US20210269497A1 - Interleukin-2 variants and methods of uses thereof - Google Patents

Interleukin-2 variants and methods of uses thereof Download PDF

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US20210269497A1
US20210269497A1 US17/254,098 US201917254098A US2021269497A1 US 20210269497 A1 US20210269497 A1 US 20210269497A1 US 201917254098 A US201917254098 A US 201917254098A US 2021269497 A1 US2021269497 A1 US 2021269497A1
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amino acid
cells
seq
treg
substitution
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Yue-Sheng Li
Lingyun Rui
Jing Xu
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Cugene Inc
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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/52—Cytokines; Lymphokines; Interferons
    • C07K14/54—Interleukins [IL]
    • C07K14/55—IL-2
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K47/00—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient
    • A61K47/50—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates
    • A61K47/51—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent
    • A61K47/68—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an antibody, an immunoglobulin or a fragment thereof, e.g. an Fc-fragment
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K47/00—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient
    • A61K47/50—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates
    • A61K47/51—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent
    • A61K47/68—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an antibody, an immunoglobulin or a fragment thereof, e.g. an Fc-fragment
    • A61K47/6801—Drug-antibody or immunoglobulin conjugates defined by the pharmacologically or therapeutically active agent
    • A61K47/6803—Drugs conjugated to an antibody or immunoglobulin, e.g. cisplatin-antibody conjugates
    • A61K47/6811—Drugs conjugated to an antibody or immunoglobulin, e.g. cisplatin-antibody conjugates the drug being a protein or peptide, e.g. transferrin or bleomycin
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P29/00—Non-central analgesic, antipyretic or antiinflammatory agents, e.g. antirheumatic agents; Non-steroidal antiinflammatory drugs [NSAID]
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P37/00—Drugs for immunological or allergic disorders
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K35/00—Medicinal preparations containing materials or reaction products thereof with undetermined constitution
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • C07K2319/01—Fusion polypeptide containing a localisation/targetting motif
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • C07K2319/30—Non-immunoglobulin-derived peptide or protein having an immunoglobulin constant or Fc region, or a fragment thereof, attached thereto
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • C07K2319/31—Fusion polypeptide fusions, other than Fc, for prolonged plasma life, e.g. albumin

Definitions

  • Interleukin 2 was the first growth factor described for T cells. Since its discovery it has been shown to promote proliferation and survival of T cells in vitro (Smith, K A. (1988) Science. 240, 1169-76) and the ability to boost immune response in the context of T viral infections (Blattman, J N, et al. (2003) Nat Med 9, 540-7) or vaccines (Fishman, M., et al. (2008) J Immunother. 31, 72-80, Kudo-Saito, C., et al. (2007) Cancer Immunol Immunother. 56, 1897-910; Lin, C T., et al. (2007) Immunol Lett. 114, 86-93).
  • IL-2 has been used in cancer therapy. Recombinant human IL-2 is an effective immunotherapy for metastatic melanoma and renal cancer, with durable responses in approximately 10% of patients. However short half-life and severe toxicity limits the optimal dosing of IL-2. Further, IL-2 also binds to its heterotrimeric receptor IL-2R ⁇ with greater affinity, which preferentially expands immunosuppressive regulatory T cells (Tregs) expressing high constitutive levels of IL-2Ra. Expansion of Tregs represents an undesirable effect of IL-2 for cancer immunotherapy. However, the capability of IL-2 to stimulate Treg cells even at low doses could be harnessed for the treatment of autoimmune and various inflammatory disorders.
  • Tregs immunosuppressive regulatory T cells
  • Treg are central to immune system homeostasis and play a major role in maintaining peripheral immune tolerance by dampening (autoreactive) effector T cells.
  • Multiple autoimmune and inflammatory diseases have been shown to have a deficiency of Treg cell numbers or Treg function. Consequently, there is great interest in the development of therapies that boost the numbers and/or function of Treg cells.
  • One treatment approach for autoimmune diseases being investigated is employing low dose IL-2 to target Treg cells, because Treg cells respond to lower concentrations of IL-2 than many other immune cell types due to their high constitutive levels of IL-2Ra. (Klatzmann D, 2015 Nat Rev Immunol. 15:283-94).
  • IL-2 could be modified to selectively stimulate either cytotoxic effector T cells or Treg cells.
  • Various approaches have led to the generation of IL-2 variants with improved and selective immune stimulatory capacities (see, e.g., U.S. Pat. Nos. 7,186,804, 7,105,653, 6,955,807, 5,229,109, U.S. Patent Application 20050142106).
  • IL-2 variants were designed to increase the capacity of this molecule to signal mainly by the high affinity receptor (alpha, beta and gamma chains) and not by the intermediate affinity receptor (beta and gamma chains).
  • IL-2 is a highly pleiotropic cytokine which is very relevant in the biological activity of different cell populations. This property makes the IL-2 an important node in the regulation of the immune response, making it an attractive target for therapies and complex immune modulation. Further, receptor subunit-biased IL-2 variants can be made to achieve IL-2 mediated selective immune modulation to promote the expansion and activity of regulatory T-cells (Treg) while minimizing helper and cytotoxic T effector (Teff) cells and led to lower levels of pro-inflammatory signaling molecules.
  • Treg regulatory T-cells
  • Teff helper and cytotoxic T effector
  • the present invention relates to the production of mutated variants of IL-2.
  • These variants are characterized by their enhanced selectivity in stimulating Treg (T CD4+CD25+FoxP3+) cells over conventional CD4+ T cells, cytotoxic effective CD8+ T lymphocytes, and NK cells.
  • Treg T CD4+CD25+FoxP3+
  • cytotoxic effective CD8+ T lymphocytes IL-2
  • NK cells a practical solution to improve IL-2 therapy in autoimmune and inflammatory disorders.
  • the present invention relates to polypeptide which share their primary sequence with the human IL-2, except for one to several amino acids that have been mutated.
  • variants have amino acid substitutions at positions corresponding to IL-2 interaction with IL-2R ⁇ and/or ⁇ C , and consequently these variants have reduced affinity for the IL-2R ⁇ receptor complex and reduced or abolished ability to activate IL-2R ⁇ -expressing cells but retain the ability to bind IL-2R ⁇ and the ability to bind and activate the IL-2R ⁇ receptor complex.
  • the present invention also includes therapeutic uses of these mutated variants for the treatment of autoimmune as well as various inflammatory disorders.
  • the present invention relates to the production of mutated variants of IL-2.
  • These variants possess a combination of attributes with Treg-selective activity, reduced aggregation, increased expression, improved manufacturability and developability.
  • These variants also provide improved protein biophysical properties and reduced immunogenic risk associated with IL-2 molecules.
  • These variants provide a superior solution to improve IL-2 therapy and reduce toxicity in autoimmune and inflammatory disorders.
  • the present invention relates to polypeptide which share their primary sequence with the human IL-2, except for one to several amino acids that have been mutated.
  • the present invention relates to the production of mutated variants of IL-2, which are characterized by removing a proposed ‘ 19 LDL’ motif resembling a component of bacterial toxins (Baluna R, Rizo et. al., Proc Natl Acad Sci 1999; 96:3957-62).
  • This ‘toxic motif’ is responsible, in part, for direct vascular toxicity of IL-2. Mutations introduced to remove the critical residue, D20, or the flanking two residues of the toxin-like domain, are expected to eliminate the toxic motif and prevent endothelial cell damage and significantly reduce VLS.
  • the amino acid substitutions to this motif reduce their affinity for IL-2R ⁇ , and the resulting molecule would be expected to have two beneficial properties, including selectivity for activating Treg cells and reduced endothelial damage.
  • the present invention relates to polypeptides which share their primary sequence with the human IL-2, except for one to several amino acids that have been mutated.
  • the present invention also includes therapeutic uses of these mutated variants for therapy of Treg cell-deficient autoimmune and various inflammatory disorders.
  • the present invention allows for a substantial improvement of the current strategies of immunomodulation based on IL-2 in the therapy of autoimmune and various inflammatory disorders. Specifically, the replacement of the native IL-2 by the mutated variants described herein will result in CD25-biased selective stimulation of Treg cells.
  • the IL-2 variant (or mutant) comprises the sequence of the IL-2 variant (or mutant) derived from the sequence of the mature human IL-2 polypeptide as set forth in SEQ ID NO: 3.
  • the IL-2 variant functions as an IL-2 agonist.
  • the IL-2 variant functions as an IL-2 antagonist.
  • the IL-2 variants comprise the sequences set forth in SEQ ID NOS: 4-43, 108-146, and 193-197.
  • the present invention allows for a substantial improvement of the current strategies of immunomodulation based on IL-2 in the therapy of Treg cell-deficient autoimmune and various inflammatory disorders.
  • the replacement of the native IL-2 by the mutated variants described herein will result in CD25-biased selective stimulation of Treg cells and is expected to eliminate the toxic motif and prevent endothelial cell damage and significantly reduce VLS.
  • the IL-2 variant (or mutant) comprises the sequence of the IL-2 variant (or mutant) derived from the sequence of the mature human IL-2 polypeptide as set forth in SEQ ID NO: 3.
  • the IL-2 variant functions as an IL-2 agonist.
  • the IL-2 variant functions as an IL-2 antagonist.
  • the IL-2 variants comprise SEQ ID NOS: 5-14, 26-43, 108-111, 125-146 and 193-197.
  • the IL-2 variants of the present invention are attached to at least one heterologous protein.
  • 11-2 variants are fused to at least one polypeptide that confers extended half-life on the fusion molecule.
  • polypeptides include an IgG Fc or other polypeptides that bind to the neonatal Fc ⁇ /receptor, human serum albumin, or polypeptides that bind to a protein having extended serum half-life, including IgGs, non-IgG immunoglobulin, proteins and non-protein agents, that have increased in vivo half-lives due to the presence of an IgG constant domain, or a portion thereof that binds the FcRn, having one or more amino acid modifications that increase the affinity of the constant domain or fragment for FcRn.
  • proteins and molecules with increased half-lives have the advantage that smaller amounts and or less frequent dosing is required in the therapeutic, prophylactic or diagnostic use of such molecules (see, e.g., U.S. Pat. No.
  • the IL-2 variants can be linked to the N-terminus or the C-terminus of the heterologous protein.
  • the IL-2 variant is fused to an IgG Fc molecule.
  • the Fc domain is a human IgG Fc domain.
  • the Fc domain is derived from the human IgG1 heavy chain constant domain sequence set forth in SEQ ID NO: 44.
  • the Fc domain is an Fc domain having the amino acid sequence set forth in SEQ ID NO: 45.
  • the Fc domain is an Fc domain having the amino acid sequence set forth in SEQ ID NO: 46.
  • the Fc domain is an Fc domain having the amino acid sequence set forth in SEQ ID NO: 47.
  • the Fc domain is derived from the human IgG2 heavy chain constant domain sequence.
  • the Fc domain is derived from the human IgG4 heavy chain constant domain sequence.
  • Fc refers to molecule or sequence comprising the sequence of a non-antigen-binding fragment of whole antibody, whether in monomeric or multimeric form.
  • the original immunoglobulin source of the native Fc is preferably of human origin and may be any of the immunoglobulins disclosed in the art.
  • Native Fc's are made up of monomeric polypeptides that may be linked into dimeric or multimeric forms by covalent (i.e., disulfide bonds) and non-covalent association.
  • the number of intermolecular disulfide bonds between monomeric subunits of native Fc molecules ranges from 1 to 4 depending on class (e.g., IgG, IgA, IgE) or subclass (e.g., IgG1, IgG2, IgG3, IgA1, IgGA2).
  • class e.g., IgG, IgA, IgE
  • subclass e.g., IgG1, IgG2, IgG3, IgA1, IgGA2
  • One example of a native Fc is a disulfide-bonded dimer resulting from papain digestion of an IgG (see Ellison et al. (1982), Nucleic Acids Res. 10: 4071-9).
  • native Fc as used herein is generic to the monomeric, dimeric, and multimeric forms. Fc domains containing binding sites for Protein A, Protein G, various Fc receptors and complement proteins.
  • Fc variant refers to a molecule or sequence that is modified from a native Fc but still comprises a binding site for the salvage receptor, FcRn.
  • International applications WO 97/34631 published Sep. 25, 1997) and WO 96/32458 describe exemplary Fc variants, as well as interaction with the salvage receptor, and are hereby incorporated by reference.
  • a native Fc comprises sites that may be removed because they provide structural features or biological activity that are not required for the fusion molecules of the present invention.
  • the term “Fc variant” comprises a molecule or sequence that lacks one or more native Fc sites or residues that affect or are involved in (1) disulfide bond formation, (2) incompatibility with a selected host cell (3) N-terminal heterogeneity upon expression in a selected host cell, (4) glycosylation, (5) interaction with complement, (6) binding to an Fc receptor other than a salvage receptor, or (7) antibody-dependent cellular cytotoxicity (ADCC).
  • ADCC antibody-dependent cellular cytotoxicity
  • Fc domain encompasses native Fc and Fc variant molecules and sequences as defined above. As with Fc variants and native Fc's, the term “Fc domain” includes molecules in monomeric or multimeric form, whether digested from whole antibody or produced by recombinant gene expression or by other means. In various embodiments, an “Fc domain” refers to a dimer of two Fc domain monomers (SEQ ID NO: 44) that generally includes full or part of the hinge region. In various embodiments, an Fc domain may be mutated to lack effector functions. In various embodiments, each of the Fc domain monomers in an Fc domain includes amino acid substitutions in the CH2 antibody constant domain to reduce the interaction or binding between the Fc domain and an Fc ⁇ receptor.
  • each subunit of the Fc domain comprises two amino acid substitutions that reduce binding to an activating Fc receptor and/or effector function wherein said amino acid substitutions are L234A, L235A. In various embodiments, each subunit of the Fc domain comprises three amino acid substitutions that reduce binding to an activating Fc receptor and/or effector function wherein said amino acid substitutions are L234A, L235A and G237A (SEQ ID NO: 45).
  • an Fc domain may be mutated to further extend in vivo half-life.
  • each subunit of the Fc domain comprises three amino acid substitutions that enhance binding to human FcRn wherein said amino acid substitutions are M252Y, S254T, and T256E, disclosed in U.S. Pat. No. 7,658,921.
  • each subunit of the Fc domain comprises one amino acid substitution that enhanced binding to human FcRn wherein said amino acid substitution is N434A, disclosed in U.S. Pat. No. 7,371,826.
  • each subunit of the Fc domain comprises one amino acid substitution that enhanced binding to human FcRn wherein said amino acid substitutions are M428L and N434S, disclosed in U.S. Pat. No. 8,546,543.
  • half-life extension mutations can be combined with amino acid substitutions that reduce binding to an activating Fc receptor and/or effector function.
  • each of the two Fc domain monomers in an Fc domain includes amino acid substitutions that promote the heterodimerization of the two monomers.
  • heterodimerization of Fc domain monomers can be promoted by introducing different, but compatible, substitutions in the two Fc domain monomers, such as “knob-into-hole” residue pairs. The “knob-into-hole” technique is also disclosed in U.S. Pat. No. 8,216,805.
  • one Fc domain monomer includes the knob mutation T366W and the other Fc domain monomer includes hole mutations T366S, L358A, and Y407V.
  • two Cys residues were introduced (S354C on the “knob” and Y349C on the “hole” side) that form a stabilizing disulfide bridge.
  • the use of heterodimeric Fc may result in monovalent IL-2 variant construct.
  • the IL-2 variant Fc-fusion protein will be monomeric, i.e., contain only a single IL-2 mutein molecule.
  • the fusion protein is co-expressed with a heterodimeric Knob-Fc linked to an IL-2 variant and the matching heterodimeric Hole Fc.
  • the heterodimer of the two Fc-containing polypeptides forms, the resulting protein comprises only a single IL-2 variant.
  • the IL-2 variants are used to prepare the Fc-IL-2 fusion proteins set forth in SEQ ID NOS: 69-107, 147-189, and 198-208.
  • the IL-2 variants of the present invention can be attached to an antibody that confers extended half-life on the fusion molecule, such as anti-keyhole limpet hemocyanin (KLH) antibody.
  • KLH anti-keyhole limpet hemocyanin
  • the IgG class could be IgG, IgA, IgE or subclass (e.g., IgG1, IgG2, IgG3, IgA1, IgA2).
  • the heterologous protein is attached to the IL-2 variant by a linker and/or a hinge linker peptide.
  • the linker or hinge linker may be an artificial sequence of between 5, 10, 15, 20, 30, 40 or more amino acids that are relatively free of secondary structure.
  • the heterologous protein is attached to the IL-2 variant by a rigid linker peptide of between 10, 15, 20, 30, 40 or more amino acids that display ⁇ -helical conformation and may act as rigid spacers between protein domains.
  • IL-2 variant can be linked to various nonproteinaceous polymers, including, but not limited to, various polyols such as polyethylene glycol, polypropylene glycol or polyoxyalkylenes, in the manner set forth in U.S. Pat. Nos. 4,640,835; 4,496,689; 4,301,144; 4,670,417; 4,791,192 or 4,179,337.
  • amino acid substitutions may be made in various positions within the IL-2 variants to facilitate the addition of polymers such as PEG.
  • PEGylated proteins may have increased half-life and/or reduced immunogenicity over the non-PEGylated proteins.
  • polyethylene glycol or “PEG” is meant a polyalkylene glycol compound or a derivative thereof, with or without coupling agents or derivatization with coupling or activating moieties (e.g., with aldehyde, hydroxysuccinimidyl, hydrazide, thiol, triflate, tresylate, azirdine, oxirane, orthopyridyl disulphide, vinylsulfone, iodoacetamide or a maleimide moiety).
  • PEG includes substantially linear, straight chain PEG, branched PEG, or dendritic PEG.
  • PEG is a well-known, water soluble polymer that is commercially available or can be prepared by ring-opening polymerization of ethylene glycol according to methods well known in the art (Sandler and Karo, Polymer Synthesis, Academic Press, New York, Vol. 3, pages 138-161).
