EP4243931A1 - Bifunktionelle antagonisten von activin/tgf-beta und rankl und verwendungen davon - Google Patents

Bifunktionelle antagonisten von activin/tgf-beta und rankl und verwendungen davon

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Publication number
EP4243931A1
EP4243931A1 EP21892613.7A EP21892613A EP4243931A1 EP 4243931 A1 EP4243931 A1 EP 4243931A1 EP 21892613 A EP21892613 A EP 21892613A EP 4243931 A1 EP4243931 A1 EP 4243931A1
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European Patent Office
Prior art keywords
seq
amino acid
antibody
acid sequence
set forth
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English (en)
French (fr)
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Hq Han
Xiaolan Zhou
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Individual
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Individual
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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C07K16/28—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
    • C07K16/2875—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants against the NGF/TNF superfamily, e.g. CD70, CD95L, CD153, CD154
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P19/00—Drugs for skeletal disorders
    • A61P19/08—Drugs for skeletal disorders for bone diseases, e.g. rachitism, Paget's disease
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides
    • A61K38/16—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • A61K38/17—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • A61K38/1703—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates
    • A61K38/1709—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K45/00—Medicinal preparations containing active ingredients not provided for in groups A61K31/00 - A61K41/00
    • A61K45/06—Mixtures of active ingredients without chemical characterisation, e.g. antiphlogistics and cardiaca
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P19/00—Drugs for skeletal disorders
    • A61P19/08—Drugs for skeletal disorders for bone diseases, e.g. rachitism, Paget's disease
    • A61P19/10—Drugs for skeletal disorders for bone diseases, e.g. rachitism, Paget's disease for osteoporosis
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C07K16/22—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against growth factors ; against growth regulators
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K2039/505—Medicinal preparations containing antigens or antibodies comprising antibodies
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/30—Immunoglobulins specific features characterized by aspects of specificity or valency
    • C07K2317/31—Immunoglobulins specific features characterized by aspects of specificity or valency multispecific
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/70—Immunoglobulins specific features characterized by effect upon binding to a cell or to an antigen
    • C07K2317/76—Antagonist effect on antigen, e.g. neutralization or inhibition of binding
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/90—Immunoglobulins specific features characterized by (pharmaco)kinetic aspects or by stability of the immunoglobulin
    • C07K2317/92—Affinity (KD), association rate (Ka), dissociation rate (Kd) or EC50 value

Definitions

  • the receptor activator of nuclear factor-kappa B ligand (RANKL) signaling pathway plays a central role in the regulation of bone mass by stimulating osteoclast activity and increasing bone resorption, even though RANKL has no direct influence on osteoblast activity and bone formation.
  • RANKL nuclear factor-kappa B ligand
  • Activin/TGF-p signaling pathway can also powerfully regulate bone mass. Remarkably, activation of Activin/TGF-p signaling not only stimulates osteoclast activity and bone resorption but also suppresses osteoblast activity and bone formation. Thus, Activin/TGF-p signaling pathway plays a dual action to regulate both bone resorption and bone formation. Recent studies demonstrated that pharmacological inhibition of Activin/TGF-p signaling pathway in vivo profoundly decreased bone resorption and at the same time markedly increased bone formation.
  • RANKL signaling pathway activation of either RANKL signaling pathway or Activin/TGF-p signaling pathway can strongly induce epithelial-mesenchymal transition (EMT), a remodeling process that is critical for metastasis.
  • EMT epithelial-mesenchymal transition
  • RANKL and Activin/TGF- P have been shown to be elevated in bone metastasis, suggesting that increased RANKL and Activin/TGF-p signaling activities act in parallel to drive pathogenesis and progression of bone metastatic diseases in cancer.
  • muscle mass plays an important role in maintaining healthy bone. It has been shown that in wasting disease states, such as cancer cachexia, age-related sarcopenia and neuromuscular diseases, muscle wasting is intimately correlated with bone loss. Recent studies suggest that increased RANKL signaling as well as increased Activin/TGF-p signaling can both trigger muscle loss. Thus, inhibiting RANKL and Activin/TGF-p can enhance muscle mass and thereby indirectly benefit bone
  • novel bifunctional inhibitors to inhibit both RANKL signaling and Activin/TGF-p signaling for the treatment of bone disorders.
  • Such novel bifunctional antagonists may achieve better efficacy and better response rate for treating certain bone disorders, such as bone metastasis and bone fragility, by inhibiting two major disease pathways at the same time.
  • the present invention provides novel polypeptide-based bifunctional antagonists designed to simultaneously neutralize RANKL signaling and Activin/TGF-p signaling in a potent manner.
  • the bifunctional antagonist molecule is designed as depicted in FIGS. 1-5.
  • the bifunctional antagonist molecule is a bifunctional polypeptide comprising a first antigen-binding molecule which specifically binds RANKL (“RANKL-Binding Polypeptide”) and a second antigen-binding molecule which specifically binds to either Activin ligand (“Activin-Binding Polypeptide”) or TGF-p ligand (“TGF-p-Binding Polypeptide”), which are capable of sequestering RANKL and Activin or TGF-p in parallel.
  • RANKL-Binding Polypeptide a first antigen-binding molecule which specifically binds RANKL
  • Activin-Binding Polypeptide Activin-Binding Polypeptide
  • TGF-p-Binding Polypeptide TGF-p ligand
  • the “RANKL-Binding Polypeptide” is selected from any polypeptide that is capable binding RANKL, which includes, but is not limited to, an anti-RANKL antibody or fragment of anti-RANKL antibody, wild-type osteoprotegerin (OPG) as well as modified OPG, and phage display-derived polypeptide capable of binding and sequestering RANKL.
  • the “Activin-Binding Polypeptide” is selected from any polypeptide that is capable binding Activin (i.e. , Activin A, Activin B or Activin AB) and/or Activin-related ligand (i.e.
  • GDF8 or GDF11 which includes, but is not limited to, an anti-Activin antibody (including anti-Activin A antibody and anti-Activin B antibody), a fragment of anti-Activin antibody, wild-type Activin Type 2A Receptor (ActRIIA) or Activin Type 2B Receptor (ActRIIB) extracellular domains (ECDs), modified ActRIIA and ActRIIB extracellular domains, wild-type and modified native Activin- binding proteins such as follistatin , follistatin-like protein and propeptide, and a phage display- derived polypeptide targeting Activin or Activin-related ligand.
  • an anti-Activin antibody including anti-Activin A antibody and anti-Activin B antibody
  • ActRIIA wild-type Activin Type 2A Receptor
  • ActRIIB Activin Type 2B Receptor
  • ECDs extracellular domains
  • modified ActRIIA and ActRIIB extracellular domains wild-type and modified native
  • the “TGF-p-Binding Polypeptide” is selected from the group consisting of an anti-TGF-p antibody, a fragment of anti-TGF-p antibody, wild-type TGF-p type-2 receptors (including TGFpRIlA and TGFpRIlB) extracellular domains (ECDs), modified TGFpRIlA and TGFpRIlB extracellular domains, and a phage display-derived antagonistic polypeptide targeting TGF-p ligand.
  • the bifunctional antagonist molecule comprises an isolated antibody, or antigen-binding fragment thereof, that specifically binds to RANKL, and an isolated antibody, or antigen-binding fragment thereof, that specifically binds to either Activin or Activin-related ligand or to TGF-p ligand.
  • the isolated antibody or antigen-binding fragment thereof is selected from the group consisting of monoclonal Abs (mAbs), polyclonal Abs, Ab fragments (e.g., Fab, Fab', F(ab')2, Fv, Fc, etc.), chimeric Abs, mini- Abs or domain Abs (dAbs), dual specific Abs, bispecific Abs, heteroconjugate Abs, single chain Abs (SCA), single chain variable region fragments (ScFv), humanized Abs, fully human Abs, and any other modified configuration of the immunoglobulin (Ig) molecule that comprises an antigen recognition site of the required specificity.
  • the bifunctional molecule comprises an isolated antibody or antigen-binding fragment thereof selected from the group consisting of a fully human, humanized and chimeric antibody.
  • the second antigen-binding molecule specifically binds an Activin or Activin-related ligand comprising an amino acid sequence set forth in SEQ ID NO: 1. In various embodiments, the second antigen-binding molecule specifically binds an Activin or Activin-related ligand comprising an amino acid sequence set forth in SEQ ID NO: 2. In various embodiments, the second antigen-binding molecule specifically binds an Activin or Activin- related ligand comprising an amino acid sequence set forth in SEQ ID NO: 3. In various embodiments, the second antigen-binding molecule specifically binds an Activin or Activin- related ligand comprising an amino acid sequence set forth in SEQ ID NO: 4.
