA (Nishimasu et al., Cell, 156(5):935-49 (2014)). The PAM-Interacting domain spans residues 1099-1368 finds the PAM sequence on the target DNA and initiates binding to the target DNA (Anders et al., Nature, 513(7519):569-73 (2014); Nishimasu et al., Cell, 156(5):935-49 (2014), Sternberg et al., Nature, 507(7490):62-7 (2014)). The HNH and RuvC 45845704.1 77ATTORNEY DOCKET NO. MSD PC 139 PCT

[0445] domains are nuclease domains that cut single-stranded DNA (Jinek, et al., Science, 343(6176): 1247997 (2014) and Nishimasu et al., Cell, 156(5):935-49 (2014)). The RuvC domain, including RuvCI, RuvCII, and RuvCIII, span residues 1-59, 718-769, and 909-1098, and have RNase H activity, and cuts single- stranded DNA for the non-complementary strand of the target DNA. The HNH domain spans residues 775-908 and cuts single-stranded DNA for the complementary strand of the target DNA. The structure of Cas9 proteins are described in further details in Jiang and Doudna, Annual Review of Biophysics, 46:505-529 (2017); Jiang and Doudna, Curr Opin Struct Biol, 30:100-111 (2015); Huai et al., Nature Communications, 8(1): 1375 (2017), all of which are incorporated herein by reference in their entireties.

[0446] In some forms, the Cas9 protein is derived from Streptococcus pyogenes, Streptococcus aureus, Campylobacter jejuni, Streptococcus thermophilus, or Treponema denticola. Thus, in some forms, the Cas9 protein is a Streptococcus pyogenes Cas9 (SpCas9), Campylobacter jejuni Cas9 (CjCas9), Streptococcus canis (ScCas9), Streptococcus thermophilus Cas9 (StCas9), Staphylococcus aureus Cas9 (SaCas9), and Neisseria meningitides Cas9 (NmCas9), or any variant thereof.

[0447] In some forms, the Cas9 protein is a naturally occurring Cas9 protein. Exemplary naturally occurring Cas9 proteins include but are not limited to SpCas9, ScCas9, and SaCas9. In some forms, the Cas9 protein is a variant of a naturally occurring Cas9 protein. Examples of suitable variants of SpCas9 proteins include but are not limited to SpCas9-NRRH, SpG, SpCas9-NRCH, SpCas9-NRTH, and variants thereof. Examples of suitable variants of SaCas9 proteins include but are not limited to efSaCas9, KKHSaCas9, SaCas9-HF, and variants thereof. Examples of suitable variants of ScCas9 proteins include but are not limited to SpCas9++, SpCas9n++, SpCas9+, and variants thereof.

[0448] In some forms, the Cas9 protein is an artificially engineered Cas9 protein. Exemplary artificially engineered Cas9 proteins include but are not limited to XCas9, ThermoCas9, dCas9, eSpCas9, Cas9-DD, SpCas9-VQR, SpCas9-EQR, and HypaCas9. In some forms, the Cas9 protein is a variant of an artificially engineered Cas9 protein. In some forms, a variant is at least about 70%, about 80%, about 85%, about 90%, about 95%, about 96%, about 97%, about 98%, or about 99% identical to an artificially engineered Cas9 protein.

[0449] In some forms, the Cas9 protein requires the presence of a protospacer adjacent motif (PAM) directly downstream of the target sequence in the genomic DNA, on the non-target strand (Karvelis et al., Genome Biology, 16: Article number 253 (2015)). In some forms, when the Cas9 protein is derived from Streptococcus pyogenes, the PAM motif is NGG or 45845704.1 78ATTORNEY DOCKET NO. MSD PC 139 PCT

[0450] NAG, preferably 5’-NGG-3’, where “N” represents any nucleotide. In some forms, when the Cas9 protein is derived from Streptococcus thermophilus, the PAM motif is NGGNG, where “N” represents any nucleotide. In some forms, when the Cas9 protein is derived from Staphylococcus aureus, the PAM motif is NNGRRT or NNGRR(N), where “N” represents any nucleotide. In some forms, when the Cas9 protein is derived from Neisseria meningitides, the PAM motif is NNNNGATT or NNNNGCTT, where “N” represents any nucleotide. In some forms, when the Cas9 protein is derived from Streptococcus canis, the PAM motif is NNG, where “N” represents any nucleotide. In some forms, when the Cas9 protein is derived from Geobacillus thermodenitrificans T12 e.g., ThermoCas9, the PAM motif is CRAA, where “R” is A or G.

[0451] The Cas9 protein in the CRISPR-Cas expression vector requires a guide RNA i.e., a single strand of RNA that forms a T-shape containing one tetraloop and two or three stem loops to become active and perform its catalytic functions. The guide RNA is engineered to have a 5' end that is complimentary to the target DNA sequence (Jinek, et al., Science, 343(6176): 1247997 (2014) and Nishimasu et al., Cell, 156(5):935-49 (2014)). This artificial guide RNA binds to the Cas9 protein and, upon binding, induces a conformational change in the protein. The conformational change converts the inactive Cas9 protein into its active form. Theoretically, steric interactions or weak binding between protein side chains and RNA bases may induce the conformational change. Once the Cas9 protein is activated, it stochastically searches for target DNA by binding with sequences that match its protospacer adjacent motif (PAM) sequence (Sternberg et al., Nature, 507(7490):62-7 (2014)). Exemplary PAMs are provided above. When the Cas9 protein finds a potential target sequence with the appropriate PAM, the protein will melt the bases immediately upstream of the PAM and pair them with the complementary region on the guide RNA (Sternberg et al., Nature, 507(7490):62-7 (2014)). If the complementary region and the target region pair properly, the RuvC and HNH nuclease domains will cut the target DNA after the third nucleotide base upstream of the PAM (Anders et al., Nature, 513(7519):569-73 (2014). The mechanism of function of Cas9 proteins are described in further details in Jiang and Doudna, Annual Review of Biophysics, 46:505-529 (2017); Jiang and Doudna, Curr Opin Struct Biol, 30:100-111 (2015); Huai et al., Nature Communications, 8(1): 1375 (2017), all of which are incorporated herein by reference in their entireties.

[0452] The orientation and design of the spacer sequence allow for its use in various genomic contexts, making it adaptable to study DSB repair anywhere in the genome. The spacer sequence can be engineered or rationally designed to provide flexibility and adaptability and 45845704.1 79ATTORNEY DOCKET NO. MSD PC 139 PCT

[0453] to mimic known double stranded breaks at any location for interrogation. Thus, the assay can be used to interrogate the repair enzymes at particular common break points and / or to interrogate mutant enzyme activity and / or the impact of drugs and / or other exogenous treatments.

[0454] b. Transcription Activator-Like Effector Nucleases (TALEN)

[0455] In some forms, TALEN can be used. In some forms, the element that induces a mutation is a nucleic acid construct or constructs encoding a transcription activator-like effector nuclease (TALEN). TALENs have an overall architecture similar to that of ZFNs, with the main difference that the DNA-binding domain comes from TAL effector proteins, transcription factors from plant pathogenic bacteria. The DNA-binding domain of a TALEN is a tandem array of amino acid repeats, each about 34 residues long. The repeats are very similar to each other; typically they differ principally at two positions (amino acids 12 and 13, called the repeat variable diresidue, or RVD). Each RVD specifies preferential binding to one of the four possible nucleotides, meaning that each TALEN repeat binds to a single base pair, though the NN RVD is known to bind adenines in addition to guanine. TAL effector DNA binding is mechanistically less well understood than that of zinc-finger proteins, but their seemingly simpler code could prove very beneficial for engineered-nuclease design. TALENs also cleave as dimers, have relatively long target sequences (the shortest reported so far binds 13 nucleotides per monomer) and appear to have less stringent requirements than ZFNs for the length of the spacer between binding sites. Monomeric and dimeric TALENs can include more than 10, more than 14, more than 20, or more than 24 repeats.

[0456] Methods of engineering TAL to bind to specific nucleic acids are described in Cermak, et al, Nucl. Acids Res. 1-11 (2011). US Published Application No. 2011 / 0145940, which discloses TAL effectors and methods of using them to modify DNA. Miller et al. Nature Biotechnol 29: 143 (2011) reported making TALENs for site-specific nuclease architecture by linking TAL truncation variants to the catalytic domain of Fokl nuclease. The resulting TALENs were shown to induce gene modification in immortalized human cells. General design principles for TALE binding domains can be found in, for example, WO 2011 / 072246.

[0457] c. Zinc Finger Nucleases (ZFN)

[0458] In some forms, ZFN can be used to generate mutations. In some forms, the element that induces a mutation is a nucleic acid construct or constructs encoding a zinc finger nucleases (ZFNs). ZFNs are typically fusion proteins that include a DNA-binding domain derived from a zinc-finger protein linked to a cleavage domain.

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[0460] The most common cleavage domain is the Type IIS enzyme Fokl. Fokl catalyzes double- stranded cleavage of DNA, at 9 nucleotides from its recognition site on one strand and 13 nucleotides from its recognition site on the other. See, for example, U. S. Pat. Nos. 5,356,802; 5,436, 150 and 5,487,994; as well as Li et al. Proc., Natl. Acad. Sci. USA 89 (1992):4275-4279; Li et al. Proc. Natl. Acad. Sci. USA, 90:2764-2768 (1993); Kim et al. Proc. Natl. Acad. Sci. USA. 91:883-887 (1994a); Kim et al. J. Biol. Chem. 269:31,978-31,982 (1994b). One or more of these enzymes (or enzymatically functional fragments thereof) can be used as a source of cleavage domains.

[0461] The DNA-binding domain, which can, in principle, be designed to target any genomic location of interest, can be a tandem array of Cys2His2 zinc fingers, each of which generally recognizes three to four nucleotides in the target DNA sequence. The Cys2His2 domain has a general structure: Phe (sometimes Tyr)-Cys-(2 to 4 amino acids)-Cys-(3 amino acids)-Phe(sometimes Tyr)-(5 amino acids)-Leu-(2 amino acids)-His-(3 amino acids)-His. By linking together multiple fingers (the number varies: three to six fingers have been used per monomer in published studies), ZFN pairs can be designed to bind to genomic sequences 18-36 nucleotides long.

[0462] Engineering methods include, but arc not limited to, rational design and various types of empirical selection methods. Rational design includes, for example, using databases including triplet (or quadruplet) nucleotide sequences and individual zinc finger amino acid sequences, in which each triplet or quadruplet nucleotide sequence is associated with one or more amino acid sequences of zinc fingers which bind the particular triplet or quadruplet sequence. See, for example, U. S. Pat. Nos. 6, 140,081; 6,453,242; 6,534,261; 6,610,512; 6,746,838; 6,866,997; 7,067.617; U. S. Published Application Nos. 2002 / 0165356;

[0463] 2004 / 0197892; 2007 / 0154989; 2007 / 0213269; and International Patent Application Publication Nos. WO 98 / 53059 and WO 2003 / 016496.

[0464] d. Other tools for generating DSBs

[0465] Beyond CRISPR, TALENs, and ZFNs, several tools can be used for generating mutations disclosed in this application. Meganucleases, such as I-Scel, are naturally occurring enzymes that recognize long DNA sequences (14-40 bp) and cleave DNA at specific sites but require the presence of native recognition sequences. Chemical-induced DSBs involve compounds like etoposide or bleomycin, which disrupt DNA by inhibiting topoisomerase activity or inducing direct strand breaks, commonly used for studying DNA damage responses. Radiation methods, such as gamma rays or UV light, cause random DSBs and are useful for analyzing repair mechanisms. Recombinase systems, including Cre-loxP or 45845704.1 g |ATTORNEY DOCKET NO. MSD PC 139 PCT

[0466] FLP-FRT, create site-specific recombination events that result in DSBs, often used in conditional gene editing. Nickase-paired approaches employ mutated nucleases to create two single-strand nicks close together, leading to a DSB. Restriction enzymes recognize short, specific DNA sequences and cleave DNA precisely but lack programmability for previously unrecognized target sites. These tools provide both targeted and untargeted DNA editing and repair systems.

[0467] Site-Directed Mutagenesis technique can be used to make amino acid mutations by changing the nucleotides in the cDNA that encodes the protein using e.g., Agilent Site-Directed Mutagenesis Kit (QuickChange Kit). Alternatively, a cDNA or a segment of cDNA can be synthesized with desired nucleotide changes, leading to amino acid changes in the protein.

[0468] 2. Methods of Treatment and Diseases to be Treated

[0469] There are three pathways of complement activation, the classical pathway, the alternative pathway, and the lectin pathway. Described herein are examples of complement factor B protein analogs and fusion proteins and dimers and multimers of the instant disclosure. In some forms, these complement factor B protein analogs and fusion proteins and dimers and multimcrs can attenuate the alternative pathway of complement activation. However, based on the way all three complement pathways intersect, these and fusion proteins and dimers and multimers can diminish inflammation caused by any of the three complement pathways and thereby provide therapy for any illness whose etiology involves, at least in part, complement activation. These include, but are not limited to, paroxysmal nocturnal hemoglobinuria (PNH), rheumatoid arthritis, juvenile rheumatoid arthritis, systemic lupus erythematosus (SLE), lupus nephritis, pediatric SLE, C3 glomerulopathy, early AMD, wet AMD, and geographic atrophy, multiple sclerosis, IgA nephropathy, vasculitis, and atherosclerosis.