  • 11-2 variants can be linked non-covalently or covalently to an IgG Fc or other polypeptides that bind to the neonatal Fc ⁇ /receptor, human serum albumin, or polypeptides that bind to a protein having extended serum half-life, or various nonproteinaceous polymers at either the N-terminus or C-terminus.
  • the present disclosure provides a pharmaceutical composition
  • a pharmaceutical composition comprising the isolated IL-2 variants in admixture with a pharmaceutically acceptable carrier.
  • IL-2 variants can be formulated for slow release, such as covalently or non-covalently attached to hydrogels, nanoparticle, etc.
  • the present disclosure provides a method for treating an autoimmune disease in a subject, comprising administering a therapeutically effective amount of the pharmaceutical compositions of the invention to a subject in need thereof.
  • the subject is a human subject.
  • An autoimmune disease as pertains to the present invention, is a disease or disorder arising from and directed against an individual's own tissues or a co-segregate or manifestation thereof or resulting condition therefrom.
  • the autoimmune disease includes, but is not limited to, Graft Versus Host Disease (GvHD), Immune related adverse events (irAE), arthritis (including rheumatoid arthritis, reactive arthritis), systemic lupus erythematosus (SLE), atopic dermatitis, psoriasis and inflammatory bowel disease (IBD), encephalomyelitis, uveitis, myasthenia gravis, multiple sclerosis, insulin dependent diabetes (type 1 diabetes), various dermatitis, Addison's disease, celiac disease, chronic fatigue syndrome, autoimmune hepatitis, autoimmune alopecia, ankylosing spondylitis, ulcerative colitis, Crohn's disease, fibromyalgia, pemphigus vulgaris, Sjogren's syndrome, Kawasaki's Disease, hyperthyroidism/Graves disease, hypothyroidism/Hashimoto's disease, endometriosis, s
  • the present disclosure provides a method for treating an autoimmune disease in a subject, comprising administering a therapeutically effective amount of the pharmaceutical compositions of the invention in combination with a second therapeutic agent capable of treating an autoimmune disease.
  • the present disclosure provides a method for treating an inflammatory disease in a subject, comprising administering a therapeutically effective amount of the pharmaceutical compositions of the invention to a subject in need thereof.
  • the subject is a human subject.
  • the inflammatory disease to be treated includes, but is not limited to, Crohn's disease, colitis, dermatitis, psoriasis, diverticulitis, hepatitis, irritable bowel syndrome (IBS), lupus erythematous, nephritis, Parkinson's disease, ulcerative colitis, collagenous colitis, lymphocytic colitis, ischemic colitis, diversion colitis, Behcet's syndrome and indeterminate colitis multiple sclerosis (MS), Alzheimer's disease, arthritis, rheumatoid arthritis, asthma, and various cardiovascular diseases such as atherosclerosis and vasculitis.
  • the inflammatory disease is selected from the group consisting of rheumatoid arthritis
  • the present disclosure provides a method for treating an inflammatory disease in a subject, comprising administering a therapeutically effective amount of the pharmaceutical compositions of the invention in combination with a second therapeutic agent capable of treating an inflammatory disease.
  • the present disclosure provides methods for organ transplantation or associated graft-versus-host disease in a subject, comprising administering a therapeutically effective amount of the pharmaceutical compositions of the invention to a subject in need thereof.
  • the subject is a human subject.
  • the transplantation is selected from organ transplantations of the heart, kidneys, liver, lungs, pancreas, intestine and thymus or from tissues transplantations of the bones, tendons, cornea, skin, heart valves, nerves and veins.
  • the disclosure provides uses of the IL-2 variants for the preparation of a medicament for the treatment of an autoimmune disease.
  • the disclosure provides uses of the IL-2 variants for the preparation of a medicament for the treatment of organ transplantation and GvHD.
  • the disclosure provides uses of the IL-2 variants for the preparation of a medicament for the treatment of inflammatory disorders.
  • the present disclosure provides isolated nucleic acid molecules comprising a polynucleotide encoding an IL-2 variant of the present disclosure.
  • the present disclosure provides vectors comprising the nucleic acids described herein.
  • the vector is an expression vector.
  • the present disclosure provides isolated cells comprising the nucleic acids of the disclosure.
  • the cell is a host cell comprising the expression vector of the disclosure.
  • methods of making the IL-2 variants are provided by culturing the host cells under conditions promoting expression of the proteins or polypeptides.
  • FIG. 1 depicts size exclusion chromatogram of exemplary IL-2 Fc fusion proteins A) P-0250, B) P-0318, C) P-0317, D) P-0447, and E) P-0511 after protein A purification.
  • FIG. 1D and FIG. 1E also illustrate the SDS-PAGE of respective samples in the absence (Lane 2) and presence of reducing agent (Lane 3).
  • FIG. 2 depicts differential effects of Fc fusion proteins of IL-2 variants with amino acid substitutions of aspartic acid at position 20 (D20 ⁇ ) on induction of STAT5 phosphorylation in CD4+ Treg (A) vs Tconv (B) cells in comparison with the wild type fusion protein (P-0250) in human PBMC assay.
  • FIG. 3 depicts differential effects of Fc fusion proteins of IL-2 variants P-0375 (N88Q) on induction of STAT5 phosphorylation in CD4+ Treg (A) vs Tconv (B) cells in comparison with the wild type (P-0250) and the benchmark proteins in human PBMC assay.
  • FIG. 4 depicts differential effects on STAT5 phosphorylation by Fc fusion proteins of IL-2 variants with amino acid substitutions at position 19 in comparison with the wild type (P-0250).
  • the ability to induce STAT5 phosphorylation in CD4+ Treg (A and C) and Tconv (B and D) cells was determined in human PBMC assay by FACS analysis.
  • FIG. 5 depicts differential effects on STAT5 phosphorylation by Fc fusion proteins of IL-2 variants with individual amino acid substitution at either position 19 (P-0372) or position 126 (P-0303), or combination mutant (P-0419) in comparison with the wild type (P-0250) or the Benchmark-1 protein.
  • the ability to induce STAT5 phosphorylation in CD4+ Treg (A, C, and E) and CD4+ Tconv (B, D &F) cells was determined by FACS analysis.
  • FIG. 6 depicts differential effects on STAT5 phosphorylation by Fc fusion proteins of IL-2 variants harboring different combination of dual amino acid substitutions (P-0419, P-0464, P-0471, P-0474, P-0417 and P-0322) in comparison with the wild type (P-0250).
  • the biological activity of P-0417 and P-0322 was also compared to their counterparts with single amino acid substitution, P-0373 and P-0363, respectively.
  • the ability to induce STAT5 phosphorylation in CD4+ Treg (A & C) and CD4+ Tconv (B & D) cells was determined in human PBMC assay by FACS analysis.
  • FIG. 7 depicts differential effects on STAT5 phosphorylation by Fc fusion proteins of IL-2 variants with individual amino acid substitution at either position 19 (P-0424) or position 126 (P-0303), or combination mutant (P-0447) in comparison with the wild type (P-0250), and differential effects on STAT5 phosphorylation by Fc fusion proteins of IL-2 variants harboring different combinational amino acid substitutions (P-0419, P-0447, P-0448, and P-0449) in comparison with the wild type (P-0250) and benchmark Fc fusion proteins.
  • the ability to induce STAT5 phosphorylation in CD4+ Treg (A and C) and CD4+ Tconv (B and D) cells was determined in human PBMC assay by FACS analysis.
  • FIG. 8 depicts pSTAT5 stimulation activity of IL-2 fusion proteins P-0250, P-0424, and P-447 in comparison to their respective counterparts harboring S125I substitution, P-0531, P-0491, and P-0511.
  • the ability to induce STAT5 phosphorylation in CD4+ Treg (A, C, and E) and CD4+ Tconv (B, D, and F) cells was determined in human PBMC assay by FACS analysis.
  • FIG. 9 depicts differential effects on STAT5 phosphorylation by IL-2 variant Fc fusions (P-0511 and P-0512) in comparison with the wild type (P-0250) and three benchmark molecules in three subsets of CD4+ T cells; A) CD4+FoxP3+CD25+ Treg cells, B) CD4+FoxP3 ⁇ CD25+ activated Tconv cells, and C) CD4+FoxP3 ⁇ CD25 ⁇ na ⁇ ve Tconv cells.
  • the ability to induce STAT5 phosphorylation was determined in human PBMC assay by FACS analysis.
  • FIG. 10 depicts differential effects on stimulating proliferation of A) CD8+ T cells and B) NK cells by P-0511 and P-0512 in comparison with the wild type (P-0250) and benchmark molecules.
  • Cell proliferation was determined in human PBMC assay by FACS analysis of CFSE dilution and expressed as a percent of divided cells.
  • FIGS. 11A-D depict differential effects on inducing STAT5 phosphorylation by IL-2 variant Fc fusion P-0511 in comparison to the wild-type equivalent P-0531 in different cells types.
  • the ability to induce STAT5 phosphorylation in A) CD4+ Treg, B) CD4+ Tconv, C) CD8+ T cells, and D) NK cells was determined in human PBMC assay by FACS analysis.
  • FIG. 11E depicts binding strength of P-511 to IL-2R ⁇ and ⁇ c complex in comparison to P-0531 and Benchmark-1 in ELISA assay.
  • FIG. 12 depicts the proliferation and expansion of Treg cells in mice treated with Fc fusion proteins of IL-2 variants and the benchmarks after a single subcutaneous injection. Blood was collected at the indicated time points for measurement of proliferation and lymphocytes phenotyping.
  • A Percentage of the proliferation marker Ki67 positive Treg cells
  • B Percentage of Treg cells in total CD4+ T cell population
  • C Percentage of Treg cells in total blood lymphocytes. Data are expressed as mean ⁇ SEM. Statistical analysis was performed by one-way anova followed by Tukey's post hoc test. **** p ⁇ 0.0001; *** p ⁇ 0.001 compared to PBS group at respective time point.
  • FIG. 13 depicts the proliferation of effector T cells and NK cells in mice treated with IL-2 mutant Fc fusion proteins and the benchmarks after a single subcutaneous injection. Blood was collected at the indicated time points for measurement of lymphocyte proliferation.
  • A Percentage of Ki67 positive CD4+ T conventional (Tconv) cells;
  • B Percentage of Ki67 positive CD8+ T cells;
  • C Percentage of Ki67 positive NK cells. Data are expressed as mean ⁇ SEM. Statistical analysis was performed by one-way anova followed by Tukey's post hoc test. **** p ⁇ 0.0001; *** p ⁇ 0.001 compared to PBS group at respective time point.
  • FIG. 14 depicts the expansion of effector T cells and NK cells in mice treated with IL-2 mutant Fc fusion proteins and the benchmarks after a single subcutaneous injection.
  • A-B Percentage of CD4+ T conventional (Tconv) cells in total CD4+ T cells (A) and total blood lymphocytes (B).
  • C Percentage of CD8+ T cells in total blood lymphocytes;
  • D Percentage of NK cells in total blood lymphocytes. Data are expressed as mean ⁇ SEM.
  • FIG. 15 depicts the ratio of Treg to Tconv cells based on A) percentage of Ki67 positive expression, and B) cell numbers in mice treated with IL-2 mutant Fc fusion proteins, and the benchmarks. Data were acquired with FACS and are expressed as mean ⁇ SEM. Statistical analysis was performed by one-way anova followed by Tukey's post hoc test. **** p ⁇ 0.0001; * p ⁇ 0.05 compared to PBS group at respective time point.
  • FIG. 16 depicts the expression of CD25 and Foxp3 on Treg cells in mice treated with IL-2 mutant Fc fusion proteins and the benchmarks after a single subcutaneous injection.
  • the expression level of A) Foxp3, and B) CD25 was analyzed by FACS analysis and expressed as mean fluorescent intensity (MFI). Data are expressed as mean ⁇ SEM. **** p ⁇ 0.0001, compared to PBS group at respective time point.
  • FIG. 17 depicts dose-dependent increases in the proliferation and expansion of Treg cells in mice following a single injection of IL-2 variant Fc fusion protein P-0511.
  • Blood was collected at the indicated time points for lymphocyte phenotyping and measurement of Ki67 proliferation marker.
  • A Percentage of the proliferation marker Ki67 positive Treg cells
  • B Percentage of Treg cells in total CD4+ T cells
  • C number of Treg cells per microliter of whole blood
  • D Fold change of Treg cell numbers from the baseline for each group. Data were expressed as mean ⁇ SEM. Statistical analysis was performed by one-way anova followed by Tukey's post hoc test. **** p ⁇ 0.0001, *** p ⁇ 0.001, ** p ⁇ 0.01, * p ⁇ 0.05 compared to PBS group at respective time point.
  • FIG. 18 depicts dose-dependent effect of IL-2 variant Fc fusion protein P-0511 on the percentage of Treg cells (A), CD4+ Tconv cells (B), CD8 T cells (C), and NK cells (D) over total lymphocytes in mice following a single injection.
  • Blood was collected at the indicated time points for lymphocyte phenotyping. Data were determined by FACS analysis and are expressed as mean ⁇ SEM. Statistical analysis was performed by one-way anova followed by Tukey's post hoc test. **** p ⁇ 0.0001, ** p ⁇ 0.01, * p ⁇ 0.05 compared to PBS group at respective time point.
  • FIG. 19 depicts dose-dependent increases in A) ratio of Treg to T cony cell numbers, B) expression of CD25 on Treg cells, and C) expression of Foxp3 on Treg cells in mice following a single injection of P-0511. Data were determined by FACS analysis and are expressed as mean ⁇ SEM. Statistical analysis was performed by one-way anova followed by Tukey's post hoc test. **** p ⁇ 0.0001, *** p ⁇ 0.001, ** p ⁇ 0.01 compared to PBS group at respective time point.
  • FIG. 20 depicts the sustained proliferation and expansion of Treg cells in mice receiving repeated doses of Fc fusion proteins of IL-2 variants (P-0511 and P-0512), but not the wild type (P-0531) and the benchmark.
  • Compounds were given s.c. once every three days (Q3D) and blood was collected 3 days post the 1st and the 3rd injection for lymphocyte phenotyping and measurement of proliferation marker Ki67.
  • A Percentage of Ki67 positive Treg cells
  • B Percentage of Treg cells in total CD4+ T cells
  • C Percentage of Treg cells in total blood lymphocytes.
  • Data were determined by FACS analysis and are expressed as mean ⁇ SEM. Statistical analysis was performed by one-way anova followed by Tukey's post hoc test. **** p ⁇ 0.0001, * p ⁇ 0.05 compared to respective PBS group.
  • FIG. 21 depicts the sustained elevation of Treg cell counts in mice receiving repeated dosing of Fc fusion proteins of IL-2 variants (P-0511 and P-0512), but not the wild type (P-0531) and the benchmark.
  • Compounds were given s.c. once every three days (Q3D) and blood was collected 3 days post the 1 st and the 3 rd injection for lymphocyte phenotyping and measurement of proliferation marker Ki67.
  • A Number of Treg cells per microliter of whole blood
  • B Fold change of the Treg numbers compared to the PBS control group. Data were determined by FACS analysis and are expressed as mean ⁇ SEM. Statistical analysis was performed by one-way anova followed by Tukey's post hoc test. **** p ⁇ 0.0001, *** p ⁇ 0.001, p ⁇ 0.01, compared to respective PBS group.
  • FIG. 22 depicts the retaining of the elevated ratio of Treg to Tconv in mice receiving repeated dosing of Fc fusion proteins of IL-2 variants (P-0511 and P-0512), but not the wild type (P-0531) and the benchmark.
  • Compounds were given s.c. once every three days (Q3D) and blood was collected 3 days post the 1 st and the 3 rd injection for Treg and Tconv cell phenotyping. The ratio was calculated based on the % Treg and % Tconv in total CD4 cells. Data were determined by FACS analysis and are expressed as mean ⁇ SEM. Statistical analysis was performed by one-way anova followed by Tukey's post hoc test. **** p ⁇ 0.0001, compared to respective PBS group.
  • FIG. 23 depicts the suppression of antigen-driven inflammation by P-0511 in a mouse model of delayed-type hypersensitivity (DTH) induced by keyhole limpet hemocyanin (KLH) antigen.
  • DTH delayed-type hypersensitivity
  • KLH keyhole limpet hemocyanin
  • Mice were KLH immunized on day 0 and re-challenged in right ear on day 5. Mice were treated with P-0511 either Q3D or Q5D starting at Day ⁇ 2.
  • Kinetics of the DTH response using the change in ear thickness relative to baseline values (A ear thickness) at various times after KLH challenge was illustrated for A) Q3D, and B) Q5D dosing schedules. Data are expressed as mean ⁇ SEM.
  • Statistical analysis was performed by one-way anova followed by Tukey's post hoc test. **** p ⁇ 0.0001, *** p ⁇ 0.001, ** p ⁇ 0.01, * p ⁇ 0.05, compared to respective PBS group at respective timepoint
  • FIG. 24 depicts the suppression of antigen-driven inflammation by P-0511 in comparison with a benchmark molecule (Benchmark-1) in a mouse model of DTH induced by KLH antigen.
  • Mice were KLH immunized on day 0 and re-challenged in right ear on day 5. Mice were treated with the compound Q5D starting on day ⁇ 2.
  • Kinetics of the DTH response using the change in ear thickness relative to baseline values ( ⁇ ear thickness) at various times after KLH challenge was illustrated. Data are expressed as mean ⁇ SEM.
  • Statistical analysis was performed by one-way anova followed by Tukey's post hoc test. **** p ⁇ 0.0001, ** p ⁇ 0.01, * p ⁇ 0.05, compared to respective PBS group at respective timepoint.
  • the present invention relates to polypeptides which share primary sequence with human IL-2, except for one to several amino acids that have been mutated.
  • One panel of IL-2 variants comprise mutations that preferentially promotes the proliferation, survival, activation and/or function of immunosuppressive regulatory T cells ((T CD4+CD25+FoxP3+) over effector T cells and NK cells.