  • the second antigen-binding molecule specifically binds an Activin or Activin- related ligand comprising an amino acid sequence set forth in SEQ ID NO: 5. In various embodiments, the second antigen-binding molecule specifically binds an Activin or Activin- related ligand comprising an amino acid sequence set forth in SEQ ID NO: 6. In various embodiments, the second antigen-binding molecule specifically binds an Activin or Activin- related ligand comprising an amino acid sequence set forth in SEQ ID NO: 7. In various embodiments, the second antigen-binding molecule specifically binds an Activin or Activin- related ligand comprising an amino acid sequence set forth in SEQ ID NO: 8. In various embodiments, the second antigen-binding molecule specifically binds an Activin or Activin- related ligand comprising an amino acid sequence set forth in SEQ ID NO: 9.
  • the second antigen-binding molecule that specifically binds to Activin or Activin-related ligand is an isolated antibody selected from the group consisting of an antibody comprising the heavy chain amino acid sequence set forth in SEQ ID NO: 10; an antibody comprising the light chain amino acid sequence set forth in SEQ ID NO: 11 ; an antibody comprising the heavy chain amino acid sequence set forth in SEQ ID NO: 10 and the light chain amino acid sequence set forth in SEQ ID NO: 11 ; an antibody comprising the heavy chain variable region amino acid sequence set forth in SEQ ID NO: 12; an antibody comprising the light chain variable region amino acid sequence set forth in SEQ ID NO: 13; and an antibody comprising the heavy chain variable region amino acid sequence set forth in SEQ ID NO: 12 and the light chain variable region amino acid sequence set forth in SEQ ID NO: 13.
  • the second antigen-binding molecule that specifically binds to Activin or Activin-related ligand is an isolated antibody selected from the group consisting of an antibody comprising the heavy chain amino acid sequence set forth in SEQ ID NO: 14; an antibody comprising the light chain amino acid sequence set forth in SEQ ID NO: 15; an antibody comprising the heavy chain amino acid sequence set forth in SEQ ID NO: 14 and the light chain amino acid sequence set forth in SEQ ID NO: 15; an antibody comprising the heavy chain variable region amino acid sequence set forth in SEQ ID NO: 16; an antibody comprising the light chain variable region amino acid sequence set forth in SEQ ID NO: 17; and an antibody comprising the heavy chain variable region amino acid sequence set forth in SEQ ID NO: 16 and the light chain variable region amino acid sequence set forth in SEQ ID NO: 17.
  • the second antigen-binding molecule specifically binds a TGF-p ligand comprising an amino acid sequence set forth in SEQ ID NO: 18. In various embodiments, the second antigen-binding molecule specifically binds a TGF-p ligand comprising an amino acid sequence set forth in SEQ ID NO: 19.
  • the second antigen-binding molecule that specifically binds to TGF-p ligand is an isolated antibody selected from the group consisting of an antibody comprising the heavy chain amino acid sequence set forth in SEQ ID NO: 20; an antibody comprising the light chain amino acid sequence set forth in SEQ ID NO: 21 ; an antibody comprising the heavy chain amino acid sequence set forth in SEQ ID NO: 20 and the light chain amino acid sequence set forth in SEQ ID NO: 21 ; an antibody comprising the heavy chain variable region amino acid sequence set forth in SEQ ID NO: 22; an antibody comprising the light chain variable region amino acid sequence set forth in SEQ ID NO: 23; and an antibody comprising the heavy chain variable region amino acid sequence set forth in SEQ ID NO: 22 and the light chain variable region amino acid sequence set forth in SEQ ID NO: 23.
  • the bifunctional antagonist is a polypeptide molecule comprising a second antigen-binding molecule that specifically binds to Activin ligand or to TGF- P ligand, wherein the Activin ligand binding molecule is selected from the group of polypeptides comprising the amino acid sequence set forth in SEQ ID NOs: 1-17, and the TGF-p ligand binding molecule is selected from the group of polypeptides comprising the amino acid sequence set forth in SEQ ID NOs: 18-23.
  • the RANKL-Binding Polypeptide is an isolated antibody selected from the group consisting of an antibody comprising the heavy chain amino acid sequence set forth in SEQ ID NO: 24; an antibody comprising the light chain amino acid sequence set forth in SEQ ID NO: 25; an antibody comprising the heavy chain amino acid sequence set forth in SEQ ID NO: 24 and the light chain amino acid sequence set forth in SEQ
  • the RANKL-Binding Polypeptide is osteoprotegerin (OPG) comprising the amino acid sequence set forth in SEQ ID NO: 28.
  • the bifunctional antagonist is a polypeptide molecule comprising a first antigen-binding molecule that specifically binds to RANKL and a second antigen-binding molecule that specifically binds to Activin ligand, wherein the bifunctional molecule is selected from the group consisting of: a bifunctional molecule comprising a heavy chain selected from a heavy chain comprising the amino acid sequence set forth in SEQ ID NOs: 29-37 and a light chain selected from a light chain comprising the amino acid sequence set forth in SEQ ID NO: 25.
  • the bifunctional antagonist is a polypeptide molecule comprising a first antigen-binding molecule that specifically binds to RANKL, wherein the first antigen-binding molecule is an isolated antibody comprising the heavy chain amino acid sequence set forth in SEQ ID NO: 24 and the light chain amino acid sequence set forth in SEQ ID NO: 25; and a second antigen-binding molecule that specifically binds to Activin ligand, wherein the second antigen-binding molecule is an isolated antibody comprising the heavy chain amino acid sequence set forth in SEQ ID NO: 10 and the light chain amino acid sequence set forth in SEQ ID NO: 11 .
  • the bifunctional antagonist is a polypeptide molecule comprising a first antigen-binding molecule that specifically binds to RANKL, wherein the first antigen-binding molecule is an isolated antibody comprising the heavy chain amino acid sequence set forth in SEQ ID NO: 24 and the light chain amino acid sequence set forth in SEQ ID NO: 25; and a second antigen-binding molecule that specifically binds to Activin ligand, wherein the second antigen-binding molecule is an isolated antibody comprising the heavy chain amino acid sequence set forth in SEQ ID NO: 14 and the light chain amino acid sequence set forth in SEQ ID NO: 15.
  • the bifunctional antagonist is a polypeptide molecule comprising a first antigen-binding molecule that specifically binds to RANKL and a second antigen-binding molecule that specifically binds to TGF-p ligand, wherein the bifunctional molecule is selected from the group consisting of: a bifunctional molecule comprising a heavy chain selected from a heavy chain comprising the amino acid sequence set forth in SEQ ID NOs: 38-39 and a light chain selected from a light chain comprising the amino acid sequence set forth in SEQ ID NO: 25.
  • the bifunctional antagonist is a polypeptide molecule comprising a first antigen-binding molecule that specifically binds to RANKL, wherein the first antigen-binding molecule is an isolated antibody comprising the heavy chain amino acid sequence set forth in SEQ ID NO: 24 and the light chain amino acid sequence set forth in SEQ ID NO: 25; and a second antigen-binding molecule that specifically binds to TGF-p ligand, wherein the second antigen-binding molecule is an isolated antibody comprising the heavy chain amino acid sequence set forth in SEQ ID NO: 20 and the light chain amino acid sequence set forth in SEQ ID NO: 21 .
  • the bifunctional antagonist is a polypeptide molecule comprising a first antigen-binding molecule that specifically binds to OPG ligand and a second antigen-binding molecule that specifically binds to Activin ligand, wherein the bifunctional molecule is selected from the group consisting of a polypeptide molecule comprising the amino acid sequence set forth in any one of SEQ ID NOs: 40-48.
  • the bifunctional antagonist is a polypeptide molecule comprising a first antigen-binding molecule that specifically binds to OPG ligand and a second antigen-binding molecule that specifically binds to Activin ligand, wherein the bifunctional molecule is selected from the group consisting of: a bifunctional molecule comprising a heavy chain comprising the amino acid sequence set forth in SEQ ID NO: 49 and a light chain comprising the amino acid sequence set forth in SEQ ID NO: 11 and a bifunctional molecule comprising a heavy chain comprising the amino acid sequence set forth in SEQ ID NO: 50 and a light chain comprising the amino acid sequence set forth in SEQ ID NO: 15.
  • the bifunctional antagonist is a polypeptide molecule comprising a first antigen-binding molecule that specifically binds to OPG ligand and a second antigen-binding molecule that specifically binds to TGF-p ligand, wherein the bifunctional antagonist is selected from the group consisting of a polypeptide molecule comprising the amino acid sequence set forth in any one of SEQ ID NOs: 51-52.
  • the bifunctional antagonist is a polypeptide molecule comprising a first antigen-binding molecule that specifically binds to OPG ligand and a second antigen-binding molecule that specifically binds to TGF-p ligand, wherein the bifunctional molecule comprises a heavy chain comprising the amino acid sequence set forth in SEQ ID NO: 53 and a light chain comprising the amino acid sequence set forth in SEQ ID NO: 21 .