[0470] The instant disclosure provides methods of treating a complement-mediated disease including administering to a patient a pharmaceutical preparation of the instant disclosure, a complement factor B analog or fusion protein or dimer or multimer thereof of the instant disclosure or a nucleic acid or vector encoding a complement factor B analog or fusion protein of the instant disclosure. The instant disclosure also includes methods of inhibiting complement activity, wherein the method includes administering to a human subject a mutated human complement factor B analog or fusion protein or dimer or multimer thereof in an amount sufficient to inhibit a complement pathway by compering with binding of native complement factor B in the subject.

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[0472] The instant disclosure also provides methods of inhibiting complement activity, wherein the methods include introducing to a site of the complement activity a complement factor B analog of the instant disclosure, a nucleic acid of the instant disclosure, a viral vector of the instant disclosure, a pharmaceutical composition / prcparation of the instant disclosure, or any combination thereof in an amount sufficient to inhibit the complement activity.

[0473] The instant disclosure provides methods of inhibiting complement activity, wherein the methods include introducing to a site of the complement activity a mutated human complement factor B analog or a disclosed fusion protein or dimer or multimer thereof in an amount sufficient to inhibit the complement activity by the mutated human complement factor B analog or a disclosed fusion protein or dimer or multimer thereof competing with binding of native complement factor B.

[0474] Complement pathways are a part of the immune system known as the innate immune system that provides immediate protection from infection prior to activation of the humoral and cell mediated branches of the immune system. They are activated and inactivated through cascading reactions that exhibit high order kinetics but are remarkably well-regulated. The alternative complement pathway, in particular, has evolved to cycle up with great rapidity through a positive feedback loop.

[0475] Complement factor B protein analogs and fusion proteins and dimers and multimers of the instant disclosure and / or the vectors that express them may advantageously be used for local and / or systemic administration to a mammal and / or to treat chronic diseases. In some forms of the instant disclosure, a complement factor B analog or a disclosed fusion protein or dimer or multimer thereof inhibits a complement pathway by competing with binding of the native complement factor B, e.g., to C3b protein. This can allow attenuation of complement activity as opposed to complete blockade of the pathway. Therefore, it may be possible to downregulate complement activity to a level that is therapeutic (e.g., alleviates some symptoms or their severity) without completely blocking complement activity. Thus, avoiding or decreasing the risks associated with blockage of complement activity, such as increased risk of infection. Therefore, the present instant disclosure provides methods for treating a complement mediated disease (e.g., a chronic disease) by local or systemic administration (e.g., i.v., subcutaneous, intravitreal, subretinal, intraperitoneal or oral) of a complement factor B protein analog or fusion protein or dimer or multimer of the instant disclosure.

[0476] In some forms, the present disclosure provides compositions and methods for modulating, regulating, and / or inhibiting a complement activity. Complement-related 45845704.1 83ATTORNEY DOCKET NO. MSD PC 139 PCT

[0477] pathways include, but are not limited to, the classical, lectin and alternative complement pathways. In some cases, a complement-related pathway may play a role in a particular condition, disease or diseases. Therefore, some forms of the instant disclosure provide methods of regulating, modifying, curing, inhibiting, preventing, ameliorating, slowing progression of and / or treating a disease state mediated by one or more complement-related pathways by administering a complement factor B analog or a disclosed fusion protein or dimer or multimer thereof of the instant disclosure or a nucleic acid or vector encoding a complement factor B analog or fusion protein of the instant disclosure. Such disease states or conditions include, but are not limited to, drusen formation, macular degeneration, AMD, geographic atrophy, dry eye, corneal ulcers, atherosclerosis, diabetic retinopathy, vitreoretinopathy (Grisanti et al. Invest. Ophthalmol. Vis. Sci. 32:2711-2717), corneal inflammation, airway hyperresponsiveness, immune-related diseases, autoimmune-related diseases, lupus nephritis, systemic lupus erythematosus (SLE), C3 glomerulopathy, arthritis (e.g., rheumatoid arthritis), rheumatologic diseases, anti-phospholipid antibody syndrome, intestinal and renal I / R injury, asthma, atypical hemolytic-uremic syndrome, Type II membranoproliferative glomerulonephritis, non-proliferative glomerulonephritis, fetal loss (e.g., spontaneous fetal loss), glaucoma, uveitis, ocular hypertension, brain injury (e.g., traumatic brain injury), stroke (e.g., see Arumugam et al. PNAS 93(12):5872-6 (1996)), post-traumatic organ damage, thermal trauma (e.g., burn injury), post infarction organ damage (e.g., cardiac, neurological), vasculitis, Kawasaki disease, hereditary angioedema (HAE), paroxysmal nocturnal hemoglobinuria (PNH, sometimes referred to as Marchiafava- Micheli syndrome), colitis, inflammatory bowel disease, tumor metastasis, ischemic-reperfusion injury, cerebrovascular accident, Alzheimer's disease, transplant rejection (e.g., xeno and allo), infections, sepsis, septic shock, Sjogren’s syndrome, myasthenia gravis, antibody-mediated skin diseases, all antibody-mediated organ-specific diseases (including Type I and Type II diabetes mellitus, thyroiditis, idiopathic thrombocytopenic purpura and hemolytic anemia, and neuropathies), insulin resistance syndrome (e.g., see Weyer et al. (2000) Diabetes Care, 23(6):779-785), gestational diabetes, multiple sclerosis, psoriasis, cardiopulmonary bypass injury, polyarteritis nodosa, Henoch Schonlein puipura, serum sickness, Goodpasture's disease, systemic necrotizing vasculitis, post streptococcal glomerulonephritis, idiopathic pulmonary fibrosis (usual interstitial pneumonitis), membranous glomerulonephritis, myocarditis (e.g., autoimmune myocarditis) (Kaya et al. Nat Immunol. 2001;2(8):739-45), myocardial infarction, muscular dystrophy (e.g., associated

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[0479] with dystrophin-deficiency), acute shock lung syndrome, adult respiratory distress syndrome, reperfusion, and / or a complement mediated disease.

[0480] In some forms, a complement-mediated disease is Lupus Nephritis. In some forms, a complement factor B analog or a disclosed fusion protein or dimer or multimer thereof or pharmaceutical composition thereof is administered via subcutaneously or intravenously, wherein the pharmaceutical composition includes a complement factor B analog or fusion protein or dimer or multimer thereof.

[0481] In some forms, a complement-mediated disease is a disease of the eye. In some forms, a complement factor B analog or a disclosed fusion protein or dimer or multimer thereof or a pharmaceutical composition thereof is administered to the eye, for example, by intravitreal injection, subretinal injection, injection to the intra- anterior chamber of the eye, injection or application locally to the cornea, subconjunctival injection, subtenon injection, or by eye drops. In some forms, a pharmaceutical composition is administered to the eye, wherein the pharmaceutical composition includes is a complement factor B analog or fusion protein or dimer or multimer thereof.

[0482] Age-related macular degeneration (AMD) is the most common cause of decreased vision in individuals over 65 years of age in the developed world. Dry AMD is characterized by a progressive degeneration of the macula causing central field visual loss. A more acute debilitating AMD includes choroidal neovascularization (CNV) and extravasation in the retina, known as wet AMD.

[0483] A characteristic of AMD is the accumulation of drusen, located between the basal lamina of the retinal pigment epithelium (RPE) and the inner layer of Bruch’s membrane (Pauleikhoff et al., 1990 Am. I. Ophthalmol. 109, 38-43; Bressler et al., 1990 Arch.

[0484] Ophthalmol. 108, 1442-1447). Drusen, as well as other age-related changes that occur proximal to Bruch’s membrane, are believed to contribute to the dysfunction and degeneration of the RPE and retina by inducing ischemia as well as restricting the exchange of nutrient and waste products between the retina and choroid (reviewed by Bird, 1992 Pathophysiology of AMD. In Age-Related Macular Degeneration: Principles and Practice (Hampton, G., and Nelsen, P. T., eds.) Chap. 3, Raven Press, New York). Several studies have indicated immune-mediated processes in the development of AMD. Importantly, autoantibodies were detected in the sera of AMD patients (Penfold et al., 1990 Graefes Arch. Clin. Exp. Ophthalmol. 228, 270-274), as predicted by the hypothesis that immune and inflammatory-mediated processes are involved in the development and / or removal of drusen.

[0485] 45845704.1 85ATTORNEY DOCKET NO. MSD PC 139 PCT

[0486] The formation of drusen in the eye can be associated with various diseases such as macular degeneration. In some cases, drusen formation and / or its association with a disease has been implicated to be related to complement activity. Some forms of the instant disclosure provide compositions and methods for modulating, regulating, inhibiting, reducing, retarding and / or reversing the formation or growth of drusen in an animal, such as a human. For example, compositions or molecules of the instant disclosure may be delivered to drusen (e.g., by direct injection into drusen (intradrusen injection), adjacent to drusen or intravitreal injection). Some forms of the instant disclosure can be utilized to slow the progression of macular degeneration, possibly by inhibiting drusen formation. Vitronectin, an abundant component of drusen, is also a component of extracellular deposits associated with atherosclerosis (Niculescu et al., 1989 Atherosclerosis, 78, 197-203), amyloidosis (Dahlback et al., 1993 J. Invest. Dermatol. 100, 166-170), elastosis (Dahlback et al., 1988 Acta Derm. Venereol. 68, 107-115), and MPGN type II (Jansen et al., 1993 Am. J. Pathol. 143, 1356-1365). Vitronectin is a multifunctional protein that functions in cell adhesion, maintenance of hemostasis, and inhibition of complement-induced cell lysis (Preissner, 1991 Ann. Rev. Cell Biol. 7, 275-310). Furthermore, atherosclerotic plaques share a number of other constituents with drusen, such as complement components and apoliproprotcin E. An association between advanced AMD and atherosclerosis of carotid arteries was reported in an epidemiological study (Vingerling et al., 1995 Am. J. Epidemiol. 142, 404-409) and another study identified a notable correlation between elastotic degeneration of nonsolar-exposed dermis and choroidal neovascularization in AMD patients (Blumenkranz et al., 1986 Ophthalmology, 93, 552-558). Finally, amyloid 0 peptide, a major constituent of neuritic plaques in Alzheimer’s disease, is also found in drusen (Johnson et al., 2002 Proc. Natl. Acad. Sci. USA, 99, 11830-11835). Amyloid 0 peptide has been implicated as a primary activator of complement (Bradt et al., 1998 J. Exp. Med. 188, 431-438).

[0487] Comprehensive analysis of the molecular composition of human drusen, as well as of the RPE cells that flank or overlie drusen, demonstrated immunoreactivity to immunoglobulins and components of the complement system that are associated with immune complex deposition (Johnson et al., 2000 Exp. Eye Res. 70, 441-449). Drusen also contains multifunctional proteins such as vitronectin (Hageman et al., 1999 FASEB J. 13, 477-484) and apolipoprotein E (Anderson et al., 2001 Am. J. Ophthalmol. 131, 767-781) that play a role in immune system modulation. In addition, molecules involved in the acute phase response to inflammation, such as amyloid P component and ou-antitrypsin, have also been identified in drusen (Mullins et al., 2000 The FASEB Journal, 14, 835-846), as well as 45845704.1 86ATTORNEY DOCKET NO. MSD PC 139 PCT

[0488] proteins involved in coagulation and fibrinolysis (factor X, thrombin, and fibrinogen) (Mullins et al., 2000 The FASEB Journal, 14, 835-846). Drusen formation and associated RPE pathology were indicated to contribute to a chronic inflammatory response that activates the complement cascade (Hageman et al., 2001 Prog. Rctin, Eye Res. 20, 705-732; Johnson et al., 2001 Exp. Eye Res. 73, 887-896).

[0489] One other form of an optic disorder arising from AMD and resulting in perturbations of the retina is geographic atrophy, which leads to death of patches of rod and cone cells, as well as of the RPE cells. Although two complement inhibitors have been recently approved for the treatment of geographic atrophy, these therapies, SYFOVRE (PEGylated anti-C3 peptide) and IZERVAY (PEGylated anti-C5 aptamer), have limited therapeutic efficacy and carry notable side effects to the patients. Not wishing to be bound by theory, limited efficacy and notable side effects associated with these approved drugs may be mainly due to their undesirable mechanisms of action as they inhibit all three complement pathways indiscriminately.

[0490] Atherosclerosis has been shown to typically involve complement related pathways, e.g., see Niculescu et al. Immunologic Research, 30(11:73-80(8) (2004) and Niculescu and Horca, Immunologic Research 30(l):73-80 (2004) and Liszcwski and Atkinson, Immunol Rev 313:60-63 (2024). Complement activation and C5b-9 deposition typically occurs both in human and experimental atherosclerosis. C5b-9 may be responsible for cell lysis, and sublytic assembly of C5b-9 induces smooth muscle cell (SMC) and endothelial cell (EC) activation and proliferation. Complement C6 deficiency has a protective effect on diet- induced atherosclerosis, indicating that C5b-9 assembly is required for, or at least plays a notable role, in the progression of atherosclerotic lesions, e.g.. see Niculescu and Horea, Immunologic Research 30(l):73-80 (2004). Some forms of the instant disclosure may be used to inhibit the formation of C5b-9 and / or inhibit atherosclerosis. In some forms, a complement factor B protein analog or a disclosed fusion protein or dimer or multimer thereof of the instant disclosure is administered to a site or potential site of atherosclerosis. This complement factor B protein analog or a disclosed fusion protein or dimer or multimer thereof inhibits a pathway (e.g., the classical and / or alternative complement pathway) which in turn inhibits the formation or activation of C5b-9 or another complement pathway related compound involved in atherosclerosis. There may be other complement related proteins involved in atherosclerosis whose formation and / or activation may be inhibited or blocked in a similar manner.