  • the present invention also includes therapeutic uses of such IL-2 selective agonist, used alone, or in combination with disease tissue targeting proteins or peptides to treat autoimmune and various inflammatory disorders.
  • Another panel of IL-2 variants comprise mutations substantially reduce the ability of these polypeptides to stimulate either Treg or Tconv cells while may having receptor binding activity and make them effective as IL-2 antagonists.
  • the present invention relates to pharmaceutical compositions comprising the polypeptides disclosed.
  • the present invention relates to the therapeutic use of the polypeptides and pharmaceutical compositions disclosed due to their selective modulating effect of the immune system on diseases like autoimmune and inflammatory disorders.
  • polypeptide refers to a polymer of amino acid residues.
  • peptides polypeptides
  • proteins are chains of amino acids whose alpha carbons are linked through peptide bonds.
  • the terminal amino acid at one end of the chain (amino terminal) therefore has a free amino group, while the terminal amino acid at the other end of the chain (carboxy terminal) has a free carboxyl group.
  • amino terminus refers to the free ⁇ -amino group on an amino acid at the amino terminal of a peptide or to the ⁇ -amino group (Amino group when participating in a peptide bond) of an amino acid at any other location within the peptide.
  • carboxy terminus refers to the free carboxyl group on the carboxy terminus of a peptide or the carboxyl group of an amino acid at any other location within the peptide.
  • Peptides also include essentially any polyamino acid including, but not limited to, peptide mimetics such as amino acids joined by an ether as opposed to an amide bond.
  • Polypeptides of the disclosure include polypeptides that have been modified in any way and for any reason, for example, to: (1) reduce susceptibility to proteolysis, (2) reduce susceptibility to oxidation, (3) alter binding affinity for forming protein complexes, (4) alter binding affinities, and (5) confer or modify other physicochemical or functional properties.
  • amino acid substitution refers to the replacement in a polypeptide of one amino acid at a particular position in a parent polypeptide sequence with a different amino acid.
  • Amino acid substitutions can be generated using genetic or chemical methods well known in the art. For example, single or multiple amino acid substitutions (e.g., conservative amino acid substitutions) may be made in the naturally occurring sequence (e.g., in the portion of the polypeptide outside the domain(s) forming intermolecular contacts).
  • a “conservative amino acid substitution” refers to the substitution in a polypeptide of an amino acid with a functionally similar amino acid. The following six groups each contain amino acids that are conservative substitutions for one another:
  • non-conservative amino acid substitution refers to the substitution of a member of one of these classes for a member from another class.
  • the hydropathic index of amino acids may be considered. Each amino acid has been assigned a hydropathic index on the basis of its hydrophobicity and charge characteristics.
  • hydropathic amino acid index in conferring interactive biological function on a protein is understood in the art (see, for example, Kyte et al., 1982, J. Mol. Biol. 157:105-131). It is known that certain amino acids may be substituted for other amino acids having a similar hydropathic index or score and still retain a similar biological activity.
  • the substitution of amino acids whose hydropathic indices are within +2 is included. In various embodiments, those that are within +1 are included, and in various embodiments, those within +0.5 are included.
  • the substitution of like amino acids can be made effectively on the basis of hydrophilicity, particularly where the biologically functional protein or peptide thereby created is intended for use in immunological embodiments, as disclosed herein.
  • the greatest local average hydrophilicity of a protein as governed by the hydrophilicity of its adjacent amino acids, correlates with its immunogenicity and antigenicity, i.e., with a biological property of the protein.
  • hydrophilicity values have been assigned to these 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); threonine ( ⁇ 0.4); proline ( ⁇ 0.5.+ ⁇ .1); 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) and tryptophan ( ⁇ 3.4).
  • the substitution of amino acids whose hydrophilicity values are within ⁇ 2 is included, in various embodiments, those that are within ⁇ 1 are included, and in various embodiments, those within ⁇ 0.5 are included.
  • a skilled artisan will be able to determine suitable variants of polypeptides as set forth herein using well-known techniques.
  • one skilled in the art may identify suitable areas of the molecule that may be changed without destroying activity by targeting regions not believed to be important for activity.
  • the skilled artisan can identify residues and portions of the molecules that are conserved among similar polypeptides.
  • even areas that may be important for biological activity or for structure may be subject to conservative amino acid substitutions without destroying the biological activity or without adversely affecting the polypeptide structure.
  • One skilled in the art can also analyze the three-dimensional structure and amino acid sequence in relation to that structure in similar polypeptides. In view of such information, one skilled in the art may predict the alignment of amino acid residues of a polypeptide with respect to its three-dimensional structure. In various embodiments, one skilled in the art may choose to not make radical changes to amino acid residues predicted to be on the surface of the polypeptide, since such residues may be involved in important interactions with other molecules. Moreover, one skilled in the art may generate test variants containing a single amino acid substitution at each desired amino acid residue. The variants can then be screened using activity assays known to those skilled in the art. Such variants could be used to gather information about suitable variants.
  • polypeptide fragment and “truncated polypeptide” as used herein refers to a polypeptide that has an amino-terminal and/or carboxy-terminal deletion as compared to a corresponding full-length protein.
  • fragments can be, e.g., at least 5, at least 10, at least 25, at least 50, at least 100, at least 150, at least 200, at least 250, at least 300, at least 350, at least 400, at least 450, at least 500, at least 600, at least 700, at least 800, at least 900 or at least 1000 amino acids in length.
  • fragments can also be, e.g., at most 1000, at most 900, at most 800, at most 700, at most 600, at most 500, at most 450, at most 400, at most 350, at most 300, at most 250, at most 200, at most 150, at most 100, at most 50, at most 25, at most 10, or at most 5 amino acids in length.
  • a fragment can further comprise, at either or both of its ends, one or more additional amino acids, for example, a sequence of amino acids from a different naturally-occurring protein (e.g., an Fc or leucine zipper domain) or an artificial amino acid sequence (e.g., an artificial linker sequence).
  • polypeptide variant refers to a polypeptide that comprises an amino acid sequence wherein one or more amino acid residues are inserted into, deleted from and/or substituted into the amino acid sequence relative to another polypeptide sequence.
  • the number of amino acid residues to be inserted, deleted, or substituted can be, e.g., at least 1, at least 2, at least 3, at least 4, at least 5, at least 10, at least 25, at least 50, at least 75, at least 100, at least 125, at least 150, at least 175, at least 200, at least 225, at least 250, at least 275, at least 300, at least 350, at least 400, at least 450 or at least 500 amino acids in length.
  • Hybrids of the present disclosure include fusion proteins.
  • a “derivative” of a polypeptide is a polypeptide that has been chemically modified, e.g., conjugation to another chemical moiety such as, for example, polyethylene glycol, albumin (e.g., human serum albumin), phosphorylation, and glycosylation.
  • another chemical moiety such as, for example, polyethylene glycol, albumin (e.g., human serum albumin), phosphorylation, and glycosylation.
  • % sequence identity is used interchangeably herein with the term “% identity” and refers to the level of amino acid sequence identity between two or more peptide sequences or the level of nucleotide sequence identity between two or more nucleotide sequences, when aligned using a sequence alignment program.
  • 80% identity means the same thing as 80% sequence identity determined by a defined algorithm and means that a given sequence is at least 80% identical to another length of another sequence.
  • the % identity is selected from, e.g., at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or at least 99% or more sequence identity to a given sequence.
  • the % identity is in the range of, e.g., about 60% to about 70%, about 70% to about 80%, about 80% to about 85%, about 85% to about 90%, about 90% to about 95%, or about 95% to about 99%.
  • % sequence homology is used interchangeably herein with the term “% homology” and refers to the level of amino acid sequence homology between two or more peptide sequences or the level of nucleotide sequence homology between two or more nucleotide sequences, when aligned using a sequence alignment program.
  • 80% homology means the same thing as 80% sequence homology determined by a defined algorithm, and accordingly a homologue of a given sequence has greater than 80% sequence homology over a length of the given sequence.
  • the % homology is selected from, e.g., at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or at least 99% or more sequence homology to a given sequence. In various embodiments, the % homology is in the range of, e.g., about 60% to about 70%, about 70% to about 80%, about 80% to about 85%, about 85% to about 90%, about 90% to about 95%, or about 95% to about 99%.
  • the BLASTX program is preferred for searching nucleic acid sequences that have been translated in all reading frames against amino acid sequences in the GenBank Protein Sequences and other public databases. Both BLASTP and BLASTX are run using default parameters of an open gap penalty of 11.0, and an extended gap penalty of 1.0, and utilize the BLOSUM-62 matrix.
  • the BLAST algorithm In addition to calculating percent sequence identity, the BLAST algorithm also performs a statistical analysis of the similarity between two sequences (see, e.g., Karlin & Altschul, Proc. Nat'l. Acad. Sci. USA, 90:5873-5787, 1993).
  • One measure of similarity provided by the BLAST algorithm is the smallest sum probability (P(N)), which provides an indication of the probability by which a match between two nucleotide or amino acid sequences would occur by chance.
  • P(N) the smallest sum probability
  • a nucleic acid is considered similar to a reference sequence if the smallest sum probability in a comparison of the test nucleic acid to the reference nucleic acid is, e.g., less than about 0.1, less than about 0.01, or less than about 0.001.
  • modification refers to any manipulation of the peptide backbone (e.g. amino acid sequence) or the post-translational modifications (e.g. glycosylation) of a polypeptide.
  • knob-into-hole modification refers to a modification within the interface between two immunoglobulin heavy chains in the CH3 domain.
  • the “knob-into-hole modification” comprises the amino acid substitution T366W and optionally the amino acid substitution S354C in one of the antibody heavy chains, and the amino acid substitutions T366S, L368A, Y407V and optionally Y349C in the other one of the antibody heavy chains.
  • the knob-into-hole technology is described e.g. in U.S. Pat. Nos. 5,731,168; 7,695,936; Ridgway et al., Prot Eng 9, 617-621 (1996) and Carter, J Immunol Meth 248, 7-15 (2001).
  • fusion protein refers to a fusion polypeptide molecule comprising two or more genes that originally coded for separate proteins, wherein the components of the fusion protein are linked to each other by peptide-bonds, either directly or through peptide linkers.
  • fused refers to components that are linked by peptide bonds, either directly or via one or more peptide linkers.
  • Linker refers to a molecule that joins two other molecules, either covalently, or through ionic, van der Waals or hydrogen bonds, e.g., a nucleic acid molecule that hybridizes to one complementary sequence at the 5′ end and to another complementary sequence at the 3′ end, thus joining two non-complementary sequences.
  • a “cleavable linker” refers to a linker that can be degraded or otherwise severed to separate the two components connected by the cleavable linker.
  • Cleavable linkers are generally cleaved by enzymes, typically peptidases, proteases, nucleases, lipases, and the like. Cleavable linkers may also be cleaved by environmental cues, such as, for example, changes in temperature, pH, salt concentration, etc.
  • peptide linker refers to a peptide comprising one or more amino acids, typically about 2-20 amino acids. Peptide linkers are known in the art or are described herein. Suitable, non-immunogenic linker peptides include, for example, (G 4 S) n , (SG 4 ) n or G 4 (SG 4 )n peptide linkers. “n” is generally a number between 1 and 10, typically between 2 and 4.
  • “Pharmaceutical composition” refers to a composition suitable for pharmaceutical use in an animal.
  • a pharmaceutical composition comprises a pharmacologically effective amount of an active agent and a pharmaceutically acceptable carrier.
  • “Pharmacologically effective amount” refers to that amount of an agent effective to produce the intended pharmacological result.
  • “Pharmaceutically acceptable carrier” refers to any of the standard pharmaceutical carriers, vehicles, buffers, and excipients, such as a phosphate buffered saline solution, 5% aqueous solution of dextrose, and emulsions, such as an oil/water or water/oil emulsion, and various types of wetting agents and/or adjuvants.
  • a “pharmaceutically acceptable salt” is a salt that can be formulated into a compound for pharmaceutical use including, e.g., metal salts (sodium, potassium, magnesium, calcium, etc.) and salts of ammonia or organic amines.
  • treatment refers to clinical intervention in an attempt to alter the natural course of a disease in the individual being treated and can be performed either for prophylaxis or during the course of clinical pathology. Desirable effects of treatment include, but are not limited to, preventing occurrence or recurrence of disease, alleviation of symptoms, diminishment of any direct or indirect pathological consequences of the disease, preventing metastasis, decreasing the rate of disease progression, amelioration or palliation of the disease state, and remission or improved prognosis.
  • references herein to “alleviate” a disease, disorder or condition means reducing the severity and/or occurrence frequency of the symptoms of the disease, disorder, or condition.
  • references herein to “treatment” include references to curative, palliative and prophylactic treatment.
  • an effective amount refers to an amount of a compound or composition sufficient to treat a specified disorder, condition or disease such as ameliorate, palliate, lessen, and/or delay one or more of its symptoms.
  • an effective amount comprises an amount sufficient to: (i) reduce the number of cancer cells; (ii) reduce tumor size; (iii) inhibit, retard, slow to some extent and preferably stop cancer cell infiltration into peripheral organs; (iv) inhibit (i.e., slow to some extent and preferably stop) tumor metastasis; (v) inhibit tumor growth; (vi) prevent or delay occurrence and/or recurrence of tumor; and/or (vii) relieve to some extent one or more of the symptoms associated with the cancer.
  • An effective amount can be administered in one or more administrations.
  • administering refers to the actions taken by a medical professional (e.g., a physician), or a person controlling medical care of a patient, that control and/or permit the administration of the agent(s)/compound(s) at issue to the patient.
  • Causing to be administered can involve diagnosis and/or determination of an appropriate therapeutic regimen, and/or prescribing particular agent(s)/compounds for a patient.
  • Such prescribing can include, for example, drafting a prescription form, annotating a medical record, and the like. Where administration is described herein, “causing to be administered” is also contemplated.
  • patient may be used interchangeably and refer to a mammal, preferably a human or a non-human primate, but also domesticated mammals (e.g., canine or feline), laboratory mammals (e.g., mouse, rat, rabbit, hamster, guinea pig), and agricultural mammals (e.g., equine, bovine, porcine, ovine).
  • the patient can be a human (e.g., adult male, adult female, adolescent male, adolescent female, male child, female child) under the care of a physician or other health worker in a hospital, psychiatric care facility, as an outpatient, or other clinical context.
  • the patient may be an immunocompromised patient or a patient with a weakened immune system including, but not limited to patients having primary immune deficiency, AIDS; cancer and transplant patients who are taking certain immunosuppressive drugs; and those with inherited diseases that affect the immune system (e.g., congenital agammaglobulinemia, congenital IgA deficiency).
  • the patient has an immunogenic cancer, including, but not limited to bladder cancer, lung cancer, melanoma, and other cancers reported to have a high rate of mutations (Lawrence et al., Nature, 499(7457): 214-218, 2013).
  • Fc domain or “Fc region” as used herein is used to define a C-terminal region of an immunoglobulin heavy chain that contains at least a portion of the constant region.
  • the term includes native sequence Fc regions and variant Fc regions.
  • An IgG Fc region comprises an IgG CH2 and an IgG CH3 domain.
  • the CH3 region herein may be a native sequence CH3 domain or a variant CH3 domain (e.g. a CH3 domain with an introduced “protuberance” (“knob”) in one chain thereof and a corresponding introduced “cavity” (“hole”) in the other chain thereof; see U.S. Pat. No. 5,821,333, expressly incorporated herein by reference).
  • Such variant CH3 domains may be used to promote heterodimerization of two non-identical immunoglobulin heavy chains as herein described. Unless otherwise specified herein, numbering of amino acid residues in the Fc region or constant region is according to the EU numbering system.
  • effector functions refers to those biological activities attributable to the Fc region of an immunoglobulin, which vary with the immunoglobulin isotype.
  • immunoglobulin effector functions include: C1q binding and complement dependent cytotoxicity (CDC), Fc receptor binding, antibody-dependent cell-mediated cytotoxicity (ADCC), antibody-dependent cellular phagocytosis (ADCP), cytokine secretion, immune complex-mediated antigen uptake by antigen presenting cells, down regulation of cell surface receptors (e.g. B cell receptor), and B cell activation.
  • Treg cell a specialized type of CD4+ T cell that can suppress the responses of other T cells (effector T cells).
  • Treg cells are characterized by expression of CD4, the ⁇ -subunit of the IL-2 receptor (CD25), and the transcription factor forkhead box P3 (FOXP3) (Sakaguchi, Annu Rev Immunol 22, 531-62 (2004)) and play a critical role in the induction and maintenance of peripheral self-tolerance to antigens, including those expressed by tumors.
  • CD4+ T cells are conventional CD4+ T cells other than regulatory T cells.
  • Treg cells activation of Treg cells essentially without concomitant activation of other T cell subsets (such as CD4+ T helper cells, CD8+ cytotoxic T cells) or natural killer (NK) cells. Methods for identifying and distinguishing these cell types are described in the Examples. Activation may include induction of IL-2 receptor signaling (as measured e.g. by detection of phosphorylated STAT5), induction of proliferation (as measured e.g. by detection of Ki-67), and/or up-regulation of expression of activation markers (such as e.g. CD25), and expansion of cell numbers.
  • T cell subsets such as CD4+ T helper cells, CD8+ cytotoxic T cells
  • NK natural killer
  • ELISA enzyme-linked immunosorbent assay
  • SPR Surface Plasmon Resonance
  • affinity refers to the strength of the sum total of non-covalent interactions between a single binding site of a molecule (e.g. an antibody) and its binding partner (e.g. an antigen).
  • the affinity of a molecule X for its partner Y can generally be represented by the dissociation constant (KD), which is the ratio of dissociation and association rate constants (koff and kon, respectively).
  • KD dissociation constant
  • a particular method for measuring affinity is Surface Plasmon Resonance (SPR).
  • reduced binding refers to a decrease in affinity for the respective interaction, as measured for example by SPR. Conversely, “increased binding” refers to an increase in binding affinity for the respective interaction.