  • the present disclosure provides a pharmaceutical composition
  • a pharmaceutical composition comprising the isolated bifunctional antagonist molecules in admixture with a pharmaceutically acceptable carrier.
  • the novel bifunctional antagonists of the present invention have broad applications for the treatment of various disorders whose pathogenesis involves the activation of both RANKL-NFKB and Activin/TGFp-Smad2/3 signaling pathways including, but not limited to bone metastasis and skeletal-related events in cancer, including breast cancer, multiple myeloma, prostate cancer, lung cancer, kidney cancer, lymphoma, thyroid cancer, and other malignancies; osteolytic neoplasm, such as Giant Cell Tumor of Bone (GCTB); bone fractures, such as hip fracture; osteoporosis; glucocorticoid therapy induced bone loss; androgen deprivation therapy induced bone loss; muscle wasting disorders with bone loss, such as cancer cachexia, sarcopenia, muscular dystrophy, spinal muscular atrophy; and osteogenesis imperfecta.
  • the disorder is selected from the group consisting of bone metastasis, bone loss in cancer, bone fragility in neuromuscular diseases, osteogenesis
  • the disclosure provides uses of the bifunctional antagonist molecules for making a medicament for the treatment of any disorder or condition as described herein.
  • the present disclosure provides isolated nucleic acid molecules comprising a polynucleotide encoding a bifunctional antagonist molecule of the present disclosure.
  • the isolated nucleic acid molecules comprise the polynucleotides described herein, and further comprise a polynucleotide encoding at least one heterologous protein described herein.
  • the nucleic acid molecules further comprise polynucleotides encoding the linkers or hinge linkers described herein.
  • 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 bifunctional antagonist molecules are provided by culturing the host cells under conditions promoting expression of the proteins or polypeptides.
  • a method for producing a bifunctional antagonist molecule comprising a first antigen-binding molecule that specifically binds to RANKL and a second antigen-binding molecule that specifically binds to Activin/TGF-p as described herein, comprising the steps of a) transforming a host cell with vectors comprising polynucleotides encoding said bifunctional antagonist molecule, b) culturing the host cell according under conditions suitable for the expression of the bifunctional antagonist molecule and c) recovering the bifunctional antagonist molecule from the culture.
  • the invention also encompasses a bifunctional antagonist molecule produced by the method of the invention.
  • FIG. 1 depicts a representative bifunctional antagonist molecule of the present invention capable of inhibiting RANKL and Activin or TGFp through fusion between RANKL- binding polypeptide (fusion partner A) and Activin- or TGFp-binding polypeptide (fusion partner B).
  • the “RANKL-binding polypeptide”, as illustrated in this schematic, refers to any polypeptide that is capable binding RANKL, which includes, but not limited to, 1) anti-RANKL antibody or fragment of anti-RANKL antibody, 2) wild-type as well as modified osteoprotegerin (OPG), and 3) phage display-derived polypeptide capable of binding and sequestering RANKL.
  • Activin- or TGFp-binding polypeptide refers to any polypeptide that is capable binding Activin (i.e. , Activin A, Activin B or Activin AB), or TGFp (i.e.
  • TGFpi TGFpi , TGFP2 or TGFP3
  • TGFpi TGFpi , TGFP2 or TGFP3
  • anti-Activin antibody or fragment of anti-Activin antibody and anti-TGFp antibody or fragment of anti-TGFp antibody B extracellular domains (ECDs) of wild-type as well as modified Activin type-2 receptors (including ActRIIA and ActRIIB) and extracellular domains (ECDs) of wild-type or modified TGFp type-2 receptors (including TGFpRIlA and TGFpRIlB), 3) Wild-type and modified follistatin proteins that bind and neutralize activin, and 4) phage display-derived antagonistic polypeptides capable of binding and neutralizing Activin or TGFp.
  • the “Linker”, as shown in this schematic, refers to various methods for fusing different polypeptide fusion partners to generate bispecific and multi-specific molecules, which includes, but not limited to, the use of any peptide linker or chemical linker. [034] FIGS.
  • 2A and 2B depict two representative bifunctional antagonist molecules of the present invention wherein: (A) the RANKL-binding polypeptide is an anti-RANKL antibody and the Activin-binding polypeptide is an Activin Receptor ECD attached via a linker to the heavy chain CH3 of the anti-RANKL antibody; or (B) the RANKL-binding polypeptide is an anti- RANKL antibody and the TGF-p-binding polypeptide is a TGF-p Receptor ECD attached via a linker to the heavy chain CH3 of the anti-RANKL antibody.
  • the Activin Receptor ECD (or TGF-p Receptor ECD) is attached to the anti-Activin antibody (or anti- TGF-p antibody) via a linker at the heavy chain variable region (VH) of the antibody.
  • the Activin Receptor ECD (or TGF-p Receptor ECD) is attached to the anti-Activin antibody (or anti-TGF-p antibody) via a linker at the light chain variable region (VL) of the antibody.
  • the Activin Receptor ECD (or TGF-p Receptor ECD) is attached to the anti-Activin antibody (or anti-TGF-p antibody) via a linker at an internal site rather than at the heavy chain CH3, VL, or VH sites of the antibody.
  • FIGS. 3A and 3B depict two representative bifunctional antagonist molecules of the present invention wherein: (A) the Activin-binding polypeptide is an anti-Activin antibody and the RANKL-binding polypeptide is OPG attached via a linker to the heavy chain CH3 of the anti- Activin antibody; or (B) the TGF-p-binding polypeptide is an anti-TGF-p antibody and the RANKL-binding polypeptide is a OPG attached via a linker to the heavy chain CH3 of the anti- TGF-p antibody.
  • the OPG is attached to the anti-Activin antibody (or anti-TGF-p antibody) via a linker at the heavy chain variable region (VH) of the antibody.
  • the OPG is attached to the anti-Activin antibody (or anti-TGF-p antibody) via a linker at the light chain variable region (VL) of the antibody.
  • the OPG is attached to the anti-Activin antibody (or anti-TGF-p antibody) via a linker at an internal site rather than at the heavy chain CH3, VL, or VH sites of the antibody.
  • 4A and 4B depict two representative bifunctional antagonist molecules of the present invention wherein: (A) the RANKL-binding polypeptide is OPG and the Activin- binding polypeptide is an Activin Receptor ECD attached via an Fc domain; or (B) the RANKL- binding polypeptide is OPG and the TGF-p-binding polypeptide is an TGF-p Receptor ECD attached via an Fc domain.
  • FIGS. 5A and 5B depict two representative bifunctional antagonist molecules of the present invention in the form of a bispecific antibody, wherein the bispecific antibody comprises (A) variable regions (VH and VL) of an anti-activin A antibody and the variable regions (VH and VL) of an anti-RANKL antibody, or (B) variable regions (VH and VL) of an anti- TGF-p antibody and variable regions (VH and VL) of an anti-RANKL antibody. Note that although the bispecific antibody examples illustrated in FIG.
  • bispecific antibodies comprising variable regions derived from both anti-activin A antibody and anti-anti-RANKL antibody or from both anti-TGF-p and anti-RANKL antibody can be constructed in a wide variety of configurations by those that are skilled in the art.
  • FIG. 6 depicts line graphs showing that bifunctional antagonist molecule A112 potently neutralizes Activin A, Activin B, Activin AB and Myostatin in cell-based assays.
  • the IC50 values were calculated and plotted using Prism software (GraphPad Software).
  • FIG. 7 depicts the photographs of RAW 264.7 cells showing the induction of osteoclastogenesis in response to RANKL and activin A and the ability of bifunctional antagonist A1 12 in compararion to anti-RANKL antibody or ActRIIA-Fc to inhibit the RANKL- and activin A- induced osteoclast formation.
  • FIG. 8 depicts bar graphs on osteoclast counts in RAW 264.7 cell cultures showing that in the presence RANKL and TGF-pi , bifunctional antagonist A1 12 was more effective than anti-RANKL antibody or ActRIIA-Fc in suppressing osteoclast formation.
  • FIG. 9 depicts the photographs of RAW 264.7 cell cultures showing the induction of osteoclast formation in response to RANKL and TGF-pi and the effect of bifunctional antagonist A240 in compararion to anti-RANKL antibody or TGFRII-Fc in inhibiting the RANKL- and activin A-induced osteoclast formation.
  • FIG. 10 depicts bar graphs on osteoclast counts in RAW 264.7 cells showing that in the presence RANKL and TGF-pi , bifunctional antagonist A240 was more effective than anti- RANKL antibody or TGFRII-Fc in preventing osteoclast formation.
  • FIG. 1 1 depicts the representative microCT images of bone volume of the distal femur in the different mouse groups showing a marked bone loss resulting from dexamethasone and a complete prevention of the bone loss by the combination treatment with ActRIIA-Fc and anti-murine RANKL antibody.