[0491] 45845704.1 87ATTORNEY DOCKET NO. MSD PC 139 PCT

[0492] Airway hyperresponsiveness (AHR) is characteristic of various diseases including, but not limited to, asthma (e.g., allergic asthma). AHR has been shown to typically involve complement related pathways, e.g., see Taube et al., 2006 PNAS 103(21):8084-8089; Park et al., American Journal of Respiratory and Critical Care Medicine 169:726-732, (2004);

[0493] Thurman and Holers, J Immunology 176:1305-1310 (2006). Park et al. showed that Crry -Ig administered by intraperitoneal injection had an effect on AHR. Some forms of the instant disclosure provide compositions and methods for modulating, regulating, inhibiting and / or reducing AHR in an animal, such as a human. Specific AHR related diseases that may be treated, alleviated, inhibited and / or ameliorated include, but are not limited to, asthma, chronic obstructive pulmonary' disease (COPD), allergic bronchopulmonary aspergillosis, hypersensitivity pneumonia, eosinophilic pneumonia, emphysema, bronchitis, allergic bronchitis bronchiectasis, cystic fibrosis, tuberculosis, hypersensitivity pneumonitis, occupational asthma, sarcoid, reactive airway disease syndrome, interstitial lung disease, hyper-eosinophilic syndrome, rhinitis, sinusitis, exercise-induced asthma, pollution-induced asthma, cough variant asthma, parasitic lung disease, respiratory syncytial vims (RSV) infection, parainfluenza vims (PIV) infection, rhino virus (RV) infection, Hantan virus (e.g., four-comers strain) and adenovirus infection.

[0494] Immune-related diseases such as autoimmune-related diseases, HLA-B27 associated inflammatory diseases, C3 glomerulopathy, lupus nephritis and systemic lupus erythematosus (SLE) have been shown to typically involve complement related pathways, e.g., see Thurman and Holers, J Immunology 176:1305-1310 (2006) and Li et al., J. Clin Med 10:626 (2021). Lupus nephritis is one complication of SLE. It is related to the autoimmune process of lupus, where the immune system produces antibodies (antinuclear antibody and others) against body¬ components. Complexes of these antibodies and complement components typically accumulate in the kidneys and result in an inflammatory response. Some forms of the instant disclosure provide methods and compositions for regulating, modifying, curing, inhibiting, preventing, ameliorating and / or treating an immune-related disease, e.g., involving or related to a complement pathway, such as SLE.

[0495] Arthritis has been shown to typically involve complement related pathways, e.g., see Thurman and Holers, J Immunology 176: 1305-1310 (2006); Banda et al. J Immunol.

[0496] 177(3): 1904-12 (2006); and Holers and Banda, Front Immunol. 9:1057 (2018). The alternative complement pathway plays a notable role in the induction of arthritis and the alternative complement pathway may even be required. The turnover of serum complement products is accelerated in active rheumatoid arthritis. Activated complement products are 45845704.1 88ATTORNEY DOCKET NO. MSD PC 139 PCT

[0497] elevated in synovial fluid. The alternative complement pathway is a major factor in juvenile idiopathic arthritis / juvenile rheumatoid arthritis (JRA). Non-responders to anti-TNF alpha agents have higher rates of complement turnover. Some forms of the instant disclosure provide methods and compositions for regulating, modifying, curing, inhibiting, preventing, ameliorating and / or treating arthritis, e.g., rheumatoid arthritis or inflammatory arthritis. Some forms provide methods and compositions for regulating, modifying, curing, inhibiting, preventing, ameliorating and / or treating arthritis, e.g., rheumatoid arthritis or inflammatory arthritis, in patients who are refractory to treatment (i.e., refractory rheumatoid arthritis). In some forms the subject is refractory to treatment any one or more disease-modifying antirheumatic drugs (DMARDs) and / or biologic therapies. In a non-limiting example, the patient is refractory to treatment with anti-TNF alpha agents.

[0498] Glaucoma is a group of diseases of the optic nerve involving loss of retinal ganglion cells in a characteristic pattern of optic neuropathy. Approximately 25% of glaucoma patients with retinal ganglion cell loss have normal ocular pressure. Ocular hypertension (OHT) is a notable risk factor for developing glaucoma and lowering it via pharmaceuticals or surgery is currently the mainstay of glaucoma treatment. Ocular hypertension and glaucoma have been shown to typically involve complement related pathways, e.g., sec Khalyfa el al., Molecular Vision, 13:293-308 (2007); Stasi el al. IOVS 47(3): 1024-1029 (2007); Kuehn et al., Experimental Eye Research 83:620-628 (2006); and Samelska et al., Cent Eur I Immunol. 46: 111-117 (2021). Expression and / or the presence of Clq and C3 have been shown to be higher in retina subjected to OHT. Some forms of the instant disclosure provide methods and compositions for regulating, modifying, curing, inhibiting, preventing, ameliorating and / or treating glaucoma.

[0499] Uveitis has been shown to typically be associated with the complement pathway, e.g., see Mondino and Rao, Investigative Ophthalmology & Visual Science 24:380-384 (1983) and Jha et al. Molecular Immunology 44:3901-3908 (2007). Mondino and Rao found that mean values of all tested complement components in aqueous humor to serum measurements were increased in patients with a history of previous eye surgeries and were highest in patients with anterior uveitis. Some forms of the instant disclosure provide methods and compositions for regulating, modifying, curing, inhibiting, preventing, ameliorating and / or treating uveitis.

[0500] Diabetic retinopathy is one of the leading causes of vision loss in middle-aged individuals. Activation of the complement system is believed to play an important role in the pathogenesis of diabetic retinopathy, e.g., see Iha et al. Molecular Immunology 44:3901- 45845704.1 89ATTORNEY DOCKET NO. MSD PC 139 PCT

[0501] 3908 (2007) and Shahulhameed et al., Front Immunol., 11: 154 (2020). Some forms of the instant disclosure provide methods and compositions for regulating, modifying, curing, inhibiting, preventing, ameliorating and / or treating diabetic retinopathy.

[0502] Proliferative vitrcorctinopathy (PV) is one of the most common complications of retinal detachment. PV has been linked to complement activity, e.g., see Grisante et al. Invest Ophthalmol Vis Sci. 1991;32( 10):2711-7 and Grisante et al. Ophthalmologe.

[0503] 1992;89(l):50-4. Some forms of the instant disclosure provide methods and compositions for regulating, modifying, curing, inhibiting, preventing, ameliorating and / or treating PV.

[0504] Anti-phospholipid antibody syndrome, intestinal and renal ischemic reperfusion PR injury, atypical hemolytic-uremic syndrome, Type II membranoproliferative glomerulonephritis, and fetal loss (e.g., spontaneous fetal loss), have been shown to typically involve complement related pathways, e.g., see Thurman and Holers, J Immunology 176:1305-1310 (2006).

[0505] Brain injury (e.g., traumatic brain injury) has been shown to typically involve complement related pathways, e.g., see Leinhase et al., J Neuroinflammation 4:13 (2007) and BMC Neurosci.7:55 (2006). Leinhase 2006, showed that after experimental traumatic brain injury in wild-type (fB+ / +) mice, there was a time-dependent systemic complement activation. In contrast, the extent of systemic complement activation was attenuated in fB- / -mice. Some forms of the instant disclosure provide methods and compositions for regulating, modifying, curing, inhibiting, preventing, ameliorating and / or treating neuronal cell death, traumatic neural injury (e.g. brain), complement-mediated neuroinflammation and / or neuropathology.

[0506] Ischemia-reperfusion injury can cause increases in the production of or oxidation of various potentially harmful compounds produced by cells and tissues, which can lead to oxidative damage to or death of cells and tissues. For example, renal ischemia-reperfusion injury can result in histological damage to the kidneys, including kidney tubular damage and changes characteristic of acute tubular necrosis. The resultant renal dysfunction permits the accumulation of nitrogenous waste ordinarily excreted by the kidney, such as serum urea nitrogen (BUN). Ischemia-reperfusion may also cause injury to remote organs, such as the lung. Some forms of the instant disclosure utilize modulators, such as inhibitors, of a complement pathway (e.g., inhibitors of factor B activity), e.g., when administered to a patient that has, or is at risk of experiencing or developing, ischemia-reperfusion. In some forms, these modulators, prevent, reduce or inhibit at least one symptom of injury due to ischemia-reperfusion. Other types of ischemia-reperfusion injury, that can be prevented or 45845704.1 90ATTORNEY DOCKET NO. MSD PC 139 PCT

[0507] reduced using methods and compositions of the instant disclosure, include, but are not limited to, cardiac ischemia-reperfusion injury such as myocardial infarction or coronary bypass surgery, central nervous system ischemia-reperfusion injury, ischemia-reperfusion injury of the limbs or digits, ischemia-reperfusion of internal organs such as the lung, liver or intestine, or ischemia-reperfusion injury of any transplanted organ or tissue.

[0508] Complement activity appears to be involved in muscular dystrophy (e.g., associated with dystrophin-deficiency). For example, see Spuler & Engel 1998 Neurology 50:41-46, and Selcen et al. 2001 Neurology 56:1472-1481. Therefore, some forms of the instant disclosure provide methods and compositions for regulating, modifying, curing, inhibiting, preventing, ameliorating and / or treating muscular dystrophy.

[0509] Complement activity may contribute to corneal inflammation. Therefore, some forms of the instant disclosure provide methods and compositions for regulating, modifying, curing, inhibiting, preventing, ameliorating and / or treating comeal inflammation, e.g., after surgery. In some forms, a complement factor B analog or fusion protein or dimer or multimer thereof of the instant disclosure is administered via eye drops or as otherwise described herein. In some forms, complement factor B analogs, fusion proteins, or dimers or multimers thereof of the instant disclosure are used for regulating, modifying, curing, inhibiting, preventing, ameliorating and / or treating corneal neovascularization.

[0510] Some forms of the instant disclosure provide methods for enhancing the efficacy of post-coronary or peripheral artery bypass grafting or angioplasty. In some forms, a vector of the instant disclosure encoding a complement factor B protein analog of the instant disclosure or fusion protein is used to transduce cells of a blood vessel (e.g., endothelial cells). In some forms, cells of a blood vessel are transduced prior to implantation in a patient. In some forms, cells of a blood vessel are transduced in vivo.

[0511] Alleviating pain and suffering and inflammation in postoperative patients is an area of special focus in clinical medicine, especially with the growing number of out-patient operations performed each year. Complement factor B analogs, fusion proteins, or dimers or multimers thereof of the present disclosure can be utilized to inhibit inflammation, e.g., by inhibiting a complement activity. Therefore, complement factor B analogs or a disclosed fusion protein or dimer or multimer thereof can be used to reduce inflammation, e.g., in postoperative patients. In some forms, a complement factor B analog or a disclosed fusion protein or dimer or multimer thereof is administered locally (e.g., perioperative delivery) to a site of surgery to inhibit inflammation, which in some cases will reduce pain and suffering. In some forms, a complement factor B analog or fusion protein or dimer or multimer is 45845704.1 91ATTORNEY DOCKET NO. MSD PC 139 PCT

[0512] administered in a solution, e.g., in a physiologic electrolyte carrier fluid. In some forms, a complement factor B analog or fusion protein or dimer or multimer is delivered via perioperative delivery directly to a surgical site of an irrigation solution containing the composition. In some forms, due to the local perioperative delivery method of the present disclosure, a desired therapeutic effect may be achieved with lower doses of agents than are necessary when employing other methods of delivery, such as intravenous, intramuscular, subcutaneous and oral. In some forms, when used perioperatively, the solution will result in a clinically notable decrease in operative site pain and / or inflammation, thereby allowing a decrease in the patient’s postoperative analgesic (e.g., opiate) requirement and, where appropriate, allowing earlier patient mobilization of the operative site. In some forms, no extra effort on the part of the surgeon and operating room personnel is required to use the present solution relative to conventional irrigation fluids. In some forms, a composition of the instant disclosure is used (e.g., in irrigation fluid) for arthroscopy, cardiovascular and general vascular therapeutic and diagnostic procedures, urologic procedures, general surgical wounds and wounds in general. Compositions of the instant disclosure may be delivered by, but not limited to, injection e.g., via syringe), via irrigation fluid, as part of a bandage over a wound, or in a topical application such as a solution, cream, gel or the like.

[0513] In some forms of the instant disclosure, a complement factor B analog or fusion protein or dimer or multimer and / or vector of the instant disclosure is administered in combination with a complement inhibiting factor, prior to, concurrently with, or after administration of the complement factor B analog or a disclosed fusion protein or dimer or multimer thereof and / or vector. A complement inhibiting factor includes, but is not limited to, a Factor H, a Factor H-like 1, an MCP, a DAF, or a soluble form of an MCP.

[0514] In some forms of the instant disclosure, a complement factor B analog or fusion protein or dimer or multimer or vector of the instant disclosure is administered in combination with an anti-angiogenic factor. Anti-angiogenic factors include, but is not limited to, endostatin, a VEGF binding molecule, PEDF, T2-TrpRS (e.g., see U. S. Patent No.