  • polymer as used herein generally includes, but is not limited to, homopolymers; copolymers, such as, for example, block, graft, random and alternating copolymers; and terpolymers; and blends and modifications thereof. Furthermore, unless otherwise specifically limited, the term “polymer” shall include all possible geometrical configurations of the material. These configurations include, but are not limited to isotactic, syndiotactic, and random symmetries.
  • Polynucleotide refers to a polymer composed of nucleotide units.
  • Polynucleotides include naturally occurring nucleic acids, such as deoxyribonucleic acid (“DNA”) and ribonucleic acid (“RNA”) as well as nucleic acid analogs.
  • Nucleic acid analogs include those which include non-naturally occurring bases, nucleotides that engage in linkages with other nucleotides other than the naturally occurring phosphodiester bond or which include bases attached through linkages other than phosphodiester bonds.
  • nucleotide analogs include, for example and without limitation, phosphorothioates, phosphorodithioates, phosphorotriesters, phosphoramidates, boranophosphates, methylphosphonates, chiral-methyl phosphonates, 2-O-methyl ribonucleotides, peptide-nucleic acids (PNAs), and the like.
  • PNAs peptide-nucleic acids
  • Such polynucleotides can be synthesized, for example, using an automated DNA synthesizer.
  • the term “nucleic acid” typically refers to large polynucleotides.
  • oligonucleotide typically refers to short polynucleotides, generally no greater than about 50 nucleotides.
  • nucleotide sequence is represented by a DNA sequence (i.e., A, T, G, C)
  • this also includes an RNA sequence (i.e., A, U, G, C) in which “U” replaces “T.”
  • the left-hand end of a single-stranded polynucleotide sequence is the 5′-end; the left-hand direction of a double-stranded polynucleotide sequence is referred to as the 5′-direction.
  • the direction of 5′ to 3′ addition of nucleotides to nascent RNA transcripts is referred to as the transcription direction.
  • the DNA strand having the same sequence as an mRNA is referred to as the “coding strand”; sequences on the DNA strand having the same sequence as an mRNA transcribed from that DNA and which are located 5′ to the 5′-end of the RNA transcript are referred to as “upstream sequences”; sequences on the DNA strand having the same sequence as the RNA and which are 3′ to the 3′ end of the coding RNA transcript are referred to as “downstream sequences.”
  • “Complementary” refers to the topological compatibility or matching together of interacting surfaces of two polynucleotides.
  • the two molecules can be described as complementary, and furthermore, the contact surface characteristics are complementary to each other.
  • a first polynucleotide is complementary to a second polynucleotide if the nucleotide sequence of the first polynucleotide is substantially identical to the nucleotide sequence of the polynucleotide binding partner of the second polynucleotide, or if the first polynucleotide can hybridize to the second polynucleotide under stringent hybridization conditions.
  • Hybridizing specifically to” or “specific hybridization” or “selectively hybridize to”, refers to the binding, duplexing, or hybridizing of a nucleic acid molecule preferentially to a particular nucleotide sequence under stringent conditions when that sequence is present in a complex mixture (e.g., total cellular) DNA or RNA.
  • stringent conditions refers to conditions under which a probe will hybridize preferentially to its target subsequence, and to a lesser extent to, or not at all to, other sequences.
  • Stringent hybridization and “stringent hybridization wash conditions” in the context of nucleic acid hybridization experiments such as Southern and northern hybridizations are sequence-dependent and are different under different environmental parameters.
  • highly stringent hybridization and wash conditions are selected to be about 5° C. lower than the thermal melting point (Tm) for the specific sequence at a defined ionic strength and pH.
  • Tm is the temperature (under defined ionic strength and pH) at which 50% of the target sequence hybridizes to a perfectly matched probe.
  • Very stringent conditions are selected to be equal to the Tm for a particular probe.
  • An example of stringent hybridization conditions for hybridization of complementary nucleic acids which have more than about 100 complementary residues on a filter in a Southern or northern blot is 50% formalin with 1 mg of heparin at 42° C., with the hybridization being carried out overnight.
  • An example of highly stringent wash conditions is 0.15 M NaCl at 72° C. for about 15 minutes.
  • An example of stringent wash conditions is a 0.2 ⁇ SSC wash at 65° C. for 15 minutes. See Sambrook et al. for a description of SSC buffer. A high stringency wash can be preceded by a low stringency wash to remove background probe signal.
  • An exemplary medium stringency wash for a duplex of, e.g., more than about 100 nucleotides, is 1 ⁇ SSC at 45° C. for 15 minutes.
  • An exemplary low stringency wash for a duplex of, e.g., more than about 100 nucleotides is 4-6 ⁇ SSC at 40° C. for 15 minutes.
  • a signal to noise ratio of 2 ⁇ (or higher) than that observed for an unrelated probe in the particular hybridization assay indicates detection of a specific hybridization.
  • Primer refers to a polynucleotide that is capable of specifically hybridizing to a designated polynucleotide template and providing a point of initiation for synthesis of a complementary polynucleotide. Such synthesis occurs when the polynucleotide primer is placed under conditions in which synthesis is induced, i.e., in the presence of nucleotides, a complementary polynucleotide template, and an agent for polymerization such as DNA polymerase.
  • a primer is typically single-stranded but may be double-stranded. Primers are typically deoxyribonucleic acids, but a wide variety of synthetic and naturally occurring primers are useful for many applications.
  • a primer is complementary to the template to which it is designed to hybridize to serve as a site for the initiation of synthesis but need not reflect the exact sequence of the template. In such a case, specific hybridization of the primer to the template depends on the stringency of the hybridization conditions. Primers can be labeled with, e.g., chromogenic, radioactive, or fluorescent moieties and used as detectable moieties.
  • Probe when used in reference to a polynucleotide, refers to a polynucleotide that is capable of specifically hybridizing to a designated sequence of another polynucleotide.
  • a probe specifically hybridizes to a target complementary polynucleotide but need not reflect the exact complementary sequence of the template. In such a case, specific hybridization of the probe to the target depends on the stringency of the hybridization conditions.
  • Probes can be labeled with, e.g., chromogenic, radioactive, or fluorescent moieties and used as detectable moieties. In instances where a probe provides a point of initiation for synthesis of a complementary polynucleotide, a probe can also be a primer.
  • a “vector” is a polynucleotide that can be used to introduce another nucleic acid linked to it into a cell.
  • a “plasmid” refers to a linear or circular double stranded DNA molecule into which additional nucleic acid segments can be ligated.
  • a viral vector e.g., replication defective retroviruses, adenoviruses and adeno-associated viruses
  • certain vectors are capable of autonomous replication in a host cell into which they are introduced (e.g., bacterial vectors comprising a bacterial origin of replication and episomal mammalian vectors).
  • vectors e.g., non-episomal mammalian vectors
  • An “expression vector” is a type of vector that can direct the expression of a chosen polynucleotide.
  • a “regulatory sequence” is a nucleic acid that affects the expression (e.g., the level, timing, or location of expression) of a nucleic acid to which it is operably linked.
  • the regulatory sequence can, for example, exert its effects directly on the regulated nucleic acid, or through the action of one or more other molecules (e.g., polypeptides that bind to the regulatory sequence and/or the nucleic acid).
  • Examples of regulatory sequences include promoters, enhancers and other expression control elements (e.g., polyadenylation signals). Further examples of regulatory sequences are described in, for example, Goeddel, 1990, Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, Calif.
  • a nucleotide sequence is “operably linked” to a regulatory sequence if the regulatory sequence affects the expression (e.g., the level, timing, or location of expression) of the nucleotide sequence.
  • a “host cell” is a cell that can be used to express a polynucleotide of the disclosure.
  • a host cell can be a prokaryote, for example, E. coli , or it can be a eukaryote, for example, a single-celled eukaryote (e.g., a yeast or other fungus), a plant cell (e.g., a tobacco or tomato plant cell), an animal cell (e.g., a human cell, a monkey cell, a hamster cell, a rat cell, a mouse cell, or an insect cell) or a hybridoma.
  • a prokaryote for example, E. coli
  • a eukaryote for example, a single-celled eukaryote (e.g., a yeast or other fungus)
  • a plant cell e.g., a tobacco or tomato plant cell
  • an animal cell e.g.
  • a host cell is a cultured cell that can be transformed or transfected with a polypeptide-encoding nucleic acid, which can then be expressed in the host cell.
  • the phrase “recombinant host cell” can be used to denote a host cell that has been transformed or transfected with a nucleic acid to be expressed.
  • a host cell also can be a cell that comprises the nucleic acid but does not express it at a desired level unless a regulatory sequence is introduced into the host cell such that it becomes operably linked with the nucleic acid. It is understood that the term host cell refers not only to the particular subject cell but also to the progeny or potential progeny of such a cell. Because certain modifications may occur in succeeding generations due to, e.g., mutation or environmental influence, such progeny may not, in fact, be identical to the parent cell, but are still included within the scope of the term as used herein.
  • isolated molecule (where the molecule is, for example, a polypeptide or a polynucleotide) is a molecule that by virtue of its origin or source of derivation (1) is not associated with naturally associated components that accompany it in its native state, (2) is substantially free of other molecules from the same species, (3) is expressed by a cell from a different species, or (4) does not occur in nature.
  • a molecule that is chemically synthesized, or expressed in a cellular system different from the cell from which it naturally originates will be “isolated” from its naturally associated components.
  • a molecule also may be rendered substantially free of naturally associated components by isolation, using purification techniques well known in the art.
  • Molecule purity or homogeneity may be assayed by a number of means well known in the art.
  • the purity of a polypeptide sample may be assayed using polyacrylamide gel electrophoresis and staining of the gel to visualize the polypeptide using techniques well known in the art.
  • higher resolution may be provided by using HPLC or other means well known in the art for purification.
  • a protein or polypeptide is “substantially pure,” “substantially homogeneous,” or “substantially purified” when at least about 60% to 75% of a sample exhibits a single species of polypeptide.
  • the polypeptide or protein may be monomeric or multimeric.
  • a substantially pure polypeptide or protein will typically comprise about 50%, 60%, 70%, 80% or 90% W/W of a protein sample, more usually about 95%, and preferably will be over 99% pure.
  • Protein purity or homogeneity may be indicated by a number of means well known in the art, such as polyacrylamide gel electrophoresis of a protein sample, followed by visualizing a single polypeptide band upon staining the gel with a stain well known in the art. For certain purposes, higher resolution may be provided by using HPLC or other means well known in the art for purification.
  • label refers to incorporation of another molecule in the antibody.
  • the label is a detectable marker, e.g., incorporation of a radiolabeled amino acid or attachment to a polypeptide of biotinyl moieties that can be detected by marked avidin (e.g., streptavidin containing a fluorescent marker or enzymatic activity that can be detected by optical or calorimetric methods).
  • the label or marker can be therapeutic, e.g., a drug conjugate or toxin.
  • Various methods of labeling polypeptides and glycoproteins are known in the art and may be used.
  • labels for polypeptides include, but are not limited to, the following: radioisotopes or radionuclides (e.g., 3 H, 14 C, 15 N, 35 S, 90 Y, 99 Tc, 111 In, 125 I, 131 I), fluorescent labels (e.g., FITC, rhodamine, lanthanide phosphors), enzymatic labels (e.g., horseradish peroxidase, ⁇ -galactosidase, luciferase, alkaline phosphatase), chemiluminescent markers, biotinyl groups, predetermined polypeptide epitopes recognized by a secondary reporter (e.g., leucine zipper pair sequences, binding sites for secondary antibodies, metal binding domains, epitope tags), magnetic agents, such as gadolinium chelates, toxins such as pertussis toxin, taxol, cytochalasin B, gramicidin D, ethidium bromide,
  • heterologous refers to a composition or state that is not native or naturally found, for example, that may be achieved by replacing an existing natural composition or state with one that is derived from another source.
  • expression of a protein in an organism other than the organism in which that protein is naturally expressed constitutes a heterologous expression system and a heterologous protein.
  • references to “about” a value or parameter herein includes (and describes) variations that are directed to that value or parameter per se. For example, description referring to “about X” includes description of “X”.
  • Interleukin-2 a classic Th1 cytokine, is produced by T cells after activation through the T-cell antigen receptor and the co-stimulatory molecule CD28.
  • the regulation of IL-2 occurs through activation of signaling pathways and transcription factors that act on the IL-2 promoter to generate new gene transcription, but also involves modulation of the stability of IL-2 mRNA.
  • IL-2 binds to a multichain receptor, including a highly regulated ⁇ chain and ⁇ and ⁇ chains that mediate signaling through the Jak-STAT pathway.
  • IL-2 delivers activation, growth, and differentiation signals to T cells, B cells, and NK cells.
  • IL-2 is also important in mediating activation-induced cell death of T cells, a function that provides an essential mechanism for terminating immune responses.
  • IL-2 has also been suggested for administration in patients suffering from or infected with hepatitis C virus (HCV), human immunodeficiency virus (HIV), acute myeloid leukemia, non-Hodgkin's lymphoma, cutaneous T-cell lymphoma, juvenile rheumatoid arthritis, atopic dermatitis, breast cancer and bladder cancer.
  • HCV hepatitis C virus
  • HAV human immunodeficiency virus
  • acute myeloid leukemia non-Hodgkin's lymphoma
  • cutaneous T-cell lymphoma cutaneous T-cell lymphoma
  • juvenile rheumatoid arthritis atopic dermatitis
  • breast cancer and bladder cancer Unfortunately, short half-life and severe toxicity limits the optimal dosing of IL-2.
  • the terms “native IL-2” and “native interleukin-2” in the context of proteins or polypeptides refer to any naturally occurring mammalian interleukin-2 amino acid sequences, including immature or precursor and mature forms.
  • Non-limiting examples of GenBank Accession Nos. for the amino acid sequence of various species of native mammalian interleukin-2 include NP 032392.1 ( Mus musculus , immature form), NP_001040595.1 ( Macaca mulatta , immature form), NP_000577.2 (human, precursor form), CAA01199.1 (human, immature form), AAD48509.1 (human, immature form), and AAB20900.1 (human).
  • native IL-2 is the immature or precursor form of a naturally occurring mammalian IL-2. In other embodiments, native IL-2 is the mature form of a naturally occurring mammalian IL-2. In various embodiments, native IL-2 is the precursor form of naturally occurring human IL-2. In various embodiments, native IL-2 is the mature form of naturally occurring human IL-2. In various embodiments, IL-2 is derived from the amino acid sequence of the human IL-2 precursor sequence set forth in SEQ ID NO: 1:
  • IL-2 comprises the amino acid sequence of the human IL-2 mature form wild type sequence set forth in SEQ ID NO: 3, which contains substitution of cysteine at position 125 to serine, but does not alter IL-2 receptor binding compared to the naturally occurring IL-2:
  • the present invention relates to polypeptides which share primary sequence with human IL-2, except for one to several amino acids that have been mutated.
  • One panel of IL-2 variants comprise mutations that preferentially promotes the proliferation, survival, activation and/or function of immunosuppressive regulatory T cells ((T CD4+CD25+FoxP3+) over effector T cells and NK cells.
  • immunosuppressive regulatory T cells (T CD4+CD25+FoxP3+) over effector T cells and NK cells.
  • IL-2 selective agonist used alone, or in combination with disease tissue targeting protein or peptide to treat Treg cell-deficient autoimmune and various inflammatory disorders.
  • pharmaceutical compositions comprising the polypeptides disclosed.
  • the present invention relates to the therapeutic use of the polypeptides and pharmaceutical compositions disclosed due to their selective modulating effect of the immune system on diseases like autoimmune and inflammatory disorders or cancer and various infectious diseases.
  • the present invention relates to polypeptides of 100 to 500 amino acids in length, preferably of 140 residues size whose apparent molecular weight is at least 15 kD. These polypeptides maintain high sequence identity, more than 90%, with native IL-2. In these positions, these polypeptides are mutated introducing amino acid residues different from those in the same position in the native IL-2.
  • polypeptides of the present invention may be referred to as immunomodulatory polypeptides, IL-2 analogs or IL-2 variants, among other names. These polypeptides are designed based on the 3D structure of the IL-2 receptor complex (available in PDB public database), introducing mutations mainly in the positions of the IL-2 corresponding to amino acids interacting with receptor subunit(s) ⁇ or ⁇ or ⁇ .
  • the IL-2 variant (or mutant) comprises a sequence derived from the sequence of the mature human IL-2 polypeptide as set forth in SEQ ID NO: 3.
  • the IL-2 variant comprises a different amino acid sequence than the native (or wild type) IL-2 protein.
  • the IL-2 variant binds the IL-2R ⁇ polypeptide and functions as an IL-2 agonist or antagonist.
  • the IL-2 variants with agonist activity have super agonist activity.
  • the IL-2 variant can function as an IL-2 agonist or antagonist independent of its association with IL-2R ⁇ .
  • IL-2 agonists are exemplified by comparable or increased biological activity compared to wild type IL-2.
  • IL-2 antagonists are exemplified by decreased biological activity compared to wild type IL-2 or by the ability to inhibit IL-2-mediated responses.
  • the sequence of the IL-2 variant has at least one amino acid change, e.g. substitution or deletion, compared to the native IL-2 sequence, such changes resulting in IL-2 agonist or antagonist activity.
  • the IL-2 variants as Fc fusion protein have the amino acid sequence set forth in SEQ ID NOs: 4-43, 108-146, and 193-197 with reduced binding to IL-2R ⁇ and/or ⁇ C and enhanced selectivity in activating and proliferating regulatory T cells (Treg).
  • IL-2 variants are provided in Table 2A-2F:
  • the present invention also includes additional modifications to the class of IL-2 variants mentioned above and especially to those described in Tables 2A-2F.
  • additional combination mutants combining the preferred mutations described in Table 2A-2F may result in more Treg cell-selective IL-2 agonists.
  • Any further combination mutants come with the spirit and scope of the present invention whether it is to increase their affinity to specific components of the IL-2 receptor, or to improve their in vivo pharmacodynamics: increase half-life or reduce their internalization by T cells.