  • FIG. 12 depicts the quantitative bar graphs of microCT imaging data on trabecular bone thickness of the distal femur in different mouse groups as illustrated in the figure. Note that the combination treatment with ActRIIA-Fc and anti-murine RANKL antibody prevented glucocorticoid-induced bone loss more effectively compared to treatment with ActRIIA-Fc alone or anti-murine RANKL antibody alone.
  • polypeptide polypeptide
  • peptide polypeptide
  • protein protein
  • 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 oc-amino group on an amino acid at the amino terminal of a peptide or to the oc-amino group (imino 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.
  • An amino acid “substitution” as used herein 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.
  • single or multiple 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:
  • a “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.
  • 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. For example, as used herein, 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. In various embodiments, 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%.
  • BLAST programs e.g., BLASTN, BLASTX, and TBLASTX, BLASTP and TBLASTN
  • Sequence searches are typically carried out using the BLASTP program when evaluating a given amino acid sequence relative to amino acid sequences in the GenBank Protein Sequences and other public databases.
  • 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.
  • 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.
  • antigen binding molecule refers in its broadest sense to a molecule that specifically binds an antigenic determinant. Examples of antigen binding molecules are antibodies, antibody fragments and scaffold antigen binding proteins.
  • an "antigen binding molecule that binds to the same epitope" as a reference molecule refers to an antigen binding molecule that blocks binding of the reference molecule to its antigen in a competition assay by 50% or more, and conversely, the reference molecule blocks binding of the antigen binding molecule to its antigen in a competition assay by 50% or more.
  • an antigen-binding site refers to the part of the antigen binding molecule that specifically binds to an antigenic determinant. More particularly, the term “antigen-binding site” refers the part of an antibody that comprises the area which specifically binds to and is complementary to part or all of an antigen. Where an antigen is large, an antigen binding molecule may only bind to a particular part of the antigen, which part is termed an epitope.
  • An antigen-binding site may be provided by, for example, one or more variable domains (also called variable regions).
  • an antigen-binding site comprises an antibody light chain variable region (VL) and an antibody heavy chain variable region (VH).
  • antigenic determinant is synonymous with “antigen” and “epitope,” and refers to a site (e.g., a contiguous stretch of amino acids or a conformational configuration made up of different regions of non-contiguous amino acids) on a polypeptide macromolecule to which an antigen binding moiety binds, forming an antigen binding moiety- antigen complex.
  • Useful antigenic determinants can be found, for example, on the surfaces of tumor cells, on the surfaces of virus-infected cells, on the surfaces of other diseased cells, on the surface of immune cells, free in blood serum, and/or in the extracellular matrix (ECM).
  • ECM extracellular matrix
  • the proteins useful as antigens herein can be any native form the proteins from any vertebrate source, including mammals such as primates (e.g., humans) and rodents (e.g., mice and rats), unless otherwise indicated.
  • the antigen is a human protein.
  • antibody herein is used in the broadest sense and encompasses various antibody structures, including but not limited to monoclonal antibodies, polyclonal antibodies, monospecific and bifunctional antibodies (e.g., bispecific antibodies), and antibody fragments so long as they exhibit the desired antigen-binding activity.
  • chimeric antibody refers to an antibody in which a portion of the heavy and/or light chain is derived from a particular source or species, while the remainder of the heavy and/or light chain is derived from a different source or species.
  • a “humanized” antibody refers to a chimeric antibody comprising amino acid residues from non-human HVRs and amino acid residues from human FRs.
  • a humanized antibody will comprise substantially all of at least one, and typically two, variable domains, in which all or substantially all of the HVRs (e.g., CDRs) correspond to those of a non-human antibody, and all or substantially all of the FRs correspond to those of a human antibody.
  • a humanized antibody optionally may comprise at least a portion of an antibody constant region derived from a human antibody.
  • a "humanized form" of an antibody e.g., a non-human antibody, refers to an antibody that has undergone humanization.
  • Other forms of "humanized antibodies” encompassed by the present invention are those in which the constant region has been additionally modified or changed from that of the original antibody to generate the properties according to the invention, especially in regard to C1q binding and/or Fc receptor (FcR) binding.
  • a "human” antibody is one which possesses an amino acid sequence which corresponds to that of an antibody produced by a human or a human cell or derived from a non- human source that utilizes human antibody repertoires or other human antibody-encoding sequences. This definition of a human antibody specifically excludes a humanized antibody comprising non-human antigen-binding residues.
  • the term "monoclonal antibody” as used herein refers to an antibody obtained from a population of substantially homogeneous antibodies, i.e. , the individual antibodies comprising the population are identical and/or bind the same epitope, except for possible variant antibodies, e.g., containing naturally occurring mutations or arising during production of a monoclonal antibody preparation, such variants generally being present in minor amounts.
  • polyclonal antibody preparations typically include different antibodies directed against different determinants (epitopes)
  • each monoclonal antibody of a monoclonal antibody preparation is directed against a single determinant on an antigen.
  • the term "monospecific” antibody as used herein denotes an antibody that has one or more binding sites each of which bind to the same epitope of the same antigen.
  • the term “bispecific” means that the antibody is able to specifically bind to at least two distinct antigenic determinants, for example two binding sites each formed by a pair of an antibody heavy chain variable domain (VH) and an antibody light chain variable domain (VL) binding to different antigens or to different epitopes on the same antigen.
  • VH antibody heavy chain variable domain
  • VL antibody light chain variable domain
  • Such a bispecific antibody is an 1 +1 format.
  • bispecific antibody formats are 2+1 formats (comprising two binding sites for a first antigen or epitope and one binding site for a second antigen or epitope) or 2+2 formats (comprising two binding sites for a first antigen or epitope and two binding sites for a second antigen or epitope).
  • a bispecific antibody comprises two antigen binding sites, each of which is specific for a different antigenic determinant.
  • the term "valent” as used within the current application denotes the presence of a specified number of binding sites in an antigen binding molecule.
  • the terms “bivalent”, “tetravalent”, and “hexavalent” denote the presence of two binding sites, four binding sites, and six binding sites, respectively, in an antigen binding molecule.
  • the bispecific antibodies according to the invention are at least “bivalent” and may be “trivalent” or “multivalent” (e.g., "tetravalent” or "hexavalent”).
  • the antibodies of the present invention have two or more binding sites and are bispecific. That is, the antibodies may be bispecific even in cases where there are more than two binding sites (i.e. that the antibody is trivalent or multivalent).
  • the invention relates to bispecific bivalent antibodies, having one binding site for each antigen they specifically bind to.
  • full-length antibody refers to an antibody having a structure substantially similar to a native antibody structure.
  • Native antibodies refer to naturally occurring immunoglobulin molecules with varying structures.
  • native IgG-class antibodies are heterotetrameric glycoproteins of about 150,000 daltons, composed of two light chains and two heavy chains that are disulfide-bonded. From N- to C-terminus, each heavy chain has a variable region (VH), also called a variable heavy domain or a heavy chain variable domain, followed by three constant domains (CH1 , CH2, and CH3), also called a heavy chain constant region.
  • each light chain has a variable region (VL), also called a variable light domain or a light chain variable domain, followed by a light chain constant domain (CL), also called a light chain constant region.
  • the heavy chain of an antibody may be assigned to one of five types, called alpha (IgA), delta (Ig D), epsilon (IgE), gamma (IgG), or mu (IgM), some of which may be further divided into subtypes, e.g., gamma 1 (lgG1 ), gamma 2 (lgG2), gamma 3 (lgG3), gamma 4 (lgG4), alpha 1 (lgA1) and alpha 2 (lgA2).
  • the light chain of an antibody may be assigned to one of two types, called kappa and lambda, based on the amino acid sequence of its constant domain.
  • an "antibody fragment” refers to a molecule other than an intact antibody that comprises a portion of an intact antibody that binds the antigen to which the intact antibody binds.
  • antibody fragments include but are not limited to Fv, Fab, Fab', Fab'-SH, F(ab') 2 ; diabodies, triabodies, tetrabodies, cross-Fab fragments; linear antibodies; single-chain antibody molecules (e.g., scFv); bifunctional antibodies formed from antibody fragments and single domain antibodies.
  • Diabodies are antibody fragments with two antigen-binding sites that may be bivalent or bispecific, see, for example, EP 404,097; WO 1993/01161 ; Hudson et al., Nat Med 9, 129-134 (2003); and Hollinger et aL, Proc Natl Acad Sci USA 90, 6444-6448 (1993). Triabodies and tetrabodies are also described in Hudson et aL, Nat Med 9, 129-134 (2003).
  • Single-domain antibodies are antibody fragments comprising all or a portion of the heavy chain variable domain or all or a portion of the light chain variable domain of an antibody.
  • a singledomain antibody is a human single-domain antibody (Domantis, Inc., Waltham, Mass.; see e.g., U.S. Pat. No. 6,248,516 B1 ).