[0515] 7,273,844), sFLT (e.g., see Kong et al. Hum Gene Ther (1998) 9:823-833), aflibercept (VEGF Trap), VEGF Trap-eye, kininostatin, ranibizumab and bevacizumab.

[0516] In some forms, a complement factor B analog or fusion protein or dimer or multimer and / or vector of the instant disclosure is administered in combination with LUCENTIS® (ranibizumab), AVASTIN® (bevacizumab), VEGF Trap-eye, aflibercept or a molecule(s) that binds VEGF and / or that inhibits angiogenesis. LUCENTIS® is used to treat wet AMD. Some forms of the instant disclosure can also be used to treat wet AMD. Therefore, the 45845704.1 92ATTORNEY DOCKET NO. MSD PC 139 PCT

[0517] present disclosure provides methods and compositions for treating wet AMD including administering, separately or together, a composition of the instant disclosure in combination with LUCENTIS® (ranibizumab), AVASTIN® (Bevacizumab) VEGF Trap-eye, aflibercept and / or a molecule(s) that binds VEGF and / or that inhibits angiogenesis. Additionally, intraocular inflammation is one of the most common adverse reactions reported after administration of LUCENTIS®, e.g., see the “Full Prescribing Information” for LUCENTIS®. The present disclosure provides a method for inhibiting or reducing intraocular inflammation (e.g., resulting from the administration of LUCENTIS®) including administering a molecule or composition of the instant disclosure prior to, at the same time, and / or after the administration of LUCENTIS®, VEGF Trap-eye or aflibercept.

[0518] In some forms of the instant disclosure, a complement factor B analog or fusion protein or dimer or multimer or vector of the instant disclosure is administered in combination with another compound(s), such as a compound that inhibits T-cell activation, B-cells, TNF, interleukin- 1 e.g., interleukin- lb), interleukin-6 and / or interferon-gamma. A complement factor B analog or fusion protein or dimer or multimer or vector of the instant disclosure can also be administered in combination with a compound(s) that inhibits complement activity, e.g., Soliris. Compounds that can be used and which inhibit TNF include, but are not limited to, compounds that bind TNF, such as antibodies (e.g., Infliximab (REMICADE®), Golimumab (SIMPONI®) and Adalimumab (HUMIRA®)) or soluble receptors that bind TNF such as Etanercept (ENBREL®). Other compounds that can be used and which inhibit T-cell activation include, but are not limited to, compounds that bind B7 such as abatacept (ORENCIA®). Also compounds which downregulate B-cells can be used including, but not limited to, compounds that bind CD20 such as Rituximab (RITUXAN® and MABTHERA®).

[0519] In some forms, complement factor B analogs such as PC113-D and variants thereof that enhance the alternative complement pathway, can be used to treat diseases or conditions where complement activation is compromised or where further complement activation is beneficial as a therapy. In some forms, enhancing Factor B activity can help treat complement deficiency syndromes (C3, Factor D, and Properdin deficiencies), recurrent bacterial infections (Neisseria meningitidis, Gram-negative infections), chronic fungal infections (Cryptococcus, Candida), cancer (by enhancing complement-mediated tumor clearance), neurodegenerative diseases (Alzheimer’s and Parkinson’s with impaired complement function), chronic non-healing wounds, post-surgical tissue regeneration, and improving immune responses after organ transplantation. In some forms, complement factor 45845704.1 93ATTORNEY DOCKET NO. MSD PC 139 PCT

[0520] B analogs such as PCI 13-D and variants thereof can be used to treat severe viral infections such as COVID-19, pandemic flu, and Ebola where complement activities are needed to control the virus load.

[0521] Complement pathways contributing to and / or causing a disease can be modulated, regulated, inhibited and / or activated using various methods and / or complement factor B protein analogs and fusion proteins and dimers and multimers that are part of the disclosure provided herein.

[0522] a. Treatment of Complement-Mediated Diseases with PC139 or PC139-Fc Fusion Protein

[0523] The instant disclosure provides methods of treating a complement-mediated disease including administering to a patient a pharmaceutical preparation of the instant disclosure, PC139 or PC139-Fc fusion protein of the instant disclosure, or vector encoding PC139 or PC139-Fc of the instant disclosure. The instant disclosure also includes methods of inhibiting complement activity, wherein the method includes administering to a human subject PC139 or PC139-Fc, or vector encoding PC139 or PC139-Fc in an amount sufficient to inhibit a complement pathway by competing with binding of native complement factor B to C3b and factor D in the subject.

[0524] For example, PC 139 or PC139-Fc is administered to treat a patient with geographic atrophy (GA) via intraocular administration in an amount sufficient to inhibit a complement pathway, particularly overactivation of the alternative complement pathway. PC139 or PC139-Fc is administered into the patient’s eye at a dose of 5, 10, 15, 20, 25, 50, 60, 70, 80, 90, 100, 150, 200, 250, 300, 350, 400, 450, 500, 600, 700, 800, 900, or 1000 ug per treatment. The treatment is performed once every week, once every two weeks, once every three weeks, once every month, once every two months, once every three months, once every four months, once every five months, once every six months, once every year, or once every two years.

[0525] PC139 or PC139-Fc is administered systemically to treat a patient with lupus nephritis or rheumatoid arthritis via subcutaneous or intravenous administration in an amount sufficient to inhibit a complement pathway, particularly overactivation of the alternative complement pathway. PC139 or PC139-Fc is administered into a patient with GA at a dose of 0.1, 0.5, 1.0, 2.0, 3.0, 4.9, 5.0, 6.0, 7.0, 8.0, 9.0, 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, or 500 mg per kg of body weight per treatment. The treatment is performed once per day, once every two days, once every three days, once every four days, once every five days, once every six days, once every week, once every two weeks, once every three 45845704.1 94ATTORNEY DOCKET NO. MSD PC 139 PCT

[0526] weeks, once every month, once every two months, once every three months, once every four months, once every five months, once every six months, once every year, or once every two years.

[0527] PC139 or PC139-Fc is administered locally to a joint to treat a patient with rheumatoid arthritis in an amount sufficient to inhibit a complement pathway, particularly overactivation of the alternative complement pathway.

[0528] b. Treatment of Geographic Atrophy with a Gene Therapy Encoding PC139 or PC139-Fc

[0529] PC139 is delivered via AAV gene therapy vector to treat a patient with geographic atrophy via intraocular administration of the vector. The AAV vector encoding PC 139 is administered about once every year, 18 months, 2 years, 30 months, 3 years, 5 years, 10 years or as needed. The vector expresses and delivers PC139 to the retina of a patient with GA in an amount sufficient to inhibit a complement pathway, particularly overactivation of the alternative complement pathway in the retina of the patient with GA.

[0530] The AAV vector encoding PC 139 is administered by subretinal injection or intravitreal injection. About 5xl08to about IxlO9; about 5xl08to about 7.5xl08; about 7.5xl08to about IxlO9; about 6xl08to about 9xl08; about 7xl08to about 8xl08; about 9xl08; or about IxlO9; or about IxlO10; or about IxlO11; or about IxlO12vector genome copy (GC) number of the AAV vector is administered by subretinal injection. About 5xl08to about IxlO10; about 5xl08to about 5xl09; about 5x10sto about 2xl09; about 2xl09to about 5xl09; about 5xl09to about IxlO10; about IxlO10to about IxlO11; or IxlO11to about IxlO12; or IxlO12to about 5xl012GC of the AAV vector is administered by intravitreal injection. It is understood that the amount of AAV vector is sometimes measured in transducing units or in GC number. GC numbers are typically between 25-300 times higher than when the same AAV vector sample is measured for transducing units.

[0531] Alternatively, PC139 or PC139-Fc is delivered by herpes simplex virus (HSV)-based gene therapy vector to the eye of a patient with geographic atrophy.

[0532] 3. Effective Amounts

[0533] In some forms the methods administer the described factor B analog, or fusion protein or dimer or multimer in an effective amount. The effective amount or therapeutically effective amount of a pharmaceutical compositions disclosed herein can be administered in a dosage sufficient to treat, inhibit, or alleviate one or more symptoms of a disease or disorder or to otherwise provide a desired pharmacologic and / or physiologic effect, for example, reducing,

[0534] 45845704.1 95ATTORNEY DOCKET NO. MSD PC 139 PCT

[0535] inhibiting, or reversing one or more of the underlying pathophysiological mechanisms underlying a disease or disorder.

[0536] In some forms, when administration of the pharmaceutical compositions disclosed herein elicits an effective therapeutic response, the amount administered can be expressed as the amount effective to achieve a desired effect in the recipient. For example, in some forms, the amount of the pharmaceutical compositions disclosed herein, is effective to reduce the severity of the disease being treated. In some forms, the amount of the pharmaceutical composition disclosed herein is effective to reduce the symptoms of a disease in the recipient, or prevent or reduce a deficit or decline, and combinations thereof.

[0537] The effective amount of the pharmaceutical compositions disclosed herein will vary from subject to subject, depending on the species, age, weight and general condition of the subject, the severity of the disorder being treated, and its mode of administration. Thus, it is not possible to specify an exact amount for every pharmaceutical composition. However, an appropriate amount can be determined by one of ordinary skill in the art using only routine experimentation given the teachings herein. For example, effective dosages and schedules for administering the pharmaceutical compositions disclosed herein can be determined empirically, and making such determinations is within the skill in the art.

[0538] The dosage should not be so large as to cause adverse side effects, such as unwanted cross-reactions, anaphylactic reactions, and the like. Generally, the dosage will vary with the age, condition, and sex of the patient, route of administration, whether other drugs are included in the regimen, and the type, stage, and location of the disease to be treated. The dosage can be adjusted by the individual physician in the event of any counter-indications. It will also be appreciated that the effective dosage of the disclosed composition used for treatment can increase or decrease over the course of a particular treatment. Changes in dosage can result and become apparent from the results of diagnostic assays.

[0539] Dosage can vary, and can be administered in one or more dose administrations daily, for one or several days. Guidance can be found in the literature for appropriate dosages for given classes of pharmaceutical products. Optimal dosing schedules can be calculated from measurements of drug accumulation in the body of the subject or patient. Persons of ordinary skill can easily determine optimum dosages, dosing methodologies and repetition rates. Optimum dosages can vary depending on the relative potency of individual pharmaceutical compositions, and can generally be estimated based on EC50s found to be effective in in vitro and in vivo animal models.

[0540] 45845704.1 96ATTORNEY DOCKET NO. MSD PC 139 PCT

[0541] It can generally be stated that a pharmaceutical composition containing the disclosed compositions can be administered at a dosage of 10‘4mg / kg body weight to 100 mg / kg body weight, inclusive, preferably 0.1 to 10.0 mg / kg body weight, including all integer values within those ranges. In some forms, patients can be treated by infusing a disclosed pharmaceutical composition containing the disclosed compositions in the range of about 0.1 to 10.0 or more mg / kg body weight of the subject.

[0542] The infusion can be repeated as often and as many times as the patient can tolerate until the desired response is achieved. Compositions disclosed herein can also be administered once or multiple times at these dosages. The cells can be administered by using infusion techniques that are commonly known in immunotherapy (see, e.g., Rosenberg et al., New Eng. J. of Med. 319:1676, 1988). The optimal dosage and treatment regime for a particular patient can readily be determined by one skilled in the art of medicine by monitoring the patient for signs of disease and adjusting the treatment accordingly. In some forms, the unit dosage is in a unit dosage form for intravenous injection. In some forms, the unit dosage is in a unit dosage form for oral administration. In some forms, the unit dosage is in a unit dosage form for inhalation.

[0543] Treatment can be continued for an amount of time sufficient to achieve one or more desired therapeutic goals. Treatment can be continued for a desired period of time, and the progression of treatment can be monitored using any means known for monitoring the disease being treated in a patient. In some forms, administration is carried out every day of treatment, or every week, or every fraction of a week. In some forms, treatment regimens are carried out over the course of up to two, three, four or five days, weeks, or months, or for up to 6 months, or for more than 6 months, for example, up to one year, two years, three years, or up to five years.

[0544] The effectiveness of a specific dose of the pharmaceutical compositions containing the disclosed compositions, as described herein, can be assessed by reviewing the subject's medical history, clinical signs, symptoms, and relevant laboratory tests commonly used to evaluate the condition of individuals requiring treatment for diseases or conditions. These signs, symptoms, and laboratory tests will vary, depending upon the particular disease or condition being treated or prevented, as will be known to any clinician who treats such patients or a researcher conducting experimentation in this field. For example, if, based on a comparison with an appropriate control group and / or knowledge of the normal progression of the disease in the general population or the particular individual: (1) a subject’s physical condition is shown to be improved (e.g., a diseases state has partially or fully regressed), (2) 45845704.1 97ATTORNEY DOCKET NO. MSD PC 139 PCT

[0545] the progression of the disease or condition is shown to be stabilized, or slowed, or reversed, or (3) the need for other medications for treating the disease or condition is lessened or obviated, then a particular treatment regimen will be considered efficacious.

[0546] 4. Administration and Delivery

[0547] It is understood that when introduction or administration of a nucleic acid encoding a complement factor B protein analog or fusion protein is discussed, that the instant disclosure also contemplates the introduction or administration of the complement factor B protein analog or fusion protein or dimer or multimer itself. It is understood that when introduction of a complement factor B analog or fusion protein or dimer or multimer is discussed, that the instant disclosure also contemplates the introduction of a nucleic acid encoding the complement factor B protein analog or fusion protein.