  • These additional mutations may be obtained by rational design with bioinformatics tools, or by using combinatorial molecular libraries of different nature (phage libraries, libraries of gene expression in yeast or bacteria).
  • the present invention relates to a fusion protein comprising any of the immunomodulatory polypeptides described above, coupled to a carrier protein.
  • the carrier protein can be Albumin or the Fc region of human immunoglobulins.
  • Immunoglobulins of IgG class are among the most abundant proteins in human blood. Their circulation half-lives can reach as long as 21 days. Fusion proteins have been reported to combine the Fc regions of IgG with the domains of another protein, such as various cytokines and receptors (see, for example, Capon et al., Nature, 337:525-531, 1989; Chamow et al., Trends Biotechnol., 14:52-60, 1996); U.S. Pat. Nos. 5,116,964 and 5,541,087).
  • the prototype fusion protein is a homodimer protein linked through cysteine residues in the hinge region of IgG Fc, resulting in a molecule similar to an IgG molecule without the heavy chain variable and CH1 domains and light chains.
  • the dimer nature of fusion proteins comprising the Fc domain may be advantageous in providing higher order interactions (i.e. bivalent or bispecific binding) with other molecules. Due to the structural homology, Fc fusion proteins exhibit in vivo pharmacokinetic profile comparable to that of human IgG with a similar isotype.
  • Fc refers to molecule or sequence comprising the sequence of a non-antigen-binding fragment of whole antibody, whether in monomeric or multimeric form.
  • the original immunoglobulin source of the native Fc is preferably of human origin and may be any of the immunoglobulins, although IgG1 and IgG2 are preferred.
  • Native Fc's are made up of monomeric polypeptides that may be linked into dimeric or multimeric forms by covalent (i.e., disulfide bonds) and non-covalent association.
  • the number of intermolecular disulfide bonds between monomeric subunits of native Fc molecules ranges from 1 to 4 depending on class (e.g., IgG, IgA, IgE) or subclass (e.g., IgG1, IgG2, IgG3, IgA1, IgGA2).
  • class e.g., IgG, IgA, IgE
  • subclass e.g., IgG1, IgG2, IgG3, IgA1, IgGA2
  • One example of a native Fc is a disulfide-bonded dimer resulting from papain digestion of an IgG (see Ellison et al. (1982), Nucleic Acids Res. 10: 4071-9).
  • native Fc as used herein is generic to the monomeric, dimeric, and multimeric forms. Fc domains containing binding sites for Protein A, Protein G, various Fc receptors and complement proteins.
  • Fc variant refers to a molecule or sequence that is modified from a native Fc but still comprises a binding site for the salvage receptor, FcRn.
  • International applications WO 97/34631 published Sep. 25, 1997) and WO 96/32478 describe exemplary Fc variants, as well as interaction with the salvage receptor, and are hereby incorporated by reference.
  • a native Fc comprises sites that may be removed because they provide structural features or biological activity that are not required for the fusion molecules of the present invention.
  • the term “Fc variant” comprises a molecule or sequence that lacks one or more native Fc sites or residues that affect or are involved in (1) disulfide bond formation, (2) incompatibility with a selected host cell (3) N-terminal heterogeneity upon expression in a selected host cell, (4) glycosylation, (5) interaction with complement, (6) binding to an Fc receptor other than a salvage receptor, or (7) antibody-dependent cellular cytotoxicity (ADCC).
  • ADCC antibody-dependent cellular cytotoxicity
  • Fc domain encompasses native Fc and Fc variant molecules and sequences as defined above. As with Fc variants and native Fc's, the term “Fc domain” includes molecules in monomeric or multimeric form, whether digested from whole antibody or produced by recombinant gene expression or by other means. In various embodiments, an “Fc domain” refers to a dimer of two Fc domain monomers (SEQ ID NO: 44) that generally includes full or part of the hinge region. In various embodiments, an Fc domain may be mutated to lack effector functions. In various embodiments, each of the Fc domain monomers in an Fc domain includes amino acid substitutions in the CH2 antibody constant domain to reduce the interaction or binding between the Fc domain and an Fc ⁇ receptor.
  • each subunit of the Fc domain comprises two amino acid substitutions that reduce binding to an activating Fc receptor and/or effector function wherein said amino acid substitutions are L234A and L235A. In various embodiments, each subunit of the Fc domain comprises three amino acid substitutions that reduce binding to an activating Fc receptor and/or effector function wherein said amino acid substitutions are L234A, L235A and G237A (SEQ ID NO: 45).
  • each of the two Fc domain monomers in an Fc domain includes amino acid substitutions that promote the heterodimerization of the two monomers.
  • heterodimerization of Fc domain monomers can be promoted by introducing different, but compatible, substitutions in the two Fc domain monomers, such as “knob-into-hole” residue pairs. The “knob-into-hole” technique is also disclosed in U.S. Pat. No. 8,216,805.
  • one Fc domain monomer includes the knob mutation T366W and the other Fc domain monomer includes hole mutations T366S, L358A, and Y407V.
  • two Cys residues were introduced (S354C on the “knob” and Y349C on the “hole” side) that form a stabilizing disulfide bridge.
  • the use of heterodimeric Fc may result in monovalent IL-2 variant.
  • an Fc domain may be mutated to further extend in vivo half-life.
  • each subunit of the Fc domain comprises three amino acid substitutions that enhance binding to human FcRn wherein said amino acid substitutions are M252Y, S254T, and T256E, disclosed in U.S. Pat. No. 7,658,921.
  • each subunit of the Fc domain comprises one amino acid substitution that enhanced binding to human FcRn wherein said amino acid substitution is N434A, disclosed in U.S. Pat. No. 7,371,826.
  • each subunit of the Fc domain comprises one amino acid substitution that enhanced binding to human FcRn wherein said amino acid substitutions are M428L and N434S, disclosed in U.S. Pat. No. 8,546,543.
  • half-life extension mutations can be combined with amino acid substitutions that reduce binding to an activating Fc receptor and/or effector function.
  • the Fc domain sequence used to make IL-2 variant Fc-fusions is the human IgG1-Fc domain sequence with reduced/abolished effector function set forth in SEQ ID NO: 45:
  • SEQ ID NO: 45 contains amino acid substitutions (underlined) that ablate Fc ⁇ R and C1q binding.
  • the Fc domain sequence used to make IL-2 variant Fc-fusions is the IgG1-Fc domain with extended half-life and reduced/abolished effector function set forth in SEQ ID NO: 46
  • SEQ ID NO: 46 contains amino acid substitutions (underlined) that ablate Fc ⁇ R and C1q binding and substitutions (bold) that extend fusion protein serum half-life.
  • the Fc domain sequence used to make IL-2 variant Fc-fusions is the IgG1-Fc domain with reduced/abolished effector function and extended half-life and having the amino acid sequence set forth in SEQ ID NO: 47
  • SEQ ID NO: 47 contains amino acid substitutions (underlined) that ablate Fc ⁇ R and C1q binding and substitution (bold) that extends fusion protein serum half-life.
  • the heterodimeric Fc domain sequence used to make the IL-2 variant Fc-fusions is the Knob-Fc domain with extended in vivo half-life sequence set forth in SEQ ID NO: 212:
  • SEQ ID NO: 212 contains amino acid substitutions (underlined) that ablate Fc ⁇ R and C1q binding and amino acid substitution (bold) to extend half-life.
  • the heterodimeric Fc domain sequence used to make the IL-2 variant Fc-fusions is the Hole-Fc domain with extended in vivo half-life sequence set forth in SEQ ID NO: 213:
  • SEQ ID NO: 213 contains amino acid substitutions (underlined) that ablate Fc ⁇ R and C1q binding and amino acid substitution (bold) to extend half-life.
  • the heterologous protein is attached to the IL-2 variant by a linker and/or a hinge linker peptide.
  • the linker or hinge linker may be an artificial sequence of between 5, 10, 15, 20, 30, 40 or more amino acids that are relatively free of secondary structure or display ⁇ -helical conformation.
  • Peptide linker provides covalent linkage and additional structural and/or spatial flexibility between protein domains.
  • peptide linkers contain flexible amino acid residues, such as glycine and serine.
  • peptide linker may include 1-100 amino acids.
  • a spacer can contain motif of GGGSGGGS (SEQ ID NO: 55).
  • a linker can contain motif of (GGGGS)n, wherein n is an integer from 1 to 10.
  • a linker can also contain amino acids other than glycine and serine.
  • a linker can contain other protein motifs, including but not limited to, sequences of ⁇ -helical conformation such as AEAAAKEAAAKEAAAKA (SEQ ID NO: 53).
  • linker length and composition can be tuned to optimize activity or developability, including but not limited to, expression level and aggregation propensity.
  • the peptide linker can be a simple chemical bond, e.g., an amide bond (e.g., by chemical conjugation of PEG).
  • the present disclosure provides isolated nucleic acid molecules comprising a polynucleotide encoding IL-2, an IL-2 variant, an IL-2 fusion protein, or an IL-2 variant fusion protein of the present disclosure.
  • the subject nucleic acids may be single-stranded or double stranded.
  • Such nucleic acids may be DNA or RNA molecules.
  • DNA includes, for example, cDNA, genomic DNA, synthetic DNA, DNA amplified by PCR, and combinations thereof. Genomic DNA encoding IL-2 polypeptides is obtained from genomic libraries which are available for a number of species.
  • RNA may be obtained from prokaryotic expression vectors which direct high-level synthesis of mRNA, such as vectors using T7 promoters and RNA polymerase.
  • cDNA is obtained from libraries prepared from mRNA isolated from various tissues that express IL-2.
  • the DNA molecules of the disclosure include full-length genes as well as polynucleotides and fragments thereof. The full-length gene may also include sequences encoding the N-terminal signal sequence. Such nucleic acids may be used, for example, in methods for making the novel IL-2 variants.
  • the isolated nucleic acid molecules comprise the polynucleotides described herein, and further comprise a polynucleotide encoding at least one heterologous protein described herein. In various embodiments, the nucleic acid molecules further comprise polynucleotides encoding the linkers or hinge linkers described herein.
  • the recombinant nucleic acids of the present disclosure may be operably linked to one or more regulatory nucleotide sequences in an expression construct.
  • Regulatory sequences are art-recognized and are selected to direct expression of the IL-2 variant. Accordingly, the term regulatory sequence includes promoters, enhancers, and other expression control elements. Exemplary regulatory sequences are described in Goeddel; Gene Expression Technology: Methods in Enzymology, Academic Press, San Diego, Calif. (1990).
  • said one or more regulatory nucleotide sequences may include, but are not limited to, promoter sequences, leader or signal sequences, ribosomal binding sites, transcriptional start and termination sequences, translational start and termination sequences, and enhancer or activator sequences. Constitutive or inducible promoters as known in the art are contemplated by the present disclosure.
  • the promoters may be either naturally occurring promoters, or hybrid promoters that combine elements of more than one promoter.
  • An expression construct may be present in a cell on an episome, such as a plasmid, or the expression construct may be inserted in a chromosome.
  • the expression vector contains a selectable marker gene to allow the selection of transformed host cells. Selectable marker genes are well known in the art and will vary with the host cell used.
  • the subject nucleic acid is provided in an expression vector comprising a nucleotide sequence encoding an IL-2 variant and operably linked to at least one regulatory sequence.
  • expression vector refers to a plasmid, phage, virus or vector for expressing a polypeptide from a polynucleotide sequence.
  • Vectors suitable for expression in host cells are readily available and the nucleic acid molecules are inserted into the vectors using standard recombinant DNA techniques.
  • Such vectors can include a wide variety of expression control sequences that control the expression of a DNA sequence when operatively linked to it may be used in these vectors to express DNA sequences encoding an IL-2 variant.
  • Such useful expression control sequences include, for example, the early and late promoters of SV40, tet promoter, adenovirus or cytomegalovirus immediate early promoter, RSV promoters, the lac system, the trp system, the TAC or TRC system, T7 promoter whose expression is directed by T7 RNA polymerase, the major operator and promoter regions of phage lambda, the control regions for fd coat protein, the promoter for 3-phosphoglycerate kinase or other glycolytic enzymes, the promoters of acid phosphatase, e.g., PhoS, the promoters of the yeast ⁇ -mating factors, the polyhedron promoter of the baculovirus system and other sequences known to control the expression of genes of prokaryotic or eukaryotic cells or their viruses, and various combinations thereof.
  • the design of the expression vector may depend on such factors as the choice of the host cell to be transformed and/or the type of protein desired to be expressed. Moreover, the vector's copy number, the ability to control that copy number and the expression of any other protein encoded by the vector, such as antibiotic markers, should also be considered.
  • An exemplary expression vector suitable for expression of vIL-2 is the pDSRa, (described in WO 90/14363, herein incorporated by reference) and its derivatives, containing vIL-2 polynucleotides, as well as any additional suitable vectors known in the art or described below.
  • a recombinant nucleic acid of the present disclosure can be produced by ligating the cloned gene, or a portion thereof, into a vector suitable for expression in either prokaryotic cells, eukaryotic cells (yeast, avian, insect or mammalian), or both.
  • Expression vehicles for production of a recombinant IL-2 polypeptide include plasmids and other vectors.
  • suitable vectors include plasmids of the types: pBR322-derived plasmids, pEMBL-derived plasmids, pEX-derived plasmids, pBTac-derived plasmids and pUC-derived plasmids for expression in prokaryotic cells, such as E. coli.
  • Some mammalian expression vectors contain both prokaryotic sequences to facilitate the propagation of the vector in bacteria, and one or more eukaryotic transcription units that are expressed in eukaryotic cells.
  • the pcDNAI/amp, pcDNAI/neo, pRc/CMV, pSV2gpt, pSV2neo, pSV2-dhfr, pTk2, pRSVneo, pMSG, pSVT7, pko-neo and pHyg derived vectors are examples of mammalian expression vectors suitable for transfection of eukaryotic cells.
  • vectors are modified with sequences from bacterial plasmids, such as pBR322, to facilitate replication and drug resistance selection in both prokaryotic and eukaryotic cells.
  • bacterial plasmids such as pBR322
  • derivatives of viruses such as the bovine papilloma virus (BPV-1), or Epstein-Barr virus (pHEBo, pREP-derived and p205) can be used for transient expression of proteins in eukaryotic cells.
  • BBV-1 bovine papilloma virus
  • pHEBo Epstein-Barr virus
  • pREP-derived and p205 Epstein-Barr virus
  • examples of other viral (including retroviral) expression systems can be found below in the description of gene therapy delivery systems.
  • the various methods employed in the preparation of the plasmids and in transformation of host organisms are well known in the art.
  • baculovirus expression systems include pVL-derived vectors (such as pVL1392, pVL1393 and pVL941), pAcUW-derived vectors (such as pAcUW1), and pBlueBac-derived vectors (such as the B-gal containing pBlueBac III).
  • pVL-derived vectors such as pVL1392, pVL1393 and pVL941
  • pAcUW-derived vectors such as pAcUW1
  • pBlueBac-derived vectors such as the B-gal containing pBlueBac III.
  • a vector will be designed for production of the subject IL-2 variants in CHO cells, such as a Pcmv-Script vector (Stratagene, La Jolla, Calif.), pcDNA4 vectors (Invitrogen, Carlsbad, Calif.) and pCI-neo vectors (Promega, Madison, Wis.).
  • the subject gene constructs can be used to cause expression of the subject IL-2 variants in cells propagated in culture, e.g., to produce proteins, including fusion proteins or variant proteins, for purification.
  • This present disclosure also pertains to a host cell transfected with a recombinant gene including a nucleotide sequence coding an amino acid sequence for one or more of the subject IL-2 variant.
  • the host cell may be any prokaryotic or eukaryotic cell.
  • an IL-2 variant of the present disclosure may be expressed in bacterial cells such as E. coli , insect cells (e.g., using a baculovirus expression system), yeast, or mammalian cells. Other suitable host cells are known to those skilled in the art.
  • a host cell transfected with an expression vector encoding an IL-2 variant can be cultured under appropriate conditions to allow expression of the IL-2 variant to occur.
  • the IL-2 variant may be secreted and isolated from a mixture of cells and medium containing the IL-2 variant.
  • the IL-2 variant may be retained cytoplasmically or in a membrane fraction and the cells harvested, lysed and the protein isolated.
  • a cell culture includes host cells, media and other byproducts. Suitable media for cell culture is well known in the art.
  • polypeptides and proteins of the present disclosure can be purified according to protein purification techniques are well known to those of skill in the art. These techniques involve, at one level, the crude fractionation of the proteinaceous and nonproteinaceous fractions. Having separated the peptide polypeptides from other proteins, the peptide or polypeptide of interest can be further purified using chromatographic and electrophoretic techniques to achieve partial or complete purification (or purification to homogeneity).
  • isolated polypeptide” or purified polypeptide as used herein, is intended to refer to a composition, isolatable from other components, wherein the polypeptide is purified to any degree relative to its naturally-obtainable state.
  • a purified polypeptide therefore also refers to a polypeptide that is free from the environment in which it may naturally occur.
  • purified will refer to a polypeptide composition that has been subjected to fractionation to remove various other components, and which composition substantially retains its expressed biological activity.
  • substantially purified will refer to a peptide or polypeptide composition in which the polypeptide or peptide forms the major component of the composition, such as constituting about 50%, about 60%, about 70%, about 80%, about 85%, or about 90% or more of the proteins in the composition.
  • the present disclosure provides a pharmaceutical composition
  • a pharmaceutical composition comprising the IL-2 variants, or IL-2 variant fusion proteins, in admixture with a pharmaceutically acceptable carrier.
  • pharmaceutically acceptable carriers are well known and understood by those of ordinary skill and have been extensively described (see, e.g., Remington's Pharmaceutical Sciences, 18th Edition, A. R. Gennaro, ed., Mack Publishing Company, 1990).
  • the pharmaceutically acceptable carriers may be included for purposes of modifying, maintaining or preserving, for example, the pH, osmolarity, viscosity, clarity, color, isotonicity, odor, sterility, stability, rate of dissolution or release, adsorption or penetration of the composition.