  • antibody fragments comprise single chain polypeptides having the characteristics of a VH domain, namely being able to assemble together with a VL domain, or of a VL domain, namely being able to assemble together with a VH domain to a functional antigen binding site and thereby providing the antigen binding property of full-length antibodies.
  • Antibody fragments can be made by various techniques, including but not limited to proteolytic digestion of an intact antibody as well as production by recombinant host cells (e.g., E. coli or phage), as described herein.
  • Papain digestion of intact antibodies produces two identical antigen-binding fragments, called "Fab” fragments containing each the heavy- and light-chain variable domains and also the constant domain of the light chain and the first constant domain (CH1) of the heavy chain.
  • Fab fragment refers to an antibody fragment comprising a light chain fragment comprising a VL domain and a constant domain of a light chain (CL), and a VH domain and a first constant domain (CH1 ) of a heavy chain.
  • Fab' fragments differ from Fab fragments by the addition of a few residues at the carboxy terminus of the heavy chain CH1 domain including one or more cysteines from the antibody hinge region.
  • Fab'-SH are Fab' fragments wherein the cysteine residue(s) of the constant domains bear a free thiol group. Pepsin treatment yields an F(ab') 2 fragment that has two antigen-combining sites (two Fab fragments) and a part of the Fc region.
  • a "single chain Fab fragment” or “scFab” is a polypeptide consisting of an antibody heavy chain variable domain (VH), an antibody constant domain 1 (CH1), an antibody light chain variable domain (VL), an antibody light chain constant domain (CL) and a linker, wherein said antibody domains and said linker have one of the following orders in N-terminal to C-terminal direction: a) VH-CH1 -linker-VL-CL, b) VL-CL-linker-VH-CH1 , c) VH-CL-linker-VL- CH1 or d) VL-CH1-linker-VH-CL; and wherein said linker is a polypeptide of at least 30 amino acids, preferably between 32 and 50 amino acids.
  • Said single chain Fab fragments are stabilized via the natural disulfide bond between the CL domain and the CH1 domain.
  • these single chain Fab molecules might be further stabilized by generation of interchain disulfide bonds via insertion of cysteine residues (e.g., position 44 in the variable heavy chain and position 100 in the variable light chain according to Kabat numbering).
  • a "single-chain variable fragment (scFv)" is a fusion protein of the variable regions of the heavy (VH) and light chains (VL) of an antibody, connected with a short linker peptide of ten to about 25 amino acids.
  • the linker is usually rich in glycine for flexibility, as well as serine or threonine for solubility, and can either connect the N-terminus of the VH with the C- terminus of the VL, or vice versa.
  • This protein retains the specificity of the original antibody, despite removal of the constant regions and the introduction of the linker.
  • scFv antibodies are, e.g., described in Houston, J. S., Methods in EnzymoL 203 (1991) 46-96).
  • antibody fragments comprise single chain polypeptides having the characteristics of a VH domain, namely being able to assemble together with a VL domain, or of a VL domain, namely being able to assemble together with a VH domain to a functional antigen binding molecule and thereby providing the antigen binding property of full-length antibodies.
  • Fc domain or "Fc region” herein is used to define a C-terminal region of an antibody heavy chain that contains at least a portion of the constant region.
  • the term includes native sequence Fc regions and variant Fc regions.
  • a human IgG heavy chain Fc region extends from Cys226, or from Pro230, to the carboxyl-terminus of the heavy chain.
  • the C-terminal lysine (Lys447) of the Fc region may or may not be present.
  • the amino acid sequences of the heavy chains are always presented with the C-terminal lysine, however variants without the C-terminal lysine are included in the invention.
  • An IgG Fc region comprises an IgG CH2 and an IgG CH3 domain.
  • the "CH2 domain" of a human IgG Fc region usually extends from an amino acid residue at about position 231 to an amino acid residue at about position 340.
  • a carbohydrate chain is attached to the CH2 domain.
  • the CH2 domain herein may be a native sequence CH2 domain or variant CH2 domain.
  • the "CH3 domain” comprises the stretch of residues C-terminal to a CH2 domain in an Fc region (i.e. from an amino acid residue at about position 341 to an amino acid residue at about position 447 of an IgG).
  • 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 antibody heavy chains as herein described.
  • numbering of amino acid residues in the Fc region or constant region is according to the EU numbering system, also called the EU index, as described in Kabat et aL, Sequences of Proteins of Immunological Interest, 5th Ed. Public Health Service, National Institutes of Health, Bethesda, Md., 1991.
  • 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).
  • the method involves introducing a protuberance ("knob") at the interface of a first polypeptide and a corresponding cavity ("hole”) in the interface of a second polypeptide, such that the protuberance can be positioned in the cavity so as to promote heterodimer formation and hinder homodimer formation.
  • Protuberances are constructed by replacing small amino acid side chains from the interface of the first polypeptide with larger side chains (e.g., tyrosine or tryptophan).
  • Compensatory cavities of identical or similar size to the protuberances are created in the interface of the second polypeptide by replacing large amino acid side chains with smaller ones (e.g., alanine or threonine).
  • the protuberance and cavity can be made by altering the nucleic acid encoding the polypeptides, e.g., by site-specific mutagenesis, or by peptide synthesis.
  • a knob modification comprises the amino acid substitution T366W in one of the two subunits of the Fc domain
  • the hole modification comprises the amino acid substitutions T366S, L368A and Y407V in the other one of the two subunits of the Fc domain.
  • the subunit of the Fc domain comprising the knob modification additionally comprises the amino acid substitution S354C
  • the subunit of the Fc domain comprising the hole modification additionally comprises the amino acid substitution Y349C.
  • a "region equivalent to the Fc region of an immunoglobulin" is intended to include naturally occurring allelic variants of the Fc region of an immunoglobulin as well as variants having alterations which produce substitutions, additions, or deletions but which do not decrease substantially the ability of the immunoglobulin to mediate effector functions (such as antibody-dependent cellular cytotoxicity).
  • one or more amino acids can be deleted from the N-terminus or C-terminus of the Fc region of an immunoglobulin without substantial loss of biological function.
  • Such variants can be selected according to general rules known in the art so as to have minimal effect on activity (see, e.g., Bowie, J. U. et aL, Science 247:1306- 10 (1990)).
  • effector functions refers to those biological activities attributable to the Fc region of an antibody, which vary with the antibody isotype.
  • antibody 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.
  • an "activating Fc receptor” is an Fc receptor that following engagement by an Fc region of an antibody elicits signaling events that stimulate the receptor-bearing cell to perform effector functions. Activating Fc receptors include FcyRllla (CD16a), FcyRI (CD64), FcyRlla (CD32), and FcaRI (CD89). A particular activating Fc receptor is human FcyRllla (see UniProt accession no. P08637, version 141 ).
  • a “blocking" antibody or an “antagonist” antibody is one that inhibits or reduces a biological activity of the antigen it binds.
  • blocking antibodies or antagonist antibodies substantially or completely inhibit the biological activity of the antigen.
  • the bispecific antibodies of the invention block the signaling through RANKL so as to inhibit RANKL-NFKB signaling pathway and simultaneously block the signaling through TGF-p or Activin so as to inhibit TGF-p/Activin-Smad2/3 signaling pathway.
  • 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).
  • SPR Surface Plasmon Resonance
  • the term "high affinity" of an antibody refers to an antibody having a Kd of 10 -9 M or less and even more particularly 10 -10 M or less for a target antigen.
  • low affinity of an antibody refers to an antibody having a Kd of 10 -8 M or higher.
  • reduced binding refers to a decrease in affinity for the respective interaction, as measured for example by SPR.
  • increased binding refers to an increase in binding affinity for the respective interaction.
  • a bispecific antibody comprising a first antigen-binding molecule that specifically binds to RANKL and a second antigen-binding molecule that specifically binds to either Activin ligand or TGF-p ligand
  • a bispecific antibody that specifically binds RANKL and either Activin ligand or TGF-p ligand "bispecific antigen binding molecule specific for RANKL and either Activin ligand or TGF-p ligand” are used interchangeably herein and refer to a bispecific antibody that is capable of binding RANKL and either Activin ligand or TGF-p ligand with sufficient affinity such that the antibody is useful as a diagnostic and/or therapeutic agent in targeting RANKL and either Activin ligand and TGF-p ligand.
  • anti-RANKL antibody and "an antibody comprising an antigenbinding site that binds to RANKL” refer to an antibody that is capable of binding RANKL, especially a RANKL polypeptide expressed on a cell surface, with sufficient affinity such that the antibody is useful as a diagnostic and/or therapeutic agent in targeting RANKL.
  • the extent of binding of an anti-RANKL antibody to an unrelated, non-RANKL protein is less than about 10% of the binding of the antibody to RANKL as measured, e.g., by radioimmunoassay (RIA) or flow cytometry (FACS) or by a Surface Plasmon Resonance assay using a biosensor system such as a Biacore® system.