[0548] In some forms, complement factor B analogs, fusion proteins, dimers, multimers, or other compositions of the instant disclosure can be administered locally or systemically. Useful routes of administration are described herein and known in the art. Methods of introduction or administration include, but are not limited to, intradermal, intramuscular, intraperitoneal, intravenous, subcutaneous, intranasal, intratracheal, topical, inhaled, transdermal, rectal, parenteral routes, epidural, intracranial, into the brain, intraventricular, subdural, intraarticular, intrathecal, intracardiac, intracoronary, intravitreal, subretinal, intra-anterior chamber of the eye, particular, locally on the cornea, subconjunctival, subtenon injection, by applying eyedrops, oral routes, via balloon catheter, via stent or any combinations thereof. In some forms, a composition of the instant disclosure is administered to a drusen, e.g., by injecting directly into a drusen. Systemic administration may be, but is not limited to, by intravenous or intra-arterial injection or by transmucosal, subcutaneous and / or transdermal delivery. In some forms, a composition of the instant disclosure may be initially directed to a site other than a diseased site. For example, regarding AHR which occurs in the lungs of a mammal, an intraperitoneal injection of a protein, vector or nucleic acid of the instant disclosure may result in a change in AHR in the lungs, e.g., see Park et al., American Journal of Respiratory and Critical Care Medicine 169:726-732, (2004). In some forms, a dosage level and / or mode of administration of a composition may depend on the nature of the composition, the nature of a condition(s) to be treated, and / or a history of an individual patient. In some forms, cells expressing a complement factor B analog or fusion protein of the instant disclosure are administered. These cells can be a cell line, xenogeneic, allogeneic or autologous.

[0549] 45845704.1 98ATTORNEY DOCKET NO. MSD PC 139 PCT

[0550] In some forms, e.g., including administration to the eye, a complement factor B protein analog or fusion protein or dimer or multimer or vector of the instant disclosure is administered about once every week, month, 2 months, 3 months, 6 months, 9 months, year, 18 months, 2 years, 30 months, 3 years, 5 years, 10 years or as needed. In some forms, e.g., including administration to the eye, a molecule or vector of the instant disclosure is administered from about every 1 to 4 weeks, about every 4 to 8 weeks, about every 1 to 4 months, about every 3 to 6 months, about every 4 to 8 months, about every 6 to 12 months, about every 9 to 15 months, about every 12 to 18 months, about every 15 to 21 months, about every 18 to 24 months, about every 1 to 2 years, about every 1.5 to 3 years, about every 2 to 4 years, about every 3 to 5 years, about every 5 to 7 years, about every 7 to 10 years or about every 10 to 20 years. It is expected that administration of a vector coding for a complement factor B protein analog or fusion protein would be less frequent than administration of the complement factor B protein analog or fusion protein or dimer or multimer. In some forms of the instant disclosure, a pharmaceutical preparation includes a vector encoding a complement factor B analog of fusion protein of the instant disclosure and the pharmaceutical preparation is administered only once to the patient.

[0551] In some forms, e.g., including administration to the eye, a vector coding for a complement factor B analog or fusion protein is administered 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more times to a patient in their lifetime. In some forms, e.g., including administration to the eye, an AAV vector of the instant disclosure is administered 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more times to a patient in their lifetime.

[0552] In some forms, a complement factor B protein analog or fusion protein or dimer or multimer of the instant disclosure is administered by intravitreal injection to a human eye. In some forms, about 15 pg to about 5 mg; about 15 pg to about 500 pg; about 100 pg to about 900 pg; about 300 pg to about 700 pg; about 500 pg to about 1 mg; about 1 mg to about 5 mg; about Img; or about 500 pg of a complement factor B protein analog or fusion protein or dimer or multimer is administered by intravitreal injection to a human eye.

[0553] In some forms, a complement factor B protein analog or fusion protein or dimer or multimer of the instant disclosure is administered by subretinal injection or intravitreal injection of a lentiviral or adeno associated viral (AAV) vector. In some forms, about 5x106to about 5xl08; about 5xl06to about 5xl07; about 5xl07to about 5xl08; about IxlO7to about IxlO8; about 3xl07to about 5xl07; about 2.5xl07; about 5xl07; about 7.5xl07; or about 1x108transducing units of a lentiviral vector is administered by subretinal injection. In some forms, about 5xl08to about IxlO9; about 5xl08to about 7.5xl08; about 7.5xl08to about 45845704.1 99ATTORNEY DOCKET NO. MSD PC 139 PCT

[0554] IxlO9; about 6x108to about 9x108: about 7x108to about 8x108; about 5x108; about 6x108; about 7x108; about 8x108; about 9x108; about IxlO9; about IxlO10; about IxlO11; about 2x1011Vector Genome (VG) of an AAV vector is administered by subretinal injection.

[0555] In some forms, about 5x108to about IxlO10; about 5x108to about 5xl09; about 5x108to about 2xl09; about 2xl09to about 5xl09; about 5xl09to about IxlO10; about 5x108to about IxlO9; about IxlO9to about 3xl09; about 3xl09to about 6xl09; about 6xl09to about IxlO10; or about IxlO9to about IxlO10or about IxlO11to about IxlO12Vector Genome (VG) of an AAV vector is administered by intravitreal injection.

[0556] In some forms, about 50 pl to about 100 pl, about 50 pl to about 75 pl, about 75 pl to about 100 pl, about 60 pl to about 90 pl, about 70 pl to about 80 pl, about 50 pl; about 60 pl; about 70 pl; about 80 pl; about 90 pl; or about 100 pl of a complement factor B protein analog or fusion protein or dimer or multimer or a vector encoding a complement factor B protein analog or fusion protein is injected subretinally. In some forms, about 50 pl to about 1 ml, about 50 pl to about 500 pl, about 500 pl to about 1 ml, about 250 pl to about 750 pl, about 250 pl to about 500 pl, about 500 pl to about 750 pl, about 400 pl to about 600 pl, or about 750 pl to about 1 ml of a complement factor B protein analog or fusion protein or dimer or multimer or a vector encoding a complement factor B protein analog or fusion protein is injected intravitreally.

[0557] In some forms, an anti-inflammatory may be delivered in combination with a complement factor B protein analog or fusion protein or dimer or multimer, vector or nucleic acid of the instant disclosure. An anti-inflammatory may be delivered prior to, concurrently with, and / or after administration of a molecule or vector of the instant disclosure. In some forms, an anti-inflammatory is administered in the same solution and / or same syringe as a complement factor B protein analog, or fusion protein or dimer or multimer, or nucleic acid or vector of the instant disclosure. In some forms, a complement factor B protein analog or fusion protein or dimer or multimer or vector of the instant disclosure and an antiinflammatory are co-administered to the eye, e.g., as described herein.

[0558] Many anti-inflammatory drugs are known in the art and include, but are not limited to, dexamethasone, dexamethasone sodium metasulfobenzoate, dexamethasone sodium phosphate, fluorometholone, bromfenac, pranoprofen, RESTASIS™, cyclosporine ophthalmic emulsion, naproxen, glucocorticoids, ketorolac, ibuprofen, tolmetin, non-steroidal anti-inflammatory drugs, steroidal anti-inflammatory drugs, diclofenac, flurbiprofen, indomethacin, and suprofen.

[0559] 45845704.1 100ATTORNEY DOCKET NO. MSD PC 139 PCT

[0560] Some forms of the instant disclosure include administration of both a complement factor B protein analog or fusion protein or dimer or multimer and a vector encoding it. A complement factor B protein analog or fusion protein or dimer or multimer of the instant disclosure may be delivered prior to, concurrently with, and / or after administration of a vector of the instant disclosure. In some forms, a complement factor B protein analog or fusion protein or dimer or multimer of the instant disclosure is administered in the same solution and / or same syringe as a vector of the instant disclosure. In some forms, a complement factor B protein analog or fusion protein or dimer or multimer of the instant disclosure and a vector of the instant disclosure are co-administered to the eye, e.g., as described herein.

[0561] Additionally, a complement factor B analog or fusion protein or dimer or multimer or a nucleic acid encoding it can be delivered or administered to a mammal via a cell, e.g., as cell therapy. For example, this can be accomplished by administering or delivering a cell(s) expressing and secreting a complement factor B analog(s) and / or fusion protein(s). In some forms, a complement factor B analog(s) and / or fusion protein(s) is expressed from the cell via a regulatable, inducible and / or repressible promoter. In some forms, cells are administered locally e.g., in a joint, intravitreal, intraretinal, intracranially etc.) or systemically e.g., i.v.).

[0562] Cells to be administered to a mammal can be autologous, allogeneic or xenogeneic. In some forms, autologous cells are manipulated ex vivo to cause them to produce a complement factor B protein analog and / or fusion protein of the instant disclosure and, in some forms, the cells are introduced back to the animal. Transferring a nucleic acid included of a coding region to cells ex vivo can be by any method, such as, electroporation, microinjection, cell fusion, chromosome-mediated gene transfer, microcell-mediated gene transfer, spheroplast fusion, lipofection, microparticle bombardment, calcium phosphate mediated transfection, viral vectors and so on. Optionally, a selectable marker also can be introduced into the cells. If a selectable marker is utilized, the cells can be then placed under selection, e.g., to enhance expression and / or to isolate those cells that express the transferred coding region (see, e.g., Loeffler & Behr, Meth. Enzymol. 217:599-618 (1993); Cohen et al.. Meth. Enzymol. 217:618-644 (1993); and Cline, Pharmac. Ther. 29:69-92 (1985)).

[0563] Recombinant cells (e.g., autologous or allogeneic cells transduced in vitro) can be delivered to a patient by various methods known in the art. For example, cells can be encapsulated prior to administration, as known in the art. In some forms, when encapsulated, the cells are not autologous. In some forms, recombinant blood cells (e.g., hematopoietic stem and / or progenitor cells) are administered intravenously. In some forms, eye cells and / or 45845704.1 JOIATTORNEY DOCKET NO. MSD PC 139 PCT

[0564] pluripotential cells can be injected directly into the eye. The amount of cells needed depends on the desired effect, the animal’s state, etc.

[0565] In some forms of the instant disclosure, a gene delivery system can result in transduction and / or stable integration of a gene or coding region for a complement factor B analog and / or fusion into a target cell. In some forms, target cells are mammalian cells such as primate cells, and human cells. In some forms, target cells are cells of the eye, such as retinal pigment epithelial cells, retinal cells, or pluripotential cells. Target cells can be in vitro, ex vivo or in vivo. In some forms, a target cell is a stem cell. Stem cells include, but are not limited to, pluripotent stem cells, totipotent stem cells, hematopoietic stem cells, cancer stem cells and embryonic stem cells. In some forms, pluripotential cells contemplated herein are not those for propagating a living entity from a zygote or blastomere. The instant disclosure also contemplates the use of a partially undifferentiated cell for implantation into the eye of a patient in need of treatment, e.g., to regenerate cells of the eye.

[0566] 5. Combination Therapy

[0567] In some forms the methods administer the disclosed composition in combination with other therapeutic agents or treatment modalities. Any of the disclosed pharmaceutical compositions can be used alone, or in combination with other therapeutic agents or treatment modalities, for example, conventional medications. As used herein, “combination” or “combined” refer to either concomitant, simultaneous, or sequential administration of the therapeutics.

[0568] In some forms, the pharmaceutical compositions and other therapeutic agents are administered separately through the same route of administration. In other forms, pharmaceutical compositions and other therapeutic agents are administered separately through different routes of administration. The combinations can be administered either concomitantly (e.g., as an admixture), separately but simultaneously (e.g., via separate intravenous lines into the same subject; one agent is given orally while the other agent is given by infusion or injection, etc.,), or sequentially (e.g., one agent is given first followed by the second).

[0569] Examples of additional therapeutic agents include other conventional therapies known in the art for treating the desired disease, disorder or condition. In some forms, the therapeutic agent is one or more other targeted therapies.

[0570] The compositions and methods described herein may be used as a first therapy, second therapy, third therapy, or combination therapy with other types of therapies known in the art, such as chemotherapy, surgery, radiation, gene therapy, immunotherapy, bone 45845704.1 102ATTORNEY DOCKET NO. MSD PC 139 PCT

[0571] marrow transplantation, stem cell transplantation, targeted therapy, cryotherapy, ultrasound therapy, photodynamic therapy, radio-frequency ablation or the like, in an adjuvant setting or a neoadjuvant setting.

[0572] The disclosed pharmaceutical compositions and / or other therapeutic agents, procedures or modalities can be administered during periods of active disease, or during a period of remission or less active disease. The pharmaceutical compositions can be administered before the additional treatment, concurrently with the treatment, post-treatment, or during remission of the disease or disorder. When administered in combination, the disclosed pharmaceutical compositions and the additional therapeutic agents (e.g., second or third agent), or all, can be administered in an amount or dose that is higher, lower or the same than the amount or dosage of each agent used individually, e.g., as a monotherapy. In certain forms, the administered amount or dosage of the disclosed pharmaceutical composition, the additional therapeutic agent (e.g., second or third agent), or all, is lower (e.g., at least 20%, at least 30%, at least 40%, or at least 50%) than the amount or dosage of each agent used individually, e.g., as a monotherapy (e.g., required to achieve the same therapeutic effect).