  • Suitable pharmaceutically acceptable carriers include, but are not limited to, amino acids (such as glycine, glutamine, asparagine, arginine or lysine); antimicrobials; antioxidants (such as ascorbic acid, sodium sulfite or sodium hydrogen-sulfite); buffers (such as borate, bicarbonate, Tris-HCl, citrates, phosphates, other organic acids); bulking agents (such as mannitol or glycine), chelating agents (such as ethylenediamine tetraacetic acid (EDTA)); complexing agents (such as caffeine, polyvinylpyrrolidone, beta-cyclodextrin or hydroxypropyl-beta-cyclodextrin); fillers; monosaccharides; disaccharides and other carbohydrates (such as glucose, mannose, or dextrins); proteins (
  • the primary vehicle or carrier in a pharmaceutical composition may be either aqueous or non-aqueous in nature.
  • a suitable vehicle or carrier may be water for injection, physiological saline solution or artificial cerebrospinal fluid, possibly supplemented with other materials common in compositions for parenteral administration.
  • Neutral buffered saline or saline mixed with serum albumin are further exemplary vehicles.
  • Other exemplary pharmaceutical compositions comprise Tris buffer of about pH 7.0-8.5, or acetate buffer of about pH 4.0-5.5, which may further include sorbitol or a suitable substitute thereof.
  • compositions may be prepared for storage by mixing the selected composition having the desired degree of purity with optional formulation agents (Remington's Pharmaceutical Sciences, supra) in the form of a lyophilized cake or an aqueous solution. Further, the therapeutic composition may be formulated as a lyophilizate using appropriate excipients such as sucrose.
  • the optimal pharmaceutical composition will be determined by one of ordinary skill in the art depending upon, for example, the intended route of administration, delivery format, and desired dosage.
  • the therapeutic pharmaceutical compositions may be in the form of a pyrogen-free, parenterally acceptable aqueous solution comprising the desired IL-2 polypeptide or IL-2 polypeptide fusion protein, in a pharmaceutically acceptable vehicle.
  • a particularly suitable vehicle for parenteral injection is sterile distilled water in which a polypeptide is formulated as a sterile, isotonic solution, properly preserved.
  • pharmaceutical formulations suitable for injectable administration may be formulated in aqueous solutions, preferably in physiologically compatible buffers such as Hanks' solution, Ringer's solution, or physiologically buffered saline.
  • Aqueous injection suspensions may contain substances that increase the viscosity of the suspension, such as sodium carboxymethyl cellulose, sorbitol, or dextran. Additionally, suspensions of the active compounds may be prepared as appropriate oily injection suspensions. Optionally, the suspension may also contain suitable stabilizers or agents to increase the solubility of the compounds and allow for the preparation of highly concentrated solutions.
  • the therapeutic pharmaceutical compositions may be formulated for targeted delivery using a colloidal dispersion system.
  • Colloidal dispersion systems include macromolecule complexes, nanocapsules, microspheres, beads, and lipid-based systems including oil-in-water emulsions, micelles, mixed micelles, and liposomes.
  • lipids useful in liposome production include phosphatidyl compounds, such as phosphatidylglycerol, phosphatidylcholine, phosphatidylserine, phosphatidylethanolamine, sphingolipids, cerebrosides, and gangliosides.
  • Illustrative phospholipids include egg phosphatidylcholine, dipalmitoylphosphatidylcholine, and distearoylphosphatidylcholine.
  • the targeting of liposomes is also possible based on, for example, organ-specificity, cell-specificity, and organelle-specificity and is known in the art.
  • one or more therapeutic compounds of the present disclosure may be mixed with one or more pharmaceutically acceptable carriers, such as sodium citrate or dicalcium phosphate, and/or any of the following: (1) fillers or extenders, such as starches, lactose, sucrose, glucose, mannitol, and/or silicic acid; (2) binders, such as, for example, carboxymethylcellulose, alginates, gelatin, polyvinyl pyrrolidone, sucrose, and/or acacia; (3) humectants, such as glycerol; (4) disintegrating agents, such as agar-agar, calcium carbonate, potato or tapioca starch,
  • the pharmaceutical compositions may also comprise buffering agents.
  • Solid compositions of a similar type may also be employed as fillers in soft and hard-filled gelatin capsules using such excipients as lactose or milk sugars, as well as high molecular weight polyethylene glycols and the like.
  • Liquid dosage forms for oral administration include pharmaceutically acceptable emulsions, microemulsions, solutions, suspensions, syrups, and elixirs.
  • the liquid dosage forms may contain inert diluents commonly used in the art, such as water or other solvents, solubilizing agents and emulsifiers, such as ethyl alcohol, isopropyl alcohol, ethyl carbonate, ethyl acetate, benzyl alcohol, benzyl benzoate, propylene glycol, 1,3-butylene glycol, oils (in particular, cottonseed, groundnut, corn, germ, olive, castor, and sesame oils), glycerol, tetrahydrofuryl alcohol, polyethylene glycols and fatty acid esters of sorbitan, and mixtures thereof
  • the oral compositions can also include adjuvants such as wetting agents, emulsifying and suspending agents, sweetening, flavoring, coloring, perfuming, and preservative agents.
  • topical administration of the pharmaceutical compositions is contemplated.
  • the topical formulations may further include one or more of the wide variety of agents known to be effective as skin or stratum corneum penetration enhancers. Examples of these are 2-pyrrolidone, N-methyl-2-pyrrolidone, dimethylacetamide, dimethylformamide, propylene glycol, methyl or isopropyl alcohol, dimethyl sulfoxide, and azone. Additional agents may further be included to make the formulation cosmetically acceptable. Examples of these are fats, waxes, oils, dyes, fragrances, preservatives, stabilizers, and surface-active agents. Keratolytic agents such as those known in the art may also be included.
  • Dosage forms for the topical or transdermal administration include powders, sprays, ointments, pastes, creams, lotions, gels, solutions, patches, and inhalants.
  • the active compound may be mixed under sterile conditions with a pharmaceutically acceptable carrier, and with any preservatives, buffers, or propellants which may be required.
  • the ointments, pastes, creams and gels may contain, in addition to a subject compound of the disclosure (e.g., a IL-2 variant), excipients, such as animal and vegetable fats, oils, waxes, paraffins, starch, tragacanth, cellulose derivatives, polyethylene glycols, silicones, bentonites, silicic acid, talc and zinc oxide, or mixtures thereof.
  • excipients such as animal and vegetable fats, oils, waxes, paraffins, starch, tragacanth, cellulose derivatives, polyethylene glycols, silicones, bentonites, silicic acid, talc and zinc oxide, or mixtures thereof.
  • compositions contemplated for use herein include formulations involving polypeptides in sustained- or controlled-delivery formulations.
  • Techniques for formulating a variety of other sustained- or controlled-delivery means, such as liposome carriers, bio-erodible microparticles or porous beads and depot injections, are also known to those skilled in the art.
  • An effective amount of a pharmaceutical composition to be employed therapeutically will depend, for example, upon the therapeutic context and objectives.
  • One skilled in the art will appreciate that the appropriate dosage levels for treatment will thus vary depending, in part, upon the molecule delivered, the indication for which the polypeptide is being used, the route of administration, and the size (body weight, body surface or organ size) and condition (the age and general health) of the patient. Accordingly, the clinician may titer the dosage and modify the route of administration to obtain the optimal therapeutic effect.
  • a typical dosage may range from about 0.001 mg/kg to up to about 100 mg/kg or more, depending on the factors mentioned above.
  • Polypeptide compositions may be preferably injected or administered intravenously.
  • compositions may be administered every three to four days, every week, or biweekly depending on the half-life and clearance rate of the particular formulation. The frequency of dosing will depend upon the pharmacokinetic parameters of the polypeptide in the formulation used. Typically, a composition is administered until a dosage is reached that achieves the desired effect. The composition may therefore be administered as a single dose, or as multiple doses (at the same or different concentrations/dosages) over time, or as a continuous infusion. Further refinement of the appropriate dosage is routinely made. Appropriate dosages may be ascertained through use of appropriate dose-response data.
  • the route of administration of the pharmaceutical composition is in accord with known methods, e.g. orally, through injection by intravenous, intraperitoneal, intracerebral (intra-parenchymal), intracerebroventricular, intramuscular, intra-ocular, intraarterial, intraportal, intralesional routes, intramedullary, intrathecal, intraventricular, transdermal, subcutaneous, or intraperitoneal or intratumorally; as well as intranasal, enteral, topical, sublingual, urethral, vaginal, or rectal means, by sustained release systems or by implantation devices.
  • the compositions may be administered by bolus injection or continuously by infusion, or by implantation device.
  • the composition may be administered locally via implantation of a membrane, sponge, or another appropriate material on to which the desired molecule has been absorbed or encapsulated.
  • a membrane, sponge, or another appropriate material on to which the desired molecule has been absorbed or encapsulated.
  • the device may be implanted into any suitable tissue or organ, and delivery of the desired molecule may be via diffusion, timed-release bolus, or continuous administration.
  • the present disclosure provides for a method of treating an autoimmune disease in a subject, comprising administering to said subject a therapeutically effective amount (either as monotherapy or in a combination therapy regimen) of an IL-2 variant, or IL-2 variant fusion protein, of the present disclosure in pharmaceutically acceptable carrier.
  • An autoimmune disease as pertains to the present invention, is a disease or disorder arising from and directed against an individual's own tissues or a co-segregate or manifestation thereof or resulting condition therefrom.
  • the autoimmune disease includes, but is not limited to, arthritis (including rheumatoid arthritis, reactive arthritis), systemic lupus erythematosus (SLE), psoriasis and inflammatory bowel disease (IBD), encephalomyelitis, uveitis, myasthenia gravis, multiple sclerosis, insulin dependent diabetes, Addison's disease, celiac disease, chronic fatigue syndrome, autoimmune hepatitis, autoimmune alopecia, ankylosing spondylitis, ulcerative colitis, Crohn's disease, fibromyalgia, pemphigus vulgaris, Sjogren's syndrome, Kawasaki's Disease, hyperthyroidism/Graves disease, hypothyroidism/Hashimoto's disease, endometriosis, scleroderma, pernicious anemia, Goodpasture syndrome, Guillain-Barre syndrome, Wegener's disease, glomerulonephritis,
  • the present disclosure provides for a method of treating an inflammatory disease in a subject, comprising administering to said subject a therapeutically effective amount (either as monotherapy or in a combination therapy regimen) of an IL-2 variant, or IL-2 variant fusion protein, of the present disclosure in pharmaceutically acceptable carrier.
  • a therapeutically effective amount include all diseases associated with acute or various inflammation. Acute inflammation is the initial response of the body to harmful stimuli and results from an increased movement of plasma and leukocytes (such as e.g. granulocytes) from the blood into the injured tissues. A number of biochemical events propagates and matures the inflammatory response, involving the local vascular system, the immune system, and various cells within the injured tissue.
  • Prolonged inflammation is referred to as various inflammation, which leads to a progressive shift in the type of cells present at the site of inflammation and is characterized by simultaneous destruction and healing of the tissue from the inflammatory process.
  • the present disclosure provides a method for treating an inflammatory disease in a subject, comprising administering a therapeutically effective amount of the pharmaceutical compositions of the invention to a subject in need thereof.
  • the subject is a human subject.
  • the inflammatory disease to be treated includes, but is not limited to, Crohn's disease, colitis, dermatitis, psoriasis, diverticulitis, hepatitis, irritable bowel syndrome (IBS), lupus erythematous, nephritis, Parkinson's disease, ulcerative colitis, collagenous colitis, lymphocytic colitis, ischemic colitis, diversion colitis, Behcet's syndrome and indeterminate colitis multiple sclerosis (MS), Alzheimer's disease, arthritis, rheumatoid arthritis, asthma, and various cardiovascular diseases such as atherosclerosis and vasculitis.
  • the inflammatory disease is selected from the group consisting of rheumatoid arthritis, diabetes, gout, cryopyrin-associated periodic syndrome, and chronic obstructive pulmonary disorder.
  • the present disclosure provides methods for organ transplantation or associated graft-versus-host disease in a subject, comprising administering a therapeutically effective amount of the pharmaceutical compositions of the invention to a subject in need thereof.
  • the subject is a human subject.
  • the transplantation is selected from organ transplantations of the heart, kidneys, liver, lungs, pancreas, intestine and thymus or from tissues transplantations of the bones, tendons, cornea, skin, heart valves, nerves and veins.
  • graft vs. host disease or “GvHD” refers to a condition, including acute and chronic, resulting from transplanted (graft) cell effects on host cells and tissues resulting from GVH.
  • donor immune cells infused within the graft or donor immune cells that develop from the stem cells may see the patient's (host) cells as foreign and turn against them with an immune response.
  • Acute graft-versus-host disease is specifically a disorder caused by donor immune cells in patients who have had an allogeneic marrow or blood cell transplantation. The most commonly affected tissues are skin intestine and liver. In severe cases, GvHD can cause blistering in the skin or excessive diarrhea and wasting. Prednisone and/or other immunosuppressive medications are used to treat acute graft-versus-host disease.
  • a therapeutically effective dose can be estimated initially from cell culture assays by determining an EC 50 .
  • a dose can then be formulated in animal models to achieve a circulating plasma concentration range that includes the EC 50 as determined in cell culture. Such information can be used to more accurately determine useful doses in humans. Levels in plasma may be measured, for example, by HPLC. The exact composition, route of administration and dosage can be chosen by the individual physician in view of the subject's condition.
  • Dosage regimens can be adjusted to provide the optimum desired response (e.g., a therapeutic or prophylactic response). For example, a single bolus can be administered, several divided doses (multiple or repeat or maintenance) can be administered over time and the dose can be proportionally reduced or increased as indicated by the exigencies of the therapeutic situation. It is especially advantageous to formulate parenteral compositions in dosage unit form for ease of administration and uniformity of dosage.
  • Dosage unit form as used herein refers to physically discrete units suited as unitary dosages for the mammalian subjects to be treated; each unit containing a predetermined quantity of active compound calculated to produce the desired therapeutic effect in association with the required pharmaceutical carrier.
  • the specification for the dosage unit forms of the present disclosure will be dictated primarily by the unique characteristics of the antibody and the particular therapeutic or prophylactic effect to be achieved.
  • the dose and dosing regimen is adjusted in accordance with methods well-known in the therapeutic arts. That is, the maximum tolerable dose can be readily established, and the effective amount providing a detectable therapeutic benefit to a subject may also be determined, as can the temporal requirements for administering each agent to provide a detectable therapeutic benefit to the subject. Accordingly, while certain dose and administration regimens are exemplified herein, these examples in no way limit the dose and administration regimen that may be provided to a subject in practicing the present disclosure.
  • dosage values may vary with the type and severity of the condition to be alleviated and may include single or multiple doses. It is to be further understood that for any particular subject, specific dosage regimens should be adjusted over time according to the individual need and the professional judgment of the person administering or supervising the administration of the compositions, and that dosage ranges set forth herein are exemplary only and are not intended to limit the scope or practice of the claimed composition. Further, the dosage regimen with the compositions of this disclosure may be based on a variety of factors, including the type of disease, the age, weight, sex, medical condition of the subject, the severity of the condition, the route of administration, and the particular antibody employed. Thus, the dosage regimen can vary widely, but can be determined routinely using standard methods.
  • doses may be adjusted based on pharmacokinetic or pharmacodynamic parameters, which may include clinical effects such as toxic effects and/or laboratory values.
  • the present disclosure encompasses intra-subject dose-escalation as determined by the skilled artisan. Determining appropriate dosages and regimens are well-known in the relevant art and would be understood to be encompassed by the skilled artisan once provided the teachings disclosed herein.
  • An exemplary, non-limiting daily dosing range for a therapeutically or prophylactically effective amount of an IL-2 variant, or IL-2 variant fusion protein, of the disclosure can be range from about 0.1 ⁇ g/kg to 100 mg/kg or more, depending on the factors mentioned above. For repeated administrations over several days or longer, depending on the condition, the treatment would generally be sustained until a desired suppression of disease symptoms occurs.
  • the dosage would be in the range from about 0.0001 to 100 mg/kg, 0.0001 to 90 mg/kg, 0.0001 to 80 mg/kg, 0.0001 to 70 mg/kg, 0.0001 to 60 mg/kg, 0.0001 to 50 mg/kg, 0.0001 to 40 mg/kg, 0.0001 to 30 mg/kg, 0.0001 to 20 mg/kg, 0.0001 to 10 mg/kg, 0.0001 to 5 mg/kg, 0.0001 to 4 mg/kg, 0.0001 to 3 mg/kg, 0.0001 to 2 mg/kg, 0.0001 to 1 mg/kg, 0.001 to 50 mg/kg, 0.001 to 40 mg/kg, 0.001 to 30 mg/kg, 0.001 to 20 mg/kg, 0.001 to 10 mg/kg, 0.001 to 5 mg/kg, 0.001 to 4 mg/kg, 0.001 to 3 mg/kg, 0.001 to 2 mg/kg, 0.001 to 1 mg/kg, 0.010 to 50 mg/kg, 0.010 to 40 mg/kg, 0.000
  • one or more doses of about 0.5 mg/kg, 2.0 mg/kg, 5.0 mg/kg or 10 mg/kg (or any combination thereof) may be administered to the patient.
  • dosage values may vary with the type and severity of the conditions to be alleviated.
  • specific dosage regimens should be adjusted over time according to the individual need and the professional judgment of the person administering or supervising the administration of the compositions, and that dosage ranges set forth herein are exemplary only and are not intended to limit the scope or practice of the claimed composition.
  • Toxicity and therapeutic index of the pharmaceutical compositions of the disclosure can be determined by standard pharmaceutical procedures in cell cultures or experimental animals, e.g., for determining the LD 50 (the dose lethal to 50% of the population) and the ED 50 (the dose therapeutically effective in 50% of the population).
  • the dose ratio between toxic and therapeutic effective dose is the therapeutic index and it can be expressed as the ratio LD 50 /ED 50 .