  • an antigen binding molecule that binds to human RANKL has a KD value of the binding affinity for binding to human RANKL of, e.g., from 10 -8 M to 10 -13 M.
  • the respective KD value of the binding affinities is determined in a Surface Plasmon Resonance assay using the Extracellular domain (ECD) of human RANKL (RANKL-ECD) for the RANKL binding affinity.
  • ECD Extracellular domain
  • RANKL-ECD Extracellular domain of human RANKL
  • anti-RANKL antibody also encompasses bispecific antibodies that are capable of binding RANKL and a second antigen.
  • anti-Activin antibody and "an antibody comprising an antigen-binding site that binds to Activin” refer to an antibody that is capable of binding Activin, especially a Activin polypeptide expressed on a cell surface, with sufficient affinity such that the antibody is useful as a diagnostic and/or therapeutic agent in targeting Activin.
  • the extent of binding of an anti-Activin antibody to an unrelated, non-Activin protein is less than about 10% of the binding of the antibody to Activin as measured, e.g., by radioimmunoassay (RIA) or flow cytometry (FACS) or by a Surface Plasmon Resonance assay using a biosensor system such as a Biacore® system.
  • an antigen binding molecule that binds to human Activin has a KD value of the binding affinity for binding to human Activin of, e.g., from 10 -8 M to 10 -13 M.
  • the respective KD value of the binding affinities is determined in a Surface Plasmon Resonance assay using the Extracellular domain (ECD) of human Activin (Activin-ECD) for the Activin binding affinity.
  • ECD Extracellular domain
  • Activin-ECD Extracellular domain
  • anti-Activin antibody also encompasses bispecific antibodies that are capable of binding Activin and a second antigen.
  • anti-TGF-p antibody and "an antibody comprising an antigen-binding site that binds to TGF-P” refer to an antibody that is capable of binding TGF-p, especially a TGF-p polypeptide expressed on a cell surface, with sufficient affinity such that the antibody is useful as a diagnostic and/or therapeutic agent in targeting TGF-p.
  • the extent of binding of an anti-TGF-p antibody to an unrelated, non-TGF-p protein is less than about 10% of the binding of the antibody to TGF-p as measured, e.g., by radioimmunoassay (RIA) or flow cytometry (FACS) or by a Surface Plasmon Resonance assay using a biosensor system such as a Biacore® system.
  • an antigen binding molecule that binds to human TGF-p has a KD value of the binding affinity for binding to human TGF-p of, e.g., from 10 -8 M to 10 -13 M.
  • the respective KD value of the binding affinities is determined in a Surface Plasmon Resonance assay using the Extracellular domain (ECD) of human TGF-p (TGF-p-ECD) for the TGF-p binding affinity.
  • ECD Extracellular domain
  • anti-TGF-p antibody also encompasses bispecific antibodies that are capable of binding TGF-p and a second antigen.
  • 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.
  • tumor metastasis slow to some extent and preferably stop
  • tumor metastasis inhibit tumor growth;
  • 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).
  • domesticated mammals e.g., canine or feline
  • laboratory mammals e.g., mouse, rat, rabbit, hamster, guinea pig
  • 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).
  • 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).
  • immunotherapy refers to cancer treatments which include, but are not limited to, treatment using depleting antibodies to specific tumor antigens; treatment using antibody-drug conjugates; treatment using agonistic, antagonistic, or blocking antibodies to costimulatory or co-inhibitory molecules (immune checkpoints) such as CTLA-4, RANKL, OX-40, CD137, GITR, LAG3, TIM-3, SIRP, CD40, CD47, Siglec 8, Siglec 9, Siglec 15, TIGIT and VISTA; treatment using bispecific T cell engaging antibodies (BiTE®) such as blinatumomab: treatment involving administration of biological response modifiers such as IL-2, IL-12, IL-15, IL- 21 , GM-CSF, IFN-a, IFN-p and IFN-y; treatment using therapeutic vaccines such as sipuleucel- 1 T; treatment using Bacilli Calmette-Guerin (BCG); treatment using dendritic cell vaccines,
  • BCG Bacilli Calmette
  • Resistant or refractory cancer refers to tumor cells or cancer that do not respond to previous anti-cancer therapy including, e.g., chemotherapy, surgery, radiation therapy, stem cell transplantation, and immunotherapy.
  • Tumor cells can be resistant or refractory at the beginning of treatment, or they may become resistant or refractory during treatment.
  • Refractory tumor cells include tumors that do not respond at the onset of treatment or respond initially for a short period but fail to respond to treatment.
  • Refractory tumor cells also include tumors that respond to treatment with anticancer therapy but fail to respond to subsequent rounds of therapies.
  • refractory tumor cells also encompass tumors that appear to be inhibited by treatment with anticancer therapy but recur up to five years, sometimes up to ten years or longer after treatment is discontinued.
  • the anticancer therapy can employ chemotherapeutic agents alone, radiation alone, targeted therapy alone, immunotherapy alone, surgery alone, or combinations thereof.
  • chemotherapeutic agents alone, radiation alone, targeted therapy alone, immunotherapy alone, surgery alone, or combinations thereof.
  • the refractory tumor cells are interchangeable with resistant tumor.
  • 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 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 NaCI at 72°C for about 15 minutes.
  • An example of stringent wash conditions is a 0.2 x 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 x 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 x SSC at 40°C for 15 minutes.
  • a signal to noise ratio of 2 x (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. [0109] "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.
  • Probes can be labeled with, e.g., chromogenic, radioactive, or fluorescent moieties and used as detectable moieties.
  • 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).
  • 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.
  • 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.
  • 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, "Tc, 111 In, 125 l, 131 1), fluorescent labels (e.g., FITC, rhodamine, lanthanide phosphors), enzymatic labels (e.g., horseradish peroxidase, p- 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, tax
  • 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.
  • TGF-p (TGF-pi , TGF-P2 and TGF-P3) mediates Smad2/3 signaling through its binding and activation of the high-affinity receptors TGFpRII and TGFpRHB on the cell surface.
  • TGF-p plays a critical role in the regulation of a wide range of biology activities, including immune function, cell proliferation and differentiation, fibrogenesis, epithelial-mesenchymal transition, hematopoiesis, myogenesis and bone remodeling.
  • Elevated TGF-p levels and consequently increased Smad2/3 signaling have been implicated in pathogenesis and progression of many disease conditions including cancer, fibrosis, anemia, bone metastasis, bone loss, pain, muscle loss, insulin resistance, chronic kidney disease, liver disease, and cardiovascular diseases.
  • Activins and related proteins include Activin A, Activin B, Activin AB, GDF-8 and GDF-11
  • Activin and related proteins also mediate Smad2/3 signaling through binding and activation of their high-affinity receptors ActRIIA and ActRIIB on the cell surface.
  • Activin and related proteins regulate a wide range of biology activities, including immune function, cell differentiation, myogenesis, fibrogenesis, bone remodeling, hematopoiesis, and reproductive physiology.
  • Follistatin (FST) a secreted glycoprotein, binds to the Activins and Activin-related ligands to negatively control their signaling activities.
  • TGF-p/Activin-Smad2/3 signaling pathway plays a central role in the pathogenesis and progression of fibrosis.
  • a key mechanism underlying pathogenesis and progression of fibrosis is the increased TGF-p/Activin-Smad2/3 signaling, which leads to proliferation and activation of fibroblasts and consequently, overexpression of extracellular matrix components such as COL1A1 , COL1A2, COL3A1 , COL5A2, COL6A1 and COL6A3 in the disease tissue.
  • Evidence indicates that TGF-p and Activin are both upregulated during fibrosis. When elevated, either TGF-p or Activin can cause fibroblast activation, leading to fibrosis.
  • TGF-p and Activin are both elevated, it is important to inhibit not only TGF-p but also Activin in order to more effectively attenuate fibrosis.
  • Activins including Activin A, Activin B and Activin AB, and Activin-related proteins, including Myostatin (GDF-8) and GDF-11 , mediate Smad2/3 signaling through binding and activation of their high-affinity receptors ActRIIA and ActRIIB on the cell surface.
  • the Activins and related proteins play a critical role in the regulation of a wide range of biology activities, including mesoderm induction, cell differentiation, myogenesis, bone remodeling, hematopoiesis, fibrogenesis, and reproductive physiology.
  • Follistatin (FST) a secreted glycoprotein, binds to the Activins and Activin-related ligands to negatively control their signaling activities.