[0573] D. Kits

[0574] The compositions disclosed herein can be packaged in kit. The kit can include a single dose or a plurality of doses of a composition including one or more of the disclosed factor B analogs, fusion proteins, dimers and multimers, or pharmaceutical formulation thereof, and instructions for administering the compositions. Specifically, the instructions direct that an effective amount of the composition be administered to an individual with a particular symptoms, disease, defect, or impairment as indicated. The composition can be formulated as described above with reference to a particular treatment method and can be packaged in any convenient manner.

[0575] The compositions, reagents, and other materials disclosed herein can be packaged together in any suitable combination as a kit useful for performing, or aiding in the performance of the methods. It is useful if the components in a given kit are designed and adapted for use together in the method. For example, kits with one or more compositions for administration to a subject, may include a pre-measured dosage of the composition in a sterile needle, ampule, tube, container, or other suitable vessel. The kits may include instructions for dosages and dosing regimens.

[0576] In some forms, the kit includes disclosed composition within a cell and / or within a vector (e.g., a viral vector) and / or nucleic acids encoding the disclosed composition, and instructional material for use thereof. In certain forms, the kit includes a plurality of vectors, 45845704.1 103ATTORNEY DOCKET NO. MSD PC 139 PCT

[0577] where each vector independently contains disclosed composition for insertion into a host cell genome. In some forms, the kit contains a population of cells collectively containing compositions disclosed herein. The instructional material can include a publication, a recording, a diagram, or any other medium of expression which can be used to communicate the usefulness of the compositions and methods of the kit. For example, the instructional material may provide instructions for methods using the kit components, such as performing transfections, transductions, infections, and conducting screens.

[0578] The disclosed compositions, methods, and kits can be further understood through one or more of the following numbered paragraphs.

[0579] Paragraph 1. A polypeptide including a complement factor B protein analog, wherein the complement factor B analog includes the substitutions Lysine to Asparagine at position 258, Arginine to Alanine, Leucine, Glycine, or Aspartic Acid at position 259, and Lysine to Threonine or Serine at position 260 of SEQ ID NO: 1.

[0580] Paragraph 2. The polypeptide of paragraph 1, wherein the substitution at 259 is Leucine, and the substitution at 260 is Threonine.

[0581] Paragraph 3. A polypeptide including a complement factor B protein analog, wherein the complement factor B analog includes an aspartic acid substitution at the position corresponding to the arginine at position 259 of SEQ ID NO:1.

[0582] Paragraph 4. The polypeptide of paragraph 3 further including an additional mutation in a complement factor D cleavage site.

[0583] Paragraph 5. The polypeptide of any one of paragraphs 1-4 further including

[0584] a) a mutation of a free cysteine amino acid, and / or

[0585] b) a mutation in a C3b binding site.

[0586] Paragraph 6. The polypeptide of any one of paragraphs 1-5, wherein the substitutions create an N-glycosylation site that increases the in vivo half-life and / or stability of the polypeptide compared to a corresponding polypeptide without the N-glycosylation site.

[0587] Paragraph 7. The polypeptide of any one of paragraph 5 or paragraph 6, wherein the mutation of the free cysteine amino acid includes a substitution of the free cysteine, optionally wherein the free cysteine is substituted with more than one amino acid.

[0588] Paragraph 8. The polypeptide of any one of paragraphs 5-7, wherein the complement factor B protein analog is an analog of SEQ ID NO:1 and the complement factor B protein analog has cysteine amino acids that form disulfide bonds and the free cysteine amino acid has been substituted by another amino acid.

[0589] 45845704.1 104ATTORNEY DOCKET NO. MSD PC 139 PCT

[0590] Paragraph 9. The polypeptide of any one of paragraphs 5-8, wherein the free cysteine is substituted with an amino acid selected from alanine, histidine, isoleucine, leucine, methionine, phenylalanine, serine, threonine, tyrosine and valine.

[0591] Paragraph 10. The polypeptide of any one of paragraphs 5-6, wherein the mutation of the free cysteine amino acid includes a deletion of the free cysteine.

[0592] Paragraph 11. The polypeptide of any one of paragraphs 5-10, wherein the free cysteine corresponds to amino acid 292 of SEQ ID NO:1.

[0593] Paragraph 12. The polypeptide of any one of paragraphs 5-11, wherein the mutation in the C3b binding site includes:

[0594] (i) a substitution or deletion of an aspartic acid corresponding to amino acid 279 of SEQ ID NO:1, a substitution or deletion of an asparagine corresponding to amino acid 285 of SEQ ID NO:1 or both; or

[0595] (ii) an insertion of at least one amino acid next to the aspartic acid or the asparagine. Paragraph 13. The polypeptide of paragraph 12, wherein the aspartic acid, the asparagine or both are substituted with one or more amino acids.

[0596] Paragraph 14. The polypeptide of any one of paragraphs 12-13, wherein the aspartic acid is substituted with glycine, alanine or asparagine.

[0597] Paragraph 15. The polypeptide of any one of paragraphs 12-14, wherein the asparagine is substituted with glycine, alanine, or aspartic acid.

[0598] Paragraph 16. The polypeptide of any one of paragraphs 12-15, wherein the substitution includes replacing the aspartic acid with glycine and the asparagine with aspartic acid.

[0599] Paragraph 17. The polypeptide of any one of paragraphs 1-16, wherein the complement factor B protein analog exhibits increased binding affinity to C3b as compared to a binding affinity of a corresponding native complement factor B protein to C3b.

[0600] Paragraph 18. The polypeptide of any of one of paragraphs 1-17, wherein the complement factor B protein analog has increased C3b binding affinity as compared to a corresponding native complement factor B protein and the complement factor B protein analog includes (i) diminished protease activity as compared to the corresponding native complement factor B protein;

[0601] (ii) diminished ability to be cleaved by a factor D protein as compared to the corresponding native complement factor B protein; or

[0602] (iii) diminished protease activity as compared to the corresponding native complement factor B protein and diminished ability to be cleaved by a factor D protein as compared to the corresponding native complement factor B protein.

[0603] 45845704.1 105ATTORNEY DOCKET NO. MSD PC 139 PCT

[0604] Paragraph 19. The polypeptide of any one of paragraphs 1-18, wherein the mutation in the complement factor D cleavage site includes an insertion next to one or more of positions 258, 259, and 260 relative to SEQ ID NO:1.

[0605] Paragraph 20. The polypeptide of any one of paragraphs 3-19, including aspartic acid at position 259, and wherein the mutation in the complement factor D cleavage site further includes a substitution or deletion of one or both lysines corresponding to amino acid 258 or 260 of SEQ ID NO:1, optionally wherein the amino acids corresponding to amino acids 258 and 260 of SEQ ID NO:1 are each substituted with alanine.

[0606] Paragraph 21. The polypeptide of any one of paragraphs 1-20, wherein the complement factor B analog competes with binding of the native complement factor B.

[0607] Paragraph 22. The polypeptide of any one of paragraphs 1-21, wherein the complement factor B protein analog is an analog of human complement factor B protein.

[0608] Paragraph 23. The polypeptide of any one of paragraphs 1-22, wherein the complement factor B protein analog includes at least one mutation corresponding to a mutation of SEQ ID NO:1 selected from D279G, N285D and C292S.

[0609] Paragraph 24. The polypeptide of any one of paragraphs 1-23, wherein the polypeptide includes the amino acid sequence of SEQ ID NO:3 or 12 with or without a signal sequence, or a variant thereof with at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO: 3 or 12.

[0610] Paragraph 25. The polypeptide of any one of paragraphs 1-24, wherein the complement factor B protein analog, includes mutations corresponding to K258N, R259L, K260T, D279G, N285D and C292S of SEQ ID NO:1.

[0611] Paragraph 26. The polypeptide of any one of paragraphs 1-25, wherein the complement factor B protein analog includes at least one mutation corresponding to a mutation of SEQ ID NO:1 selected from K258A, K260A, D279G, N285D and C292S.

[0612] Paragraph 27. The polypeptide of paragraph 26, wherein an amino acid corresponding to amino acids 259 of SEQ ID NO: 1 is substituted with a glycine, optionally wherein the polypeptide includes the amino acid sequence of SEQ ID NO:30 with or without the signal sequence, or a variant thereof with at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO:30.

[0613] Paragraph 28. The polypeptide of paragraph 27, wherein the glycine substitution decreases or ablates cleavage of the complement factor B protein analog by factor D protein.

[0614] 45845704.1 106ATTORNEY DOCKET NO. MSD PC 139 PCT

[0615] Paragraph 29. The polypeptide of any one of paragraphs 26-28, wherein the complement factor B protein analog, includes mutations corresponding to K258A, R259G, K260A, D279G, N285D and C292S relative to SEQ ID NO:1.

[0616] Paragraph 30. The polypeptide of any one of paragraphs 1-29, wherein the polypeptide inhibits or reduces complement activity.

[0617] Paragraph 31. The polypeptide of any one of paragraphs 1-30, wherein the polypeptide inhibits the alternative complement pathway.

[0618] Paragraph 32. The polypeptide of any one of paragraphs 1-25, wherein an amino acid corresponding to amino acid 259 of SEQ ID NO:1 is substituted with an aspartic acid, optionally wherein the polypeptide includes the amino acid sequence of SEQ ID NO:31 with or without the signal sequence, or a variant thereof with at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO:31.

[0619] Paragraph 33. The polypeptide of paragraph 32, wherein the aspartic acid substitution enhances cleavage of the complement factor B protein analog by factor D protein.

[0620] Paragraph 34. The polypeptide of paragraph 32 or paragraph 33, wherein the complement factor B protein analog includes mutations corresponding to K258A, R259D, K260A, D279G, N285D and C292S of SEQ ID NO:1.

[0621] Paragraph 35. The polypeptide of any one of paragraphs 32-34, wherein the polypeptide enhances complement activity.

[0622] Paragraph 36. The polypeptide of any one of paragraphs 32-35, wherein the polypeptide enhances the alternative complement pathway.

[0623] Paragraph 37. The polypeptide of any one of paragraphs 1-29, wherein the complement factor B protein analog is at least 90%, at least 95%, at least 98% or at least 99% identical to SEQ ID NO:1, 2, 3, 5, 11, 12, 26, 28, 30, or 31, with or without the signal sequence.

[0624] Paragraph 38. A fusion protein including a first fusion partner including a complement factor B analog and a second fusion partner, wherein the N-terminus of the first fusion partner is fused directly or linked by a linker peptide or polypeptide sequence to the C-terminus of the second fusion partner.

[0625] Paragraph 39. A fusion protein including a first fusion partner including a polypeptide of any one of paragraphs 1-37 fused directly or linked by a linker peptide or polypeptide sequence to the second fusion partner.

[0626] Paragraph 40. The fusion protein of paragraph 39, wherein the first fusion partner is contiguous with the carboxyl terminus of the second fusion partner, or the second fusion partner is contiguous with the carboxyl terminus of the first fusion partner.

[0627] 45845704.1 107ATTORNEY DOCKET NO. MSD PC 139 PCT

[0628] Paragraph 41. The fusion protein of paragraph 40, wherein the first fusion partner is contiguous with the carboxyl terminus of the second fusion partner.

[0629] Paragraph 42. The fusion protein of any one of paragraphs 38-41, wherein the second fusion partner includes an immunoglobulin Fc region.

[0630] Paragraph 43. The fusion protein of paragraph 42, wherein the immunoglobulin Fc region is an IgG4 Fc.

[0631] Paragraph 44. The fusion protein of any one of paragraphs 39-43 wherein the fusion protein includes the amino acid sequence of SEQ ID NO:5 and SEQ ID NO: 17 with or without a signal sequence, or a variant thereof with at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO:5 and SEQ ID NO: 17.

[0632] Paragraph 45. The fusion protein of any of paragraphs 38-44, including a domain that mediates dimerization or multimerization of the fusion protein to form homodimers, heterodimers, homomultimers, or heteromultimers.

[0633] Paragraph 46. The fusion protein of paragraph 45, wherein the domain that mediates dimerization or multimerization is selected from one or more cysteines that are capable of forming an intermolecular disulfide bond with a cysteine on the partner fusion protein, a coiled-coil domain, an acid patch, a zinc finger domain, a calcium hand domain, a CHI region, a CL region, a leucine zipper domain, an SH2 (sre homology 2) domain, an SH3 (sre Homology 3) domain, a PTB (phosphotyrosine binding) domain, a WW domain, a PDZ domain, a 14-3-3 domain, a WD40 domain, an EH domain, a Lim domain, an isoleucine zipper domain, and a dimerization domain of a receptor dimer pair, or a combination thereof. Paragraph 47. A dimeric protein including a first and a second fusion protein, wherein the first and the second fusion proteins include the fusion protein of any of paragraphs 38-46, wherein the first and the second fusion proteins are bound to one another by covalent or noncovalent bonds to form a dimer.

[0634] Paragraph 48. The dimeric protein of paragraph 47, wherein the dimer is a homodimer including the first fusion protein including the amino acid sequence of SEQ ID NO:3, 5, 11, 12, 26, 28, 30, or 31 with or without a signal sequence, or a variant thereof with at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO:3, 5, 11, 12, 26, 28, 30, or 31 and the second fusion protein including the amino acid sequence of SEQ ID NO:3, 5, 11, 12, 26, 28, 30, or 31 with or without a signal sequence, or a variant thereof with at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO: 3, 5, 11, 12, 26, 28, 30, or 31.