  • Compositions that exhibit large therapeutic indices are generally preferred.
  • the dosing frequency of the administration of the IL-2 variant, or IL-2 variant fusion protein pharmaceutical composition depends on the nature of the therapy and the particular disease being treated.
  • the subject can be treated at regular intervals, such as twice weekly, weekly or monthly, until a desired therapeutic result is achieved.
  • Exemplary dosing frequencies include but are not limited to once weekly without break; once every 2 weeks; once every 3 weeks; weakly without break for 2 weeks, then monthly; weakly without break for 3 weeks, then monthly; monthly; monthly; once every other month; once every three months; once every four months; once every five months; or once every six months, or yearly.
  • the terms “co-administration”, “co-administered” and “in combination with”, referring to the a IL-2 variant, or IL-2 variant fusion protein, of the disclosure and one or more other therapeutic agents, is intended to mean, and does refer to and include the following: simultaneous administration of such combination of a IL-2 variant, or IL-2 variant fusion protein, of the disclosure and therapeutic agent(s) to a subject in need of treatment, when such components are formulated together into a single dosage form which releases said components at substantially the same time to said subject; substantially simultaneous administration of such combination of a IL-2 variant, or IL-2 variant fusion protein, of the disclosure and therapeutic agent(s) to a subject in need of treatment, when such components are formulated apart from each other into separate dosage forms which are taken at substantially the same time by said subject, whereupon said components are released at substantially the same time to said subject; sequential administration of such combination of a IL-2 variant, or IL-2 variant fusion protein, of the disclosure and therapeutic agent(s) to a
  • the present disclosure provides a method for treating an autoimmune disease in a subject, comprising administering a therapeutically effective amount of the pharmaceutical compositions of the invention in combination with a second therapeutic agent capable of treating an autoimmune disease.
  • the second therapeutic agent is selected from the group consisting of: immunosuppressants such as corticosteroids, cyclosporin, cyclophosphamide, prednisone, azathioprine, methotrexate, rapamycin, tacrolimus, biological agents such as TNF-alpha blockers or antagonists, IL-10 agonist or long half-life extended IL-10 (PEGylated, antibody or Fc fusion IL-10); immunosuppressive agents (e.g., antibodies against other lymphocyte surface markers (e.g., CD40, alpha-4 integrin) or against cytokines), other fusion proteins (e.g., CTLA-4-Ig (ORENCIA®), TNFR-Ig (ENBREL®)), TNF
  • immunosuppressive drugs e.g., cyclosporin A, FK506-like compounds, rapamycin compounds, or steroids
  • anti-proliferatives cytotoxic agents, or other compounds that may assist in immunosuppression.
  • interferons such as IFN-beta-1a (REBIF®.
  • the present disclosure provides a method for treating an inflammatory disease in a subject, comprising administering a therapeutically effective amount of the pharmaceutical compositions of the invention in combination with a second therapeutic agent capable of inhibiting or reducing differentiation of Th1, Th17, Th22, and/or other cells that secrete, or cause other cells to secrete, inflammatory molecules, including, but not limited to, IL-1beta, TNF-alpha, TGF-beta, IFN-gamma, IL-17, IL-6, IL-23, IL-22, IL-21, and MMPs; inhibiting or reducing activity of Th1, Th 17, Th22, and/or other cells that secrete, or cause other cells to secrete, inflammatory molecules, including, but not limited to, IL-1beta, TNF-alpha, TGF-beta, IFN-gamma, IL-17, IL-6, IL-23, IL-22, IL-21, and MMPs; inhibiting or reducing the Th1 and/or Th17 pathways
  • the second therapeutic agent is a non-steroidal anti-inflammatory agents including, without limitation, oxicams, such as piroxicam, isoxicam, tenoxicam, sudoxicam; salicylates, such as aspirin, disalcid, benorylate, trilisate, safapryn, solprin, diflunisal, and fendosal; acetic acid derivatives, such as diclofenac, fenclofenac, indomethacin, sulindac, tolmetin, isoxepac, furofenac, tiopinac, zidometacin, acematacin, fentiazac, zomepirac, clmdanac, oxepinac, felbmac, and ketorolac; fenamates, such as mefenamic, meclofenamic, flufenamic, niflumic, and tolfenamic acids; propi
  • the second therapeutic agent is a steroidal anti-inflammatory drugs including, without limitation, corticosteroids such as hydrocortisone, hydroxyl-triamcinolone, alpha-methyl dexamethasone, dexamethasone-phosphate, beclomethasone dipropionates, clobetasol valerate, desonide, desoxymethasone, desoxycorticosterone acetate, dexamethasone, dichlorisone, diflorasone diacetate, diflucortolone valerate, fluadrenolone, fluclorolone acetonide, fludrocortisone, flumethasone pivalate, fiuosinolone acetonide, fluocinonide, flucortine butylesters, fluocortolone, fluprednidene (fluprednylidene) acetate, flurandrenol
  • corticosteroids such as hydrocortisone, hydroxyl-tri
  • the combination therapy comprises administering an IL-2 variant and the second agent composition simultaneously, either in the same pharmaceutical composition or in separate pharmaceutical composition.
  • an IL-2 variant composition and the second agent composition are administered sequentially, i.e., an IL-2 variant composition is administered either prior to or after the administration of the second agent composition.
  • the administrations of an IL-2 variant composition and the second agent composition are concurrent, i.e., the administration period of an IL-2 variant composition and the second agent composition overlap with each other.
  • the administrations of an IL-2 variant composition and the second agent composition are non-concurrent.
  • the administration of an IL-2 variant composition is terminated before the second agent composition is administered.
  • the administration second agent composition is terminated before an IL-2 variant composition is administered.
  • the current invention is directed one or more mutations to attenuate the affinity of IL-2 for the IL-2R ⁇ and/or ⁇ c receptor subunits.
  • the enhanced IL-2 sensitivity of Tregs conferred by IL-2R ⁇ expression may result in a pronounced growth advantage for this cell subset.
  • these mutants could serve as Treg promoters in autoimmune and inflammatory diseases.
  • the variants were designed computationally based on the reported structure of human IL-2 in Protein Data Bank (PDB code 2B51).
  • a panel of variants were designed including 1 to 3 mutations (introducing conservative and non-conservative amino acid substitutions) in residues that are at or near the interface that make direct contact with IL-2R ⁇ or ⁇ c receptor subunits.
  • D20 is engaged in an extensive network of hydrogen bonds to receptor subunit side chains at the IL-2R ⁇ interface.
  • N88 is an energetic hot spot for the IL-2/IL-2R ⁇ interaction, engaging in critical hydrogen bonds with the receptor chain.
  • Q126 is integral to the ⁇ c interaction, and Q22 is similarly at the ⁇ c interface.
  • the present inventors postulated that mutations at the above-mentioned sites or neighboring residues may result in a defect in their ability to interact with the IL-2 intermediate affinity receptor IL-2R ⁇ .
  • a panel of IL-2 variants (SEQ ID NOs: 4-43, 108-146, and 193-197) with the following 1-3 amino acid substitutions (D20T, D20E, D20N, D20Q, D20S, D20Y, D20I, L19Y, L19N, L19R, L19Q, L19H, L19D, L19P, L19S, L21S, L21N, L21R, N88R, N88G, N88I, N88Q, N88E, N88T, N88M, Q126E, Q126L, Q126N, Q126D, Q126M, Q126K, Q126H, Q126Y, Q125E, S125K, S125H, S125W, S125I, Q22N, Q22H, Q22K, Q22Y, Q22I, D20I/N88G, D20I/N88R, D20T/N88R, D20I/N88I, D20T/Q126E
  • IL-2 variants with D20I, D20I/N88G, D20E, or L19N amino acid substitutions were also expressed as N-terminal fusions to the Fc homodimer via a rigid “AEAAAKEAAAKEAAAKA” linker (SEQ ID NO: 53).
  • SEQ ID NOS: 73-107, 147-189 and 198-211 the sequences of these IL-2 variants Fc fusion constructs are listed with SEQ ID NOS: 73-107, 147-189 and 198-211.
  • Constructs with wild-type IL-2 in the same Fc fusion formats (both C- and N-terminal) were also made (SEQ ID NOS: 71 and 72).
  • All of the above IL-2 variant Fc fusion molecules are designed to afford a growth advantage to cells that highly express IL-2R ⁇ , leading to the preference for Treg cells versus other lymphocytes proliferation, including CD4+ conventional T cells, CD8+ T cells, and NK cells.
  • the mutations at position 19, 20, or 21 are expected to eliminate the toxic motif responsible for vascular toxicity, so the resulting molecules may have two beneficial properties, including enhanced selectivity for Treg activation and reduced endothelial cell damage.
  • optimal mutation or mutation combination is critical to tune the level of impairment on activation of effector T and NK cells while maintaining high enough potency on activation of Treg cells and thus maximize the window for selective targeting of Treg subset.
  • the constructs were produced by co-transfecting HEK293-F cells growing in suspension with the mammalian expression vectors using polyethylenimine (PEI, 25,000 MW linear, Polysciences). If there were two or more expression vectors, the vectors were transfected in a 1:1 ratio.
  • HEK293 cells were cultivated in serum free FreeStyleTM 293 Expression Medium (ThermoFisher). For production in 1000 ml shaking flasks (working volume 330 mL), HEK293 cells were seeded at a density of 0.8 ⁇ 10 6 cells/ml 24 hours before transfection.
  • a total of 330 ⁇ g of DNA expression vectors were mixed with 16.7 ml Opti-mem Medium (ThermoFisher). After addition of 0.33 mg PEI diluted in 16.7 ml Opti-mem Medium, the mixture was vortexed for 15 sec and subsequently incubated for 10 min at room temperature. The DNA/PEI solution was then added to the cells and incubated at 37° C. in an incubator with 8% CO 2 . Sodium butyrate (Millipore Sigma) was added to the cells at day 4 at a final concentration of 2 mg/L to help sustain protein expression. After 6 days cultivation, supernatant was collected for purification by centrifugation for 20 min at 2200 rpm. The solution was sterile filtered (0.22 ⁇ m filter, Corning). The secreted protein was purified from cell culture supernatants using Protein A affinity chromatography.
  • Ion exchange chromatography or mix-mode chromatography including but not limited to CaptoMMC (GE Healthcare), ceramic hydroxyapatite, or ceramic fluoroapatite (Bio-Rad) was also utilized to polish the Protein A material as needed.
  • Target protein was concentrated with an Amicon® Ultra-15 concentrator 10 KDa NMWC (Merck Millipore Ltd.)
  • the purity and molecular weight of the purified constructs were analyzed by SDS-PAGE with and in the absence of a reducing agent and staining with Coomassie (Imperial® Stain).
  • the NuPAGE® Pre-Cast gel system (4-12% or 8-16% Bis-Tris, ThermoFisher) was used according to the manufacturer's instructions.
  • the protein concentration of purified protein samples was determined by measuring the UV absorbance at 280 nm (Nanodrop Spectrophotometer, ThermoFisher) divided by the molar extinction coefficient calculated on the basis of the amino acid sequence.
  • the aggregate content of the constructs was analyzed on an Agilent 1200 high-performance liquid chromatography (HPLC) system. Samples were injected onto an AdvanceBio size-exclusion column (300A, 4.6 ⁇ 150 mm, 2.7 ⁇ m, LC column, Agilent) using 150 mM sodium phosphate, pH 7.0 as the mobile phase at 25° C.
  • P-0318 is very aggregation prone: 65% high-molecular weight species, which makes the expected peak as the minor species in the chromatogram and was marked with an arrow.
  • P-0317 is relatively pure with 7.5% aggregates ( FIG. 1C ).
  • N88R mutation may reduce aggregation propensity of the resulting fusion proteins.
  • IL-2 with N88R single mutation, or D20T/N88R dual mutations the resulting fusion proteins, P-0254 (SEQ ID NO: 71) and P-0324 (SEQ ID NO: 96), respectively, were aggregation prone with 30-40% aggregates. So, the contributions of individual amino acid substitution to the protein stability seem to be context dependent.
  • Amino acid substitutions at position 125 was originally aimed at tuning IL-2 selectivity as the residue is in immediate proximity to Q126, which is integral to the ⁇ c interaction.
  • Naturally occurring IL-2 contains an unpaired cysteine at position 125, which was replaced by a serine in Proleukin, and S125 is considered as wild type IL-2 residue in the present invention.
  • IL-2 containing alanine substitution at position 125 is also widely used.
  • isoleucine substitution at position 125 of IL-2 or IL-2 variant significantly improved protein developability profile, which was demonstrated by the protein expression increase and substantial reduction of aggregation propensity of the IL-2 constructs.
  • Single amino acid substitutions were introduced to IL-2 at positions corresponding to amino acids interacting with receptor subunit(s) ⁇ or ⁇ or ⁇ . These substitutions were aimed to reduce IL-2 signaling capacity through the intermediate affinity IL-2R ⁇ complex and confer signaling specificity from the high affinity IL-2R ⁇ .
  • IL-2 variants containing single amino acid substitutions were examined for their ability to differentially stimulate STAT5 phosphorylation in CD4 positive Treg and Tconv cells.
  • STAT5 is known to be involved in the downstream signaling cascade upon IL-2 binding to the transmembrane IL-2 receptors.
  • the phosphorylation of STAT5 in defined lymphocyte subpopulations was measured using fresh human peripheral blood mononuclear cells (PBMC) and the forkhead transcription factor FOXP3 was used to identify the Treg population in FACS analysis.
  • PBMC peripheral blood mononuclear cells
  • human PBMC were isolated by Ficoll-Hypaque centrifugation from the buffy coat of a healthy donor. PBMC were starved in serum-free MACS buffer at 4° C. for 1 hour. 2 ⁇ 10 5 PBMC were then treated with serial dilutions of test compounds for 30 min at 37° C. Cells were fixed and permeabilized with Foxp3/Transcription Factor Staining Buffer Set (EBIO) by incubating with 1 ⁇ Foxp3 fixation/permeabilization working solution for 30 minutes and washing with 1 ⁇ permeabilization buffer. Cells were additionally fixed with Cytofix buffer and permeabilized with Perm Buffer III (BD Biosciences) and then washed.
  • EBIO Foxp3/Transcription Factor Staining Buffer Set
  • FIG. 2 shows the dose-response effects of exemplary Fc fusion proteins of IL-2 variants on STAT5 phosphorylation in CD4 positive Treg and Tconv cells in comparison with the wild type fusion protein.
  • the wild type IL-2 Fc fusion protein (P-0250) induced STAT5 phosphorylation in both Treg and Teff cells with EC 50 values of 0.1 pM and 25.4 pM, respectively.
  • the potency of wild type IL-2 was about 250-fold greater in Treg cells than in CD4+ Tconv cells, coinciding with the higher expression levels of the high affinity trimeric receptors in Treg cells.
  • FIG. 3 shows the ability of IL-2 variant P-0375 (N88Q) to induce STAT5 phosphorylation in CD4 positive Treg and CD4+ Tconv cells in comparison with Benchmark-1 and Benchmark-2 compounds harboring V91K and N88R mutations, respectively.
  • the activity profile of the N88Q variant was similar to that of the Benchmark-2.
  • FIG. 4 shows the biological activity of IL-2 variants harboring various mutations at position 19 in comparison with the wild type.
  • Variants P-0372 (L19Y), P-0373 (L19N), P-0374 (L19R), P-0423 (L19Q), P-0424 (L19H), and P-0427 (L19S) demonstrated similar activity as the wild type in inducing STAT5 phosphorylation in Treg cells ( FIGS. 4A and 4C ).
  • Variants P-0372, P-0374, P-0423, and P-0427 also largely retained the biological activity in CD4+ Tconv cells ( FIGS. 4B and 4D ) while such activity was reduced in CD4+ Tconv for variants P-0373 and P-0424.
  • Mutant P-0425 demonstrated slightly reduced potency in inducing STAT5 phosphorylation in Treg cells while such activity was significantly impaired in CD4+ Tconv cells ( FIGS. 4C & 4D ).
  • L19 is part of the proposed toxin-like motif, and mutations at this site is also expected to have improved safety profile with reduced VLS.
  • Example 4 It was demonstrated in Example 4 that directed mutations aimed to attenuate the affinity of IL-2 for either IL-2R ⁇ or ⁇ c receptor subunit can result in IL-2 mutants with differential selectivity towards Treg lymphocytes. It was then reasoned that modulation of the affinity of IL-2 for both IL-2R ⁇ and ⁇ c receptor subunits via combining one amino acid substitution(s) targeting ⁇ receptor and the other substitution(s) targeting ⁇ receptor may yield desired potency and a selectivity window for Treg lymphocytes.
  • FIGS. 5A and 5B show the effect of IL-2R ⁇ -targeting variant P-0372 (L19Y) on STAT5 phosphorylation in Treg and CD4+ Tconv cells in comparison with the wild type IL-2 fusion protein P-0250.
  • FIGS. 5C and 5D show the STAT5 phosphorylation activity for P-0303 (Q126E) harboring an amino acid substitution targeting to disturb the interaction with the ⁇ receptor. The data suggested that each single amino substitution minimally impacted the pSTAT5 activation potency but also only showed a modestly improved selective window for Treg lymphocyte subset relative to the wild type.
  • Treg activation potency was mainly reserved in P-0419, and the activity profile of the P-0419 variant was very comparable to that of the Benchmark-1 molecule that contains a V91K mutation. This strategy is particularly attractive as 19L is also part of the proposed toxin-like motif, and mutations at this site are also expected to have an improved safety profile with reduced VLS.
  • FIGS. 6A and 6B share the same L19Y substitution targeting the beta receptor, and the additional mutation designed to target the ⁇ c receptor is Q126E in P-0419, Q126K in P-0464, S125I in P-0471, and Q22K in P-0474, respectively. While all mutants retained comparable potency in inducing STAT5 phosphorylation in Treg cells ( FIG. 6A ), such activity varied significantly in CD4+ Tconv cells ( FIG. 6B ), demonstrating differential ability in tuning selectivity of Treg activation via combining amino acid substitutions.