  • the bifunctional molecule of the present invention is capable of binding an Activin or Activin-related ligand having an amino acid sequence selected from the group consisting of the amino acid sequences set forth in SEQ ID NOs: 1-9:
  • the bifunctional polypeptide molecule is capable of binding an Activin or Activin-related ligand having an amino acid sequence selected from the group consisting of the amino acid sequences set forth in Table 2:
  • TGF-P Transforming Growth Factor-Beta
  • TGF-P2 Transforming Growth Factor-Beta
  • TGF-p plays a critical role in the regulation of a wide range of biology activities, including immune function, cell proliferation and differentiation, epithelial-mesenchymal transition, fibrogenesis, hematopoiesis, myogenesis, bone remodeling, cancer progression and metastasis.
  • Elevated TGF-p levels and consequently increased Smad2/3 signaling have been implicated in pathogenesis and progression of many disease conditions including cancer, anemia, bone metastasis, bone loss, fibrosis, pain, muscle loss, insulin resistance, chronic kidney disease, liver disease, and cardiovascular diseases.
  • the bifunctional polypeptide molecule of the present invention is capable of binding an TGF-p ligand having an amino acid sequence selected from the group consisting of the amino acid sequences set forth in SEQ ID NOs: 18-19:
  • TGF-P Receptor ll-ECD isoform 1 TGF-P RIIB-ECD
  • TGF-P Receptor ll-ECD isoform 2 TGF-P RIIA-ECD
  • TIPPHVQKSDVEMEAQKDEIICPSCNRTAHPLRHINNDMIVTDNNGAVKFPQLCKFCDVRFSTC DNQKSCMSNCSITSICEKPQEVCVAVWRKNDENITLETVCHDPKLPYHDFILEDAASPKCIMKE KKKPGETFFMCSCSSDECNDNIIFSEEYNTSNPD SEQ ID NO: 19
  • the bifunctional polypeptide molecule is capable of binding a TGF-p ligand having an amino acid sequence selected from the group consisting of the amino acid sequences set forth in Table 3:
  • RANKL nuclear factor-kappa B ligand
  • the receptor activator of nuclear factor-kappa B ligand (RANKL) signaling pathway plays a central role in the regulation of bone mass by stimulating osteoclast activity and increasing bone resorption, even though RANKL has no direct influence on osteoblast activity and bone formation.
  • the RANKL signaling pathway can also powerfully regulate bone mass. Mounting evidence indicates that the RANKL signaling pathway is increased in various skeletal disorders, indicating their parallel contribution to pathogenesis of bone disorders.
  • EMT epithelial-mesenchymal transition
  • the bifunctional antagonist molecule is capable of binding a RANKL having an amino acid sequence selected from the group consisting of the amino acid sequences set forth in Table 4:
  • RANKL and/or Activin and/or TGF-B Antibodies and Antibody Fragments Methods of generating novel antibodies that bind to RANKL and/or Activin or Activin-related ligand and/or TGF-p ligands and/or receptors are known to those skilled in the art.
  • a method for generating a monoclonal antibody that binds specifically to RANKL and/or Activin or Activin-related ligand and/or TGF-p ligand may comprise administering to a mouse an amount of an immunogenic composition comprising RANKL and/or Activin or Activin-related ligand and/or TGF-p ligand effective to stimulate a detectable immune response, obtaining antibody-producing cells (e.g., cells from the spleen) from the mouse and fusing the antibody-producing cells with myeloma cells to obtain antibody-producing hybridomas, and testing the antibody-producing hybridomas to identify a hybridoma that produces a monoclonal antibody that binds specifically to RANKL and/or Activin or Activin-related ligand and/or TGF-p ligand.
  • antibody-producing cells e.g., cells from the spleen
  • a hybridoma can be propagated in a cell culture, optionally in culture conditions where the hybridoma-derived cells produce the monoclonal antibody that binds specifically to RANKL and/or Activin or Activin-related ligand and/or TGF-p ligand.
  • the monoclonal antibody may be purified from the cell culture. A variety of different techniques are then available for testing an antigen/antibody interaction to identify particularly desirable antibodies.
  • Antibodies can be engineered in numerous ways. They can be made as singlechain antibodies (including small modular immunopharmaceuticals or SMIPsTM), Fab and F(ab') 2 fragments, etc. Antibodies can be humanized, chimerized, deimmunized, or fully human. Numerous publications set forth the many types of antibodies and the methods of engineering such antibodies. For example, see U.S. Pat. Nos. 6,355,245; 6,180,370; 5,693,762; 6,407,213; 6,548,640; 5,565,332; 5,225,539; 6,103,889; and 5,260,203.
  • Chimeric antibodies can be produced by recombinant DNA techniques known in the art. For example, a gene encoding the Fc constant region of a murine (or other species) monoclonal antibody molecule is digested with restriction enzymes to remove the region encoding the murine Fc, and the equivalent portion of a gene encoding a human Fc constant region is substituted (see Robinson et aL, International Patent Publication PCT/US86/02269; Akira, et aL, European Patent Application 184,187; Taniguchi, M., European Patent Application 171 ,496; Morrison et aL, European Patent Application 173,494; Neuberger et aL, International Application WO 86/01533; Cabilly et aL U.S.
  • a humanized antibody has one or more amino acid residues introduced from a source that is nonhuman, in addition to the nonhuman CDRs.
  • Humanization can be essentially performed following the method of Winter and co-workers (Jones et aL, Nature, 321 :522-525, 1986; Riechmann et aL, Nature, 332:323-327, 1988; Verhoeyen et aL, Science, 239:1534-1536, 1988), by substituting hypervariable region sequences for the corresponding sequences of a human antibody. Accordingly, such "humanized" antibodies are chimeric antibodies (U.S. Patent No.
  • humanized antibodies are typically human antibodies in which some hypervariable region residues and possibly some framework region residues are substituted by residues from analogous sites in rodent antibodies.
  • U.S. Patent No. 5,693,761 to Queen et al discloses a refinement on Winter et aL for humanizing antibodies, and is based on the premise that ascribes avidity loss to problems in the structural motifs in the humanized framework which, because of steric or other chemical incompatibility, interfere with the folding of the CDRs into the binding-capable conformation found in the mouse antibody.
  • Queen teaches using human framework sequences closely homologous in linear peptide sequence to framework sequences of the mouse antibody to be humanized. Accordingly, the methods of Queen focus on comparing framework sequences between species. Typically, all available human variable region sequences are compared to a particular mouse sequence and the percentage identity between correspondent framework residues is calculated.
  • the human variable region with the highest percentage is selected to provide the framework sequences for the humanizing project. Queen also teaches that it is important to retain in the humanized framework, certain amino acid residues from the mouse framework critical for supporting the CDRs in a binding-capable conformation. Potential criticality is assessed from molecular models. Candidate residues for retention are typically those adjacent in linear sequence to a CDR or physically within 6A of any CDR residue.
  • framework shuffling Another method of humanizing antibodies, referred to as “framework shuffling", relies on generating a combinatorial library with nonhuman CDR variable regions fused in frame into a pool of individual human germline frameworks (Dall'Acqua et aL, Methods, 36:43, 2005). The libraries are then screened to identify clones that encode humanized antibodies which retain good binding.
  • a method for producing an anti-Activin antibody or antigen-binding fragment thereof comprises the steps of synthesizing a library of human antibodies on phage, screening the library with Activin polypeptide or an antibody-binding portion thereof, isolating phage that bind Activin polypeptide, and obtaining the antibody from the phage.
  • one method for preparing the library of antibodies for use in phage display techniques comprises the steps of immunizing a non-human animal comprising human immunoglobulin loci with Activin polypeptide or an antigenic portion thereof to create an immune response, extracting antibody-producing cells from the immunized animal; isolating RNA encoding heavy and light chains of antibodies of the invention from the extracted cells, reverse transcribing the RNA to produce cDNA, amplifying the cDNA using primers, and inserting the cDNA into a phage display vector such that antibodies are expressed on the phage.
  • Recombinant anti- Activin antibodies of the invention may be obtained in this way.
  • Recombinant human anti-RANKL and/or anti-Activin and/or anti-TGF-p antibodies of the invention can also be isolated by screening a recombinant combinatorial antibody library.
  • the library is a scFv phage display library, generated using human VL and VH CDNAS prepared from mRNA isolated from B cells. Methods for preparing and screening such libraries are known in the art. Kits for generating phage display libraries are commercially available (e.g., the Pharmacia Recombinant Phage Antibody System, catalog no. 27-9400-01 ; and the Stratagene SurfZAPTM phage display kit, catalog no. 240612).
  • Hybridomas 3:81-85, 1992; Huse et aL, Science, 246:1275-1281 , 1989; McCafferty et aL, Nature, 348:552-554, 1990; Griffiths et aL, EMBO J., 12:725-734, 1993; Hawkins et aL, J. Mol. Biol., 226:889-896, 1992;
  • Human antibodies are also produced by immunizing a non-human, transgenic animal comprising within its genome some or all of human immunoglobulin heavy chain and light chain loci with a human IgE antigen, e.g., a XenoMouseTM animal (Abgenix, Inc./Amgen, Inc. -Fremont, Calif.).