[0635] 45845704.1 108ATTORNEY DOCKET NO. MSD PC 139 PCT

[0636] Paragraph 49. A multimeric protein including two or more fusion proteins, wherein each of the fusion proteins include the fusion protein of any of paragraphs 38-48, wherein the fusion proteins are bound to one another by covalent or noncovalent bonds to form a multimer. Paragraph 50. The multimeric protein of paragraph 49, wherein the multimer is a homomultimer.

[0637] Paragraph 51. A heterodimeric protein including a first and a second fusion protein, wherein (i) the first fusion protein includes a first fusion partner fused to a second fusion partner, wherein the first fusion partner of the first fusion protein includes a complement Factor B analog fused directly or linked by a linker peptide or polypeptide sequence to the second fusion partner of the first fusion protein.; and

[0638] (ii) the second fusion protein includes a first fusion partner fused to a second fusion partner, wherein the first fusion partner of the second fusion protein includes an antiinflammatory molecule fused directly to a second fusion partner of the second fusion or linked by a linker peptide or polypeptide sequence to the second fusion partner of the second fusion protein.

[0639] Paragraph 52. The heterodimeric protein of paragraph 51, wherein the first fusion protein includes the fusion protein of any one of paragraphs 38-46.

[0640] Paragraph 53. A heterodimeric protein of paragraph 51 and paragraph 52, wherein the antiinflammatory molecule a blocker of an inflammatory pathway initiated by IL4, IL6, IL13, IL17, IL22, IL23, IL31, Thymic Stromal lymphopoietin (TSLP), or OX40-OX40L axis, optionally wherein the anti-inflammatory molecule is an antigen binding fragment that binds to IL4, IL6, IL13, IL17, IL22, IL23, IL31, TSLP, and 0X40 or a soluble receptors that can bind these inflammatory molecules that include, but are not limited to, IL4, IL6, IL13, IL17, IL22, IL23, IL31, TSLP, and 0X40, optionally wherein the anti-inflammatory molecule is soluble IL-17 receptor A (sIL-17RA).

[0641] Paragraph 54. The heterodimeric protein of paragraphs 51-53, wherein the second fusion partner of the second fusion protein includes an immunoglobulin Fc region.

[0642] Paragraph 55. The heterodimeric protein of paragraph 54, wherein the immunoglobulin Fc region is an IgG4 Fc.

[0643] Paragraph 56. The heterodimeric protein of any one of...

Claims

ATTORNEY DOCKET NO. MSD PC 139 PCTCLAIMSWe claim:

1. A polypeptide comprising a complement factor B protein analog, wherein the complement factor B analog comprises the substitutions Lysine to Asparagine at position 258, Arginine to Alanine, Leucine, Glycine, or Aspartic Acid at position 259, and Lysine to Threonine or Serine at position 260 of SEQ ID NO: 1.

2. The polypeptide of claim 1, wherein the substitution at 259 is Leucine, and the substitution at 260 is Threonine.

3. A polypeptide comprising a complement factor B protein analog, wherein the complement factor B analog comprises an aspartic acid substitution at the position corresponding to the arginine at position 259 of SEQ ID NO:1.

4. The polypeptide of claim 3 further comprising an additional mutation in a complement factor D cleavage site.

5. The polypeptide of any one of claims 1-4 further comprisinga) a mutation of a free cysteine amino acid, and / orb) a mutation in a C3b binding site.

6. The polypeptide of any one of claims 1-5, wherein the substitutions create an N-glycosylation site that increases the in vivo half-life and / or stability of the polypeptide compared to a corresponding polypeptide without the N-glycosylation site.

7. The polypeptide of any one of claims 5 or 6, wherein the mutation of the free cysteine amino acid comprises a substitution of the free cysteine, optionally wherein the free cysteine is substituted with more than one amino acid.

8. The polypeptide of any one of claims 5-7, wherein the complement factor B protein analog is an analog of SEQ ID NO:1 and the complement factor B protein analog has cysteine amino acids that form disulfide bonds and the free cysteine amino acid has been substituted by another amino acid.

9. The polypeptide of any one of claims 5-8, wherein the free cysteine is substituted with an amino acid selected from a group consisting of alanine, histidine, isolcucinc, leucine, methionine, phenylalanine, serine, threonine, tyrosine and valine.

10. The polypeptide of any one of claims 5-6, wherein the mutation of the free cysteine amino acid comprises a deletion of the free cysteine.

11. The polypeptide of any one of claims 5-10, wherein the free cysteine corresponds to amino acid 292 of SEQ ID NO: 1.45845704.1 144ATTORNEY DOCKET NO. MSD PC 139 PCT12. The polypeptide of any one of claims 5-11, wherein the mutation in the C3b binding site comprises:(i) a substitution or deletion of an aspartic acid corresponding to amino acid 279 of SEQ ID NO:1, a substitution or deletion of an asparagine corresponding to amino acid 285 of SEQ ID NO: 1 or both; or(ii) an insertion of at least one amino acid next to the aspartic acid or the asparagine.

13. The polypeptide of claim 12, wherein the aspartic acid, the asparagine or both are substituted with one or more amino acids.

14. The polypeptide of any one of claims 12-13, wherein the aspartic acid is substituted with glycine, alanine or asparagine.

15. The polypeptide of any one of claims 12-14, wherein the asparagine is substituted with glycine, alanine, or aspartic acid.

16. The polypeptide of any one of claims 12-15, wherein the substitution comprises replacing the aspartic acid with glycine and the asparagine with aspartic acid.

17. The polypeptide of any one of claims 1-16, wherein the complement factor B protein analog exhibits increased binding affinity to C3b as compared to a binding affinity of a corresponding native complement factor B protein to C3b.

18. The polypeptide of any of one of claims 1-17, wherein the complement factor B protein analog has increased C3b binding affinity as compared to a corresponding native complement factor B protein and the complement factor B protein analog comprises(i) diminished protease activity as compared to the corresponding native complement factor B protein;(ii) diminished ability to be cleaved by a factor D protein as compared to the corresponding native complement factor B protein; or(iii) diminished protease activity as compared to the corresponding native complement factor B protein and diminished ability to be cleaved by a factor D protein as compared to the corresponding native complement factor B protein.

19. The polypeptide of any one of claims 1-18, wherein the mutation in the complement factor D cleavage site comprises an insertion next to one or more of positions 258, 259, and 260 relative to SEQ ID NO:1.

20. The polypeptide of any one of claims 3-19, comprising aspartic acid at position 259, and wherein the mutation in the complement factor D cleavage site further comprises a substitution or deletion of one or both lysines corresponding to amino acid 258 or 260 of SEQ45845704.1 145ATTORNEY DOCKET NO. MSD PC 139 PCTID NO:1, optionally wherein the amino acids corresponding to amino acids 258 and 260 of SEQ ID NO:1 are each substituted with alanine.

21. The polypeptide of any one of claims 1-20, wherein the complement factor B analog competes with binding of the native complement factor B.

22. The polypeptide of any one of claims 1-21, wherein the complement factor B protein analog is an analog of human complement factor B protein.

23. The polypeptide of any one of claims 1-22, wherein the complement factor B protein analog comprises at least one mutation corresponding to a mutation of SEQ ID NO:1 selected from a group consisting of D279G, N285D and C292S.

24. The polypeptide of any one of claims 1-23, wherein the polypeptide comprises the amino acid sequence of SEQ ID NO:3 or 12 with or without a signal sequence, or a variant thereof with at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO:3 or 12.

25. The polypeptide of any one of claims 1-24, wherein the complement factor B protein analog, comprises mutations corresponding to K258N, R259L, K260T, D279G, N285D and C292S of SEQ ID NO:!.

26. The polypeptide of any one of claims 1-25, wherein the complement factor B protein analog comprises at least one mutation corresponding to a mutation of SEQ ID NO:1 selected from a group consisting of K258A, K260A, D279G, N285D and C292S.

27. The polypeptide of claim 26, wherein an amino acid corresponding to amino acids 259 of SEQ ID NO:1 is substituted with a glycine, optionally wherein the polypeptide comprises the amino acid sequence of SEQ ID NO:30 with or without the signal sequence, or a variant thereof with at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO:30.

28. The polypeptide of claim 27, wherein the glycine substitution decreases or ablates cleavage of the complement factor B protein analog by factor D protein.

29. The polypeptide of any one of claims 26-28, wherein the complement factor B protein analog, comprises mutations corresponding to K258A, R259G, K260A, D279G, N285D and C292S relative to SEQ ID NO:1.

30. The polypeptide of any one of claims 1-29, wherein the polypeptide inhibits or reduces complement activity.

31. The polypeptide of any one of claims 1 -30, wherein the polypeptide inhibits the alternative complement pathway.45845704.1 146ATTORNEY DOCKET NO. MSD PC 139 PCT32. The polypeptide of any one of claims 1-25, wherein an amino acid corresponding to amino acid 259 of SEQ ID NO:1 is substituted with an aspartic acid, optionally wherein the polypeptide comprises the amino acid sequence of SEQ ID NO:31 with or without the signal sequence, or a variant thereof with at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO:31.

33. The polypeptide of claim 32, wherein the aspartic acid substitution enhances cleavage of the complement factor B protein analog by factor D protein.

34. The polypeptide of claims 32 or 33, wherein the complement factor B protein analog comprises mutations corresponding to K258A, R259D, K260A, D279G, N285D and C292S of SEQ ID NOil.

35. The polypeptide of any one of claims 32-34, wherein the polypeptide enhances complement activity.

36. The polypeptide of any one of claims 32-35, wherein the polypeptide enhances the alternative complement pathway.

37. The polypeptide of any one of claims 1-29, wherein the complement factor B protein analog is at least 90%, at least 95%, at least 98% or at least 99% identical to SEQ ID NO:1, 2, 3, 5, 11, 12, 26, 28, 30, or 31, with or without the signal sequence.

38. A fusion protein comprising a first fusion partner comprising a complement factor B analog and a second fusion partner, wherein the N-terminus of the first fusion partner is fused directly or linked by a linker peptide or polypeptide sequence to the C-terminus of the second fusion partner.

39. A fusion protein comprising a first fusion partner comprising a polypeptide of any one of claims 1-37 fused directly or linked by a linker peptide or polypeptide sequence to the second fusion partner.

40. The fusion protein of claim 39, wherein the first fusion partner is contiguous with the carboxyl terminus of the second fusion partner, or the second fusion partner is contiguous with the carboxyl terminus of the first fusion partner.

41. The fusion protein of claim 40, wherein the first fusion partner is contiguous with the carboxyl terminus of the second fusion partner.

42. The fusion protein of any one of claims 38-41, wherein the second fusion partner comprises an immunoglobulin Fc region.

43. The fusion protein of claim 42, wherein the immunoglobulin Fc region is an IgG4 Fc.

44. The fusion protein of any one of claims 39-43 wherein the fusion protein comprises the amino acid sequence of SEQ ID NO:5 and SEQ ID NO: 17 with or without a signal 45845704.1 147ATTORNEY DOCKET NO. MSD PC 139 PCTsequence, or a variant thereof with at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO:5 and SEQ ID NO: 17.

45. The fusion protein of any of claims 38-44, comprising a domain that mediates dimerization or multimcrization of the fusion protein to form homodimers, hctcrodimcrs, homomultimers, or heteromultimers.

46. The fusion protein of claim 45, wherein the domain that mediates dimerization or multimerization is selected from the group consisting of one or more cysteines that are capable of forming an intermolecular disulfide bond with a cysteine on the partner fusion protein, a coiled-coil domain, an acid patch, a zinc finger domain, a calcium hand domain, a CHI region, a CL region, a leucine zipper domain, an SH2 (sre homology 2) domain, an SH3 (sre Homology 3) domain, a PTB (phosphotyrosine binding) domain, a WW domain, a PDZ domain, a 14-3-3 domain, a WD40 domain, an EH domain, a Lim domain, an isoleucine zipper domain, and a dimerization domain of a receptor dimer pair.

47. A dimeric protein comprising a first and a second fusion protein, wherein the first and the second fusion proteins comprise the fusion protein of any of claims 38-46, wherein the first and the second fusion proteins are bound to one another by covalent or noncovalent bonds to form a dimer.

48. The dimeric protein of claim 47, wherein the dimer is a homodimer comprising the first fusion protein comprising the amino acid sequence of SEQ ID NO:3, 5, 11, 12, 26, 28, 30, or 31 with or without a signal sequence, or a variant thereof with at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO:3, 5, 11, 12, 26, 28, 30, or 31 and the second fusion protein comprising the amino acid sequence of SEQ ID NO:3, 5, 11, 12, 26, 28, 30, or 31 with or without a signal sequence, or a variant thereof with at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO: 3, 5, 11, 12, 26, 28, 30, or 31.

49. A multimeric protein comprising two or more fusion proteins, wherein each of the fusion proteins comprise the fusion protein of any of claims 38-48, wherein the fusion proteins are bound to one another by covalent or noncovalent bonds to form a multimer.

50. The multimeric protein of claim 49, wherein the multimer is a homomultimer.

51. A heterodimeric protein comprising a first and a second fusion protein, wherein (i) the first fusion protein comprises a first fusion partner fused to a second fusion partner, wherein the first fusion partner of the first fusion protein comprises a complement Factor B analog fused directly or linked by a linker peptide or polypeptide sequence to the second fusion partner of the first fusion protein.; and45845704.1 148ATTORNEY DOCKET NO. MSD PC 139 PCT(ii) the second fusion protein comprises a first fusion partner fused to a second fusion partner, wherein the first fusion partner of the second fusion protein comprises an antiinflammatory molecule fused directly to a second fusion partner of the second fusion or linked by a linker peptide or polypeptide sequence to the second fusion partner of the second fusion protein.