  • All these mutants are potentially Treg-biased IL-2 agents to activate Treg cells for the treatment of autoimmune disease. Additionally, these mutants are also expected to have an improved safety profile with reduced VLS due to the elimination of the potentially toxic motif.
  • Example 3 It was shown in Example 3 that isoleucine substitution at position 125 resulted in universal improvement in developability of the IL-2 fusion constructs. To make S125I substitution a viable approach to mitigate the developability challenges of IL-2 engineering, it is important to demonstrate that such amino acid replacement does not compromise the biological activity of resulting fusion proteins in comparison to their Ser-125 counterparts.
  • the S125I substitution was then introduced into wild-type IL-2 or IL-2 variants that already harbored 1 or 2 mutations targeting receptor subunit(s) ⁇ or ⁇ or ⁇ .
  • the resulting IL-2 variants containing isoleucine at position 125 were tested for their ability to stimulate STAT5 phosphorylation in Treg and Tconv cells in comparison with their respective serine counterparts at position 125.
  • Table 5 lists the potency and selectivity of IL-2 variants in Treg cells.
  • the two molecules in the same row of Table 5 share the same other amino acid substitution(s) and differ only at position 125 with either serine or isoleucine.
  • the data demonstrated that the S125I substitution fully retained or slightly improved the biological activity of various tested IL-2 variants without altering the Treg specificity.
  • IL-2 variants containing S125I substitution retained the biological activity and Treg selectivity Serine-125 Isoleucine-125 Protein Treg Treg Protein Treg Treg ID: EC 50 (pM) Selectivity ID: EC 50 (pM) Selectivity P-0250 0.049 Yes P-0531 0.012 Yes P-0424 0.026 Yes P-0491 0.029 Yes P-0425 1 Yes P-0492 ⁇ 0.10 Yes P-0372 0.05 Yes P-0471 0.09 Yes P-0364 3.61 Yes P-0493 0.08 Yes P-0447 1.71 Yes P-0511 0.76 Yes P-0419 0.56 Yes P-0495 ⁇ 0.33 Yes P-0480 0.24 Yes P-0512 0.35 Yes
  • P-0250 is the wild-type IL-2 Fc fusion molecule
  • P-0424 contains one amino acid substitution L19H
  • P-0447 comprise two amino acid substitutions L19H/Q126E.
  • Their dose-dependent effect on STAT5 phosphorylation in Treg and CD4+ Tconv cells is illustrated in FIG. 8 .
  • S125I substitution slightly increased potency of the three tested compounds without altering Treg selectivity for P-0531 and P-0491; for P-0511, S125I substitution further widened the Treg selectivity window.
  • CD4 positive Treg CD4+/Foxp3+/CD25 high
  • Tconv CD4+/Foxp3-/CD25 low
  • two variants, P-0511 and P-0512 were further assayed for their ability to stimulate other effector T and NK cells, including CD4 positive Teff (CD4+/Foxp3 ⁇ /CD25+), CD8 cytotoxic T effector and NK cells in comparison to wild-type IL-2 (P-0250) and three IL-2 benchmark molecules containing V91 K, N88R, N88D respectively.
  • IL-2 variants of the current invention have weakened IL-2R ⁇ interaction, and the pronounced growth advantage of Treg versus CD4+ Tconv by these variants was conferred by the high constitutive IL-2R ⁇ (CD25) expression in Treg.
  • CD25 expression can be induced in CD4+ T effector cells after immune stimulation. It is thus desirable to confirm that IL-2 variants retain Treg specificity over other CD25+ lymphocyte subsets.
  • Exemplary lymphocyte subset with medium to high expression level of CD25 includes CD4+ effector T cells (Teff).
  • P-0512 has a comparable activity profile to Benchmark-1 for all the three T cell subsets, while P-511 is superior to both Benchmark-2 and -3 in terms of potency and selectivity window for Treg cells versus both Teff and na ⁇ ve CD4 T cells.
  • Benchmark-2 showed much weaker potency in activating each of the three subsets.
  • CD25 at medium to high level on Teff
  • P-0511 and P-0512 were tested for their ability to stimulate NK and CD8+ T cells proliferation in comparison with the wild type and benchmark molecules.
  • Intracellular fluorescent label carboxyfluorescein diacetate succinimidyl ester (CFSE) method was utilized. Briefly, human PBMC (1 ⁇ 10 5 cells/well) were labeled with CFSE, plated onto 96-well plates, and incubated with increasing concentrations of different IL-2 compounds. Cells were then harvested after 5 or 7 days of incubation and stained with either anti-CD56-APC antibody for NK cells or anti-CD8-APC antibody for CD8+ T cells and analyzed by flow cytometry. Data are expressed as a percent of divided cells and illustrated in FIG. 10A for CD8+ T cell proliferation and FIG. 10B for NK cell proliferation.
  • the STAT5 phosphorylation activity on other responder cells than CD4+ T cell subsets, including CD8+ T and NK, by P-0511 was compared to P-0531, the S125I equivalent of wild-type P-0250.
  • P-0511 exhibited profound activity in stimulation of STAT5 phosphorylation in Treg cells similar as P-0531 ( FIG. 11A ), while such activity was nearly completely abolished in CD4+ Tconv ( FIG. 11B ), CD8+ T ( FIG. 11C ), and NK ( FIG. 11D ) cells.
  • IL-2 receptors expressed on CD4+ Tconv, CD8+ T and NK cells are primarily dimeric IL-2Rs, comprising IL-2R6 and ⁇ c.
  • P-0511 did not show appreciable binding to IL-2R ⁇ and ⁇ c complex, indicating that the two IL-2 mutations of P-0511 at the interfaces with both ⁇ and ⁇ c receptor subunits dramatically impaired its interaction with the complex.
  • P-0511 exhibited only slightly reduced activity on Treg compared to wild-type IL-2 fusion.
  • P-0511 exemplifies IL-2 variant with desired potency and selectivity window for Treg lymphocytes.
  • IL-2 variants listed in Table 2A-2F were constructed, expressed, and tested in in vitro assays.
  • Biological activities of exemplary IL-2 variants in Treg vs other lymphocyte subsets including CD4+ Tconv, CD4+ Teff, CD8+ T and NK cells, were demonstrated in FIGS. 2-11 .
  • Many variants retained high potency for Treg cells with reduced or abolished activity for Tconv cells and other lymphocyte subsets.
  • Some variants have a similar activity profile as Benchmark-1 while others resemble the activity feature of Benchmark-2 or Benchmark-3.
  • majority of the IL-2 variants had the proposed toxin-like motif eliminated aiming to reduce VLS.
  • IL-2 variant fusions with superior developability profiles while retaining biological activity and selectivity in Treg cells.
  • These variants are potentially Treg-biased IL-2 agents for the treatment of autoimmune disease with an improved safety profile.
  • IL-2 variant Fc fusion proteins were administered to mice and their ability to preferentially proliferate and expand regulatory T cells (CD4+CD25+FoxP3+ T cells) over effector T cells and NK cells were determined in vivo.
  • mice Female C57/BL6 mice (7-week old) were received from Charles River Laboratory and acclimated in house for at least 7 days before the study.
  • Vehicle (PBS), 0.3 mg/kg of each test compounds, or IL-2 benchmark compounds were subcutaneously administered to mice on day 0.
  • Peripheral blood samples were collected into heparin-treated tubes on days 3, 5 and 7 post-treatment. Each group contained 6 mice and baseline blood was collected 2 days prior to the treatment (day ⁇ 2). After red blood cell lysis, total viable mononuclear blood cells were counted by trypan blue dead cell exclusion method and proceeded to intracellular staining for immune cell phenotype and Ki67 proliferation markers using flow cytometric analysis.
  • Benchmark-1 was of the highest potency, followed by Benchmark-3.
  • Benchmark-2 is much weaker in proliferating and expanding Treg cells. ( FIG. 12A-12C ).
  • Benchmark-1 On T effector and NK cells, Benchmark-1 showed strong Ki67 stimulation on cytotoxic CD8 T cells and NK cells, while Benchmarks-2 and -3 showed low effects on CD8 T cells and NK cells ( FIG. 13A-13C ).
  • Variant P-0514 showed similar Ki67 stimulation on CD8+ T cells as Benchmark-1, while variants P-0511 and P-0512 showed mild Ki67 stimulation on CD8 T cells and NK cells as Benchmark-2 and 3 ( FIG. 13A-13C ).
  • Data suggest variants P-0511 and P-0512 demonstrate superior biological activity and selectivity on Treg compared to Benchmarks 1 & 2.
  • Benchmark-3 was not efficacious to stimulate and expand both Treg and effector cells.
  • CD4+ T conventional cells The percentage of CD4+ T conventional cells was reduced in all IL-2 variant-treated groups due to increased Treg population ( FIG. 14A ). No significant expansion of CD4+ Tconv cells, CD8 T cells or NK cells was observed in mice treated with any of Treg biased IL-2 variants (P-0511, P-0512 and P-0514) nor the three benchmarks ( FIG. 14B-14D ).
  • variants P-0511, P-0512 and P-0514 exhibit the ability to promote activation, proliferation and expansion of immunosuppressive Treg cells while sparing CD4+ conventional cells, cytotoxic effector T cells and NK cells.
  • the data also evidenced the superiority of these three variants over benchmark molecules in terms of both efficacy and selectivity on Treg proliferation and expansion.
  • These variants may serve as therapeutic agents to combat autoimmune and inflammatory diseases as well as rejection of organ transplantation.
  • PBS vehicle
  • P-0511 1, 0.3, 0.1, or 0.03 mg/kg
  • FIG. 17 dose-dependent increases in the proliferation of Treg cells as reflected by increased percentage of Ki67 positive cells ( FIG. 17A ) were observed in mice treated with P-0511 at 1, 0.3, or 0.1 mg/kg dosing levels. Treatment at 0.03 mg/kg had minimal effect. Stimulation of Ki67 expression in Treg cells peaked on day 3 at the three higher dose levels and plateaued till day 5 before decline. As a result, P-0511 treatment resulted in elevations in the percentage of Treg over total CD4+ T cells ( FIG. 17B ), absolute Treg cell numbers ( FIG. 17C ) and fold change of cell counts from baseline ( FIG. 17D ) in a dose-dependent manner.
  • Treg cell expansion followed a similar kinetic pattern as the proliferation/activation Ki67 markers ( FIG. 17 ), namely culmination on day 3 and further extension to day 5.
  • Dosing at 1 mg/kg stimulated a greater magnitude and duration of Treg and the signals sustained to day 5.
  • Treg accounted for 4.5% of total lymphocytes with 1 mg/kg single dose treatment versus 3.1% at 0.3 mg/kg dosing and 1.4% at 0.1 mg/kg.
  • Treg represented 0.5% of the total lymphocytes ( FIG. 18A ).
  • the Treg/Tconv ratio was calculated based on cell count ( FIG. 19A ).
  • the Treg/Tconv ratio peaked at 0.27 for treatment at 1 mg/kg, 0.18 for 0.3 mg/kg, and 0.06 for 0.1 mg/kg versus 0.027 untreated ( FIG. 19A ), suggesting preferential expansion of Treg cells over Tconv cells by P-0511.
  • expression of Treg cell functional markers, including CD25 ( FIG. 19B ), and FoxP3 ( FIG. 19C ) increased dose-dependently.
  • Increases in the mean fluorescence intensity (MFI) of CD25 and FoxP3 peaked on day 3 and diminished to a lower level on day 5.
  • MFI mean fluorescence intensity
  • P-0511 exhibit potent and preferential Treg activation and expansion in a dose-dependent manner. It requires careful considerations to achieve optimized dosing strategy for maximal potency to promote activation, proliferation and expansion of immunosuppressive Treg cells while sparing cytotoxic effector T cells and NK cells.
  • mice Female Balb/C mice (7-week old) were acclimated in house for 5-7 days before the study.
  • P-0531 is the S125I equivalent of the wild type IL-2 fusion protein.
  • the Benchmark-1 contains V91 K mutation.
  • Treg cells Three days following a single subcutaneous administration of IL-2 fusion proteins, near 90% of Treg cells showed positive Ki67 expression in all tested groups and the Ki67 positive cells remained significantly high after receiving the 3rd dose of all tested compounds ( FIG. 20A ). Intriguingly, Treg cells, as expressed by % Treg over total CD4 T cells or over total lymphocytes, declined drastically to near control levels in mice treated with P-0531 and Benchmark-1, while sustained at significantly high levels in mice treated with P-0511 and P-0512 after three consecutive Q3D treatments in comparison with one treatment ( FIGS. 20B-20C ).
  • FIGS. 21A-21B Similar observations were also obtained for Treg cell counts and fold changes relative to PBS control ( FIGS. 21A-21B ), as well as Treg/Tconv ratio ( FIG. 22 ). P-0511 and P-0512 demonstrated superior capabilities to sustain Treg pool and maintain Treg selectivity compared to P-0531 and Benchmark-1.
  • P-0511 and P-0512 are superior IL-2 molecules that show preferential and sustained in vivo Treg expansion after multiple doses.
  • Tuning the dosing regimen of IL-2 variant Fc fusions, e.g., dosing amount and frequency, may further optimize the desired potency and selectivity on Treg over proinflammatory immune activation.
  • Treg cells induced by IL-2 variants were assessed in a model of delayed-type hypersensitivity (DTH).
  • DTH delayed-type hypersensitivity
  • Female Balb/C mice (7-week old) were acclimated in house for 7 days and randomized into groups.
  • Subcutaneous administration of vehicle (PBS), P-0511 at either 0.1 mg/kg or 0.3 mg/kg was initiated on day ⁇ 2 and was given either once every 3 days (Q3D) for three injections or once every 5 days (Q5D) for two injections.
  • Mice were then sensitized with a subcutaneous administration of 100 ⁇ g keyhole limpet hemocyanin (KLH) in 200 ⁇ I saline on day 0.
  • KLH keyhole limpet hemocyanin
  • mice received an intradermal challenge of KLH (5 ⁇ g in 10 ⁇ I saline) in right ear on day 5. Right ear thickness was measured using a caliper on day 5 prior KLH challenge and daily from day 6 to day 8 corresponding to 24 h, 48 h, and 72 h post KLH challenge.
  • KLH KLH
  • mice also received 5 mg/kg daily i.p. treatment of dexamethasone from day 5 to day 8 as a positive control.
  • Treg cells induced by P-0511 administration was efficacious in suppressing T cell antigen-driven inflammation in a DTH model. Additionally, Treg suppression was sustained without repeated dosing after KLH challenge. It was also evident from the example that it is critical to tune the dosing regimen to achieve optimal efficacy.
  • PK/PD properties of P-0511, an IL-2 variant Fc fusion protein, in cynomolgus monkey will be evaluated following a Q14D ⁇ 3 dosing schedule.
  • PBS subcutaneous administration of vehicle
  • the other three groups will be dosed subcutaneously with P-0511 at either 100 ⁇ g/kg, 30 ⁇ g/kg, or 10 ⁇ g/kg.
  • Blood is collected on days ⁇ 7, ⁇ 3, 2, 4, 6, 8, 11, 14, 18, 21, 28, 32, 35, 43, 50, 57.
  • Whole blood is used for FACS immunophenotyping of peripheral blood Treg, non-regulatory CD4 T cells, CD8 T cells, and NK cells, na ⁇ ve and memory, to determine pharmacodynamics. Cell activation and proliferation will also be monitored by measuring CD69 and Ki67.
  • Whole blood is also used for complete blood count (CBC) with 5-part differential: neutrophil, lymphocytes, monocytes, eosinophil, and basophil.
  • CBC complete blood count
  • PK properties of P-0511 will be assessed in the cynomolgus plasma samples by measuring full-length intact P-0511 using mouse anti-human IL-2 mAb (BD Pharmingen) to coat 96-well plates in order to capture P-0511.
  • P-0511 will be detected using goat anti-human Fc polyclonal-HRP (ThermoFisher) and its plasma concentration will be subsequently quantified.
  • three more plasma samples were collected on day 1 at 0.5 hour, 3 hours, and 6 hours post the first administration of the P-0511.
  • Plasma samples from days ⁇ 8, 8, 21, 35, 43, 57 will also be used to evaluate the following clinical chemistry parameters: aspartate aminotransferase, alanine aminotransferase, alkaline phosphatase, gamma glutamyl transferase, albumin, total bilirubin, creatinine, blood urea nitrogen, and C-reactive protein.
  • body weight and body temperature of each animal will be monitored weekly or twice weekly during the whole study period.
  • nucleic and amino acid sequences listed in the accompanying sequence listing are shown using standard letter abbreviations for nucleotide bases and one letter codes for amino acids, as defined in 37 C.F.R. 1.822.
  • SEQ ID NO: 1 is a human IL-2 precursor amino acid sequence.
  • SEQ ID NO: 2 is a human IL-2 mature form naturally occurring amino acid sequence.
  • SEQ ID NO: 3 is a human IL-2 mature form wild type amino acid sequence.
  • SEQ ID NOS: 4-43, 108-146 and 193-197 are the amino acid sequences of various IL-2 variants.
  • SEQ ID NO: 44 is a human IgG1-Fc amino acid sequence.
  • SEQ ID NO: 45 is a human IgG1-Fc with reduced/abolished effector function amino acid sequence.
  • SEQ ID NOS: 46 and 47 and 212-213 are human IgG1-Fc with reduced/abolished effector function and extended half-life amino acid sequences.
  • SEQ ID NOS: 48-67 are the amino acid sequences of various peptide linker sequences.
  • SEQ ID NO: 68 is a human IL-2 receptor alpha Sushi domain amino acid sequence.
  • SEQ ID NOS: 69-107, 147-189 and 198-211 are the amino acid sequences of various Fc-IL-2 fusion proteins.
  • SEQ ID NOS: 190-192 are the amino acid sequences of benchmark Fc-IL-2 variant fusion proteins.
  • SEQ ID NOS: 214-222 are the nucleotide sequences of various Fc-IL-2 fusion proteins.

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