  • XenoMouseTM mice are engineered mouse strains that comprise large fragments of human immunoglobulin heavy chain and light chain loci and are deficient in mouse antibody production. See, e.g., Green et aL, Nature Genetics, 7:13-21 , 1994 and U.S. Pat. Nos.
  • XenoMouseTM mice produce an adult-like human repertoire of fully human antibodies and generate antigen-specific human antibodies.
  • the XenoMouseTM mice contain approximately 80% of the human antibody V gene repertoire through introduction of megabase sized, germline configuration fragments of the human heavy chain loci and kappa light chain loci in yeast artificial chromosome (YAC).
  • YAC yeast artificial chromosome
  • XenoMouseTM mice further contain approximately all of the human lambda light chain locus.
  • the present invention provides a method for making anti-RANKL and/or anti-Activin and/or TGF-p antibodies from non-human, non-mouse animals by immunizing non-human transgenic animals that comprise human immunoglobulin loci with RANKL and/or Activin and/or TGF-p polypeptide.
  • the anti-Activin antibody is an anti-Activin A antibody that is a human antibody or antigen-binding fragment comprising the heavy chain amino acid sequence set forth in SEQ ID NO: 10:
  • HYTQKSLSLSPGK (SEQ ID NO: 10) a human antibody or antigen-binding fragment comprising the light chain amino acid sequence set forth in SEQ ID NO: 11 :
  • the invention provides antibodies, comprising a heavy chain, a light chain, or both a heavy chain and light chain; a heavy chain variable region, a light chain variable region, or both a heavy chain variable region and light chain variable region; wherein the heavy chain, light chain, heavy chain variable region, or light chain variable region comprises a sequence that has at least about 75%, at least about 80%, at least about 85%, at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or at least about 99% identity to the amino acid sequences as set forth in SEQ ID NOs: 10, 11 , 12 or 13; wherein the antibody binds specifically to human Activin A.
  • the anti-Activin antibody is an anti-Activin A antibody that is a human antibody or antigen-binding fragment comprising the heavy chain amino acid sequence set forth in SEQ ID NO: 14:
  • EIVLTQSPGTLSLSPGERATLSCRASQSVSSSYLAWYQQKPGQAPRLLIYGASSRATGIPDRFS GSGSGTDFTLTISRLEPEDFAVYYCQQYGSSPWTFGQGTKVEIK (SEQ ID NO: 17) or a human antibody or antigen-binding fragment comprising the heavy chain variable region amino acid sequence set forth in SEQ ID NO: 16 and the light chain variable region amino acid sequence set forth in SEQ ID NO: 17.
  • the invention provides antibodies, comprising a heavy chain, a light chain, or both a heavy chain and light chain; a heavy chain variable region, a light chain variable region, or both a heavy chain variable region and light chain variable region; wherein the heavy chain, light chain, heavy chain variable region, or light chain variable region comprises a sequence that has at least about 75%, at least about 80%, at least about 85%, at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or at least about 99% identity to the amino acid sequences as set forth in SEQ ID NOs: 14, 15, 16 or 17; wherein the antibody binds specifically to human Activin A.
  • the anti-TGF-p antibody is an anti-TGF-p antibody that is a human antibody or antigen-binding fragment comprising the heavy chain amino acid sequence set forth in SEQ ID NO: 20:
  • SEQ ID NO: 22 a human antibody or antigen-binding fragment comprising the light chain variable region amino acid sequence set forth in SEQ ID NO: 23:
  • ETVLTQSPGTLSLSPGERATLSCRASQSLGSSYLAWYQQKPGQAPRLLIYGASSRAPGIPDRF SGSGSGTDFTLTISRLEPEDFAVYYCQQYADSPITFGQGTRLEIK (SEQ ID NO: 23) or a human antibody or antigen-binding fragment comprising the heavy chain variable region amino acid sequence set forth in SEQ ID NO: 22 and the light chain variable region amino acid sequence set forth in SEQ ID NO: 23.
  • the invention provides antibodies, comprising a heavy chain, a light chain, or both a heavy chain and light chain; a heavy chain variable region, a light chain variable region, or both a heavy chain variable region and light chain variable region; wherein the heavy chain, light chain, heavy chain variable region, or light chain variable region comprises a sequence that has at least about 75%, at least about 80%, at least about 85%, at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or at least about 99% identity to the amino acid sequences as set forth in SEQ ID NOs: 20, 21 , 22 or 23; wherein the antibody binds specifically to human TGF-p.
  • the anti-RANKL antibody is an anti-RANKL antibody that is a human antibody or antigen-binding fragment comprising the heavy chain amino acid sequence set forth in SEQ ID NO: 24:
  • EIVLTQSPGTLSLSPGERATLSCRASQSVRGRYLAWYQQKPGQAPRLLIYGASSRATGIPDRFS GSGSGTDFTLTISRLEPEDFAVFYCQQYGSSPRTFGQGTKVEIK (SEQ ID NO: 27) or a human antibody or antigen-binding fragment comprising the heavy chain variable region amino acid sequence set forth in SEQ ID NO: 26 and the light chain variable region amino acid sequence set forth in SEQ ID NO: 27.
  • the invention provides antibodies, comprising a heavy chain, a light chain, or both a heavy chain and light chain; a heavy chain variable region, a light chain variable region, or both a heavy chain variable region and light chain variable region; wherein the heavy chain, light chain, heavy chain variable region, or light chain variable region comprises a sequence that has at least about 75%, at least about 80%, at least about 85%, at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or at least about 99% identity to the amino acid sequences as set forth in SEQ ID NOs: 24, 25, 26 or 27; wherein the antibody binds specifically to human RANKL.
  • the RANKL-Binding Polypeptide is human osteoprotegerin (OPG) comprising the amino acid sequence set forth in SEQ ID NO: 28.
  • OPG human osteoprotegerin
  • the present invention provides novel polypeptide-based bifunctional antagonist molecules specifically designed to simultaneously neutralize RANKL signaling and either Activin signaling and TGF-p signaling in a potent manner and comprising a first antigen-binding molecule that specifically binds to RANKL and a second antigen-binding molecule that specifically binds to either Activin ligand or TGF-p ligand.
  • the bifunctional antagonist_molecule comprises an isolated antibody, or antigenbinding fragment thereof, that specifically binds to RANKL and an isolated antibody, or antigenbinding fragment thereof, that specifically binds to either Activin ligand or TGF-p ligand.
  • these bifunctional antagonists also provide advantageous properties such as producibility, stability, binding affinity, biological activity, specific targeting of certain cells, targeting efficiency and reduced toxicity.
  • the bifunctional antagonist molecules of the present invention are selected from the group of molecules designed and comprising the fusion partners as described in Table 5:
  • the bifunctional antagonist molecule of the present invention specifically designed to simultaneously neutralize Activin signaling and OPG signaling in a potent manner and comprising a first antigen-binding molecule that specifically binds to Activin ligand and a second antigen-binding molecule that specifically binds to OPG ligand is selected from the group of molecules as described in Table 6:
  • the bifunctional antagonist molecule of the present invention specifically designed to simultaneously neutralize Activin signaling and OPG signaling in a potent manner and comprising a first antigen-binding molecule that specifically binds to TGF-p ligand and a second antigen-binding molecule that specifically binds to OPG ligand is selected from the group of molecules as described in Table 7:
  • the first antigen-binding molecule that specifically binds to RANKL is attached to the second antigen-binding molecule that specifically binds to either Activin ligand or TGF-p ligand 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 a-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: 67).
  • a linker can contain motif of GGGGS (SEQ ID NO: 70)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 a-helical conformation such as AEAAAKEAAAKEAAAKA (SEQ ID NO: 65).
  • 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 a bifunctional antagonist molecule 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 bifunctional antagonist molecules is obtained from genomic libraries which are available for a number of species. Synthetic DNA is available from chemical synthesis of overlapping oligonucleotide fragments followed by assembly of the fragments to reconstitute part or all of the coding regions and flanking sequences.
  • 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 a bifunctional antagonist molecule.
  • 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.
  • 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. [0159] In various embodiments, the recombinant nucleic acids of the present disclosure may be operably linked to one or more regulatory nucleotide sequences in an expression bifunctional antagonist molecule. Accordingly, the term regulatory sequence includes promoters, enhancers, and other expression control elements.
  • 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 a bifunctional antagonist molecule 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 a bifunctional antagonist molecule.
  • 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 a-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.
  • 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 bifunctional antagonist molecule 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 pAcUWI), 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 pAcUWI
  • pBlueBac-derived vectors such as the B-gal containing pBlueBac III.
  • a vector will be designed for production of the subject bifunctional antagonist molecule 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.).
  • a vector will be designed for production of the subject bifunctional antagonist molecule 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 bifunctional antagonist molecule in cells propagated in culture, e.g., to produce proteins, including fusion