52. The heterodimeric protein of claim 51, wherein the first fusion protein comprises the fusion protein of any one of claims 38-46.

53. A heterodimeric protein of claims 51 and 52, wherein the anti-inflammatory molecule comprises a blocker of an inflammatory pathway initiated by IL4, IL6, IL13, IL17, IL22, IL23, IL31, Thymic Stromal lymphopoietin (TSLP), or OX40-OX40L axis, optionally wherein the anti-inflammatory molecule is an antigen binding fragment that binds to IL4, IL6, IL13, IL17, IL22, IL23, IL31, TSLP, and 0X40 or a soluble receptors that can bind these inflammatory molecules that include, but are not limited to, IL4, IL6, IL13, IL17, IL22, IL23, IL31, TSLP, and 0X40, optionally wherein the anti-inflammatory molecule is soluble IL- 17 receptor A (sIL-17RA).

54. The heterodimeric protein of any one of claims 1-53, wherein the second fusion partner of the second fusion protein comprises an immunoglobulin Fc region.

55. The heterodimeric protein of claim 54, wherein the immunoglobulin Fc region is an IgG4 Fc.

56. The heterodimeric protein of any one of claims 1-55, wherein the first and the second fusion proteins are bound to one another by covalent or noncovalent bonds.

57. The heterodimeric protein of any one of claims 51-56, wherein the heterodimeric protein comprises the first fusion protein comprising the amino acid sequence of SEQ ID NO:3, 5, 11, 12, 26, 28, 30, or 31 with or without a signal sequence, or a variant thereof with at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO:3, 5, 11, 12, 26, 28, 30, or 31 and the second fusion protein comprises the amino acid sequence of SEQ ID NO:7 with or without a signal sequence, or a variant thereof with at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO:7.

58. A nucleic acid comprising a nucleotide sequence encoding the polypeptide of any one of claims 1-37 or the fusion protein of any one of claims 38-46.

59. A viral vector comprising the nucleic acid of claim 58.

60. The viral vector of claim 59, wherein the viral vector is selected from a group consisting of a retroviral vector, a lentiviral vector, an adenoviral vector, a Herpes viral 45845704.1 149ATTORNEY DOCKET NO. MSD PC 139 PCTvector, a Hepatitis viral vector, an SV40 viral vector, an AAV vector, an EBV vector and an NDV vector, optionally wherein the vector comprises the nucleic acid sequence of SEQ ID NO:36, or a variant thereof wherein nucleotides 1321-3615 are substituted with a coding sequence for a different complement factor B analog or fusion protein thereof, optionally wherein the complement factor B analog or fusion protein includes the amino acid sequence of any one of SEQ ID NOS:!, 2, 5, 12, 16, 29, 30, or 31, or a variant thereof.

61. The viral vector of claim 60, wherein the lenti viral vector is a BIV, HIV, EIAV, SIV or FIV vector.

62. The viral vector of claim 61, wherein the viral vector comprises a decay accelerating factor.

63. A pharmaceutical composition comprising the polypeptide of any one of claims 1-36, the fusion protein of any one of claims 38-46, the dimeric, heterodimeric or the multimeric protein of any one of claims 47-57, the nucleic acid of claim 58, the viral vector of any one of claims 59-62 or any combination thereof.

64. The pharmaceutical composition of claim 63, comprising at least one ingredient selected from the group consisting of histidine, trehalose, a polysorbate, polysorbate 20, sucrose, arginine and praline.

65. A cell comprising the nucleic acid of claim 58, the viral vector of any one of claims 59-62 or any combination thereof, wherein the cell expresses the polypeptide or fusion protein.

66. The cell of claim 65, wherein the cell is a mammalian cell.

67. The cell of any one of claims 65-66, wherein the cell is selected from the group consisting of a 293 cell, a CHO cell, a PerC6 cell or a Vero cell.

68. The cell of claim 65, wherein the cell is a prokaryotic cell.

69. The cell of claim 68, wherein the cell is an E. coli cell.

70. A method of inhibiting complement activity comprising introducing or administering to a subject in need thereof an effective amount of the pharmaceutical compositions of claims 63 or 64 to inhibit the complement activity, wherein the polypeptide inhibits the complement activity,optionally wherein the polypeptide does not comprise an aspartic acid substitution at the position corresponding to the arginine at position 259 of SEQ ID NO:1,optionally wherein the complement factor B analog comprises the substitutions Eysine to Asparagine at position 258, Arginine to Alanine, Eeucine, or Glycine at position 259, and Lysine to Threonine or Serine at position 260 of SEQ ID NO:1.45845704.1 150ATTORNEY DOCKET NO. MSD PC 139 PCT71. The method of claim 70, comprising administering to a subject the polypeptide, the fusion protein, the dimeric protein, the heterodimeric protein, the multimeric protein, the nucleic acid, the viral vector, the pharmaceutical composition or any combination thereof.

72. The method of any one of claims 70-71, wherein the polypeptide, the fusion protein, the dimeric protein, the heterodimeric protein, or the multimeric protein competes with binding of a native complement factor B.

73. A method of treating a complement mediated disease in a subject, comprising the method of any one of claims 70-72.

74. The method of claim 73, wherein the complement-mediated disease is a disease of an eye.

75. The method of claim-74, wherein the pharmaceutical composition is administered to the eye.

76. The method of claim 75, wherein the pharmaceutical composition is administered by intravitreal injection, subretinal injection, injection to intraanterior chamber of the eye, injection or application locally to cornea, subconjunctival injection, subtenon injection, or by eye drops.

77. The method of any one of claims 73-76, wherein the complement-mediated disease is macular degeneration, age-related macular degeneration (AMD), geographic atrophy, wet AMD, myocardial infarction, dry AMD, drusen formation, arthritis, stroke, ischemic reperfusion injury, diabetic retinopathy, vitreoretinopathy, traumatic organ injury, corneal inflammation, comeal neovascularization, uveitis, ocular hypertension or glaucoma.

78. The method of any one of claims 73-76, wherein the complement-mediated disease is selected from the group consisting of atherosclerosis, airway hyperresponsiveness, immune related diseases, autoimmune related diseases, lupus nephritis, systemic lupus erythematosus (SLE), arthritis, rheumatologic diseases, anti-phospholipid antibody syndrome, intestinal and renal PR injury, asthma, atypical hemolytic-uremic syndrome, Type II membranoproliferative glomerulonephritis, non-proliferative glomerulonephritis, fetal loss, brain injury, post-traumatic organ damage, post infarction organ damage, vasculitis, hereditary angioedema, paroxysmal nocturnal hemoglobinuria, cerebrovascular accident, Alzheimer's disease, Parkinson’s disease, transplant rejection, infections, sepsis, septic shock, Sjogren's syndrome, myasthenia gravis, antibody-mediated skin diseases, Type I and Type II diabetes mellitus, insulin resistance syndrome, gestational diabetes, thyroiditis, idiopathic thrombocytopenic purpura and hemolytic anemia, neuropathies, multiple sclerosis, cardiopulmonary bypass injury, polyarteritis nodosa, Henoch Schonlein puipura, serum 45845704.1 | JATTORNEY DOCKET NO. MSD PC 139 PCTsickness, Goodpasture's disease, systemic necrotizing vasculitis, post streptococcal glomerulonephritis, idiopathic pulmonary fibrosis, membranous glomerulonephritis, acute shock lung syndrome, adult respiratory distress syndrome, and reperfusion.

79. The method any one of claims 73-76, wherein the complement-mediated disease is rheumatoid arthritis.

80. 1’he method any one of claims 73-76, wherein the complement-mediated disease is lupus nephritis.

81. The method of any one of claims 73-76, wherein the complement-mediated disease is paroxysmal nocturnal hemoglobinuria.

82. The method of any one of claims 73-76, wherein the complement-mediated disease is geographic atrophy.

83. The method of any one of claims 73-82, further comprising administering to the subject, prior to, concurrently with, or after the administration of the pharmaceutical composition, a complement inhibiting factor or an anti-angiogenic factor.

84. The method of claim 83, wherein the complement inhibiting factor is selected from a group consisting of a Factor H, a Factor H-like 1, a MCP, a DAF, or a soluble form of a MCP.

85. The method of claim 83, wherein the anti-angiogenic factor is selected from a group consisting of endostatin, a VEGF binding molecule, PEDF, T2-TrpRS, sFLT, aflibercept and kininostatin.

86. The method of any one of claims 73-85, wherein an anti-inflammatory is administered prior to, concurrently with, or after the administration of the pharmaceutical composition.

87. The method of claim 86, wherein the anti-inflammatory is(i) administered concurrently with the pharmaceutical composition or(ii) the pharmaceutical composition comprises the anti-inflammatory.

88. The method of any one of claims 86-87, wherein the anti-inflammatory is administered to the eye.

89. The method of any one of claims 86-88, wherein the anti-inflammatory is selected from the group consisting of dexamethasone, dexamethasone sodium metasulfobenzoate, dexamethasone sodium phosphate, fluorometholone, bromfenac, pranoprofen, a cyclosporine ophthalmic emulsion, naproxen, glucocorticoids, ketorolac, ibuprofen, tolmetin, non-steroidal anti-inflammatory drugs, steroidal anti-inflammatory drugs, diclofenac, flurbiprofen, indomethacin, and suprofen.45845704.1 152ATTORNEY DOCKET NO. MSD PC 139 PCT90. The method of any one of claims 73-89, wherein the pharmaceutical composition optionally comprising the viral vector is administered about once every week, month, 2 months, 3 months, 6 months, 9 months, a year, 18 months, 2 years, 30 months, 3 years, 5 years, or 10 years.

91. The method of any one of claims 73-90, wherein a compound that inhibits complement activity, T-cell activation, B-cells, tumor necrosis factor (TNF), estrogen, interleukin-I or interferon-gamma is administered prior to, concurrently with, or after the administration of the pharmaceutical composition.

92. The method of claim 91, wherein the compound is selected from the group consisting of infliximab, adalimumab, golimumab, etanercept, abatacept and rituximab.

93. A method of enhancing a complement activity, wherein the method comprises introducing or administering to a subject in need thereof an effective amount of the pharmaceutical composition of claims 63 or 64 in an amount sufficient to enhance the complement activity, wherein the polypeptide enhances the complement activity, optionally wherein the polypeptide does not comprise substitutions Lysine to Asparagine at position 258, Arginine to Alanine, Leucine, or Glycine, at position 259, and Lysine to Threonine or Serine at position 260 of SEQ ID NO:1,optionally wherein the polypeptide comprises an aspartic acid substitution at the position corresponding to the arginine at position 259 of SEQ ID NO: 1.

94. The method of claim 93, wherein enhancing the alternative complement pathway is used to treat diseases or conditions where complement activation is compromised or where further complement activation is beneficial as a therapy.

95. The method of any one of claims 93-94, wherein enhancing the alternative complement pathway can be used to treat complement deficiency syndromes (C3, Factor D, and Properdin deficiencies), recurrent bacterial infections (Neisseria meningitidis, Gramnegative infections), chronic fungal infections (Cryptococcus, Candida), cancer (by enhancing complement-mediated tumor clearance), neurodegenerative diseases (Alzheimer’s and Parkinson’s with impaired complement function), chronic non-healing wounds, post-surgical tissue regeneration, viral infections, and improving immune responses after organ transplantation.

96. The method of any one of claims 93-95 for treating or wherein the subject has a viral infection.

97. The method of claim 96, wherein the virus causing the viral infection is COVID-19.45845704.1 153ATTORNEY DOCKET NO. MSD PC 139 PCT98. The method of claim 96, wherein the virus causing the viral infection is a flu such as pandemic flu.

99. The method of claim 96, wherein the virus causing the viral infection is Ebola.

100. The method of any one of claims 73-99, wherein the pharmaceutical composition optionally comprising the viral vector is administered only once to the subject.

101. The method of any one of claims 70-99, wherein the pharmaceutical composition is administered systemically to the subject.

102. The method of any one of claims 70-99, wherein the pharmaceutical composition is administered to the subject locally, optionally to a site of a complement activity.

103. A method of producing a polypeptide comprising a complement factor B protein analog, the method comprising:(i). expressing the polypeptide of any one of claims 1-37 or fusion protein of claims 38-47; and(ii). purifying the polypeptide.

104. A protein comprising the amino acid sequence of any one of claims SEQ ID NO:3, 5, 11, 12, 17, 26, 28, 30, or 31 with or without a signal sequence, or a variant thereof with at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% sequence identity thereto.

105. A vector comprising the nucleic acid sequence of SEQ ID NO:36.

106. A vector comprising the variant nucleic acid sequence of SEQ ID NO:6, wherein the variant comprises or consists of substituting nucleotides 1321-3615 of SEQ ID NO:36 with a nucleic acid sequence encoding a different complement factor B analog or fusion protein thereof.

107. The vector of claim 106, wherein the complement factor B analog or fusion protein comprises the amino acid sequence of any one of SEQ ID NOS:1, 2, 5, 12, 16, 29, 30, or 31, or a variant thereof optionally with at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% sequence identity thereto.45845704.1 154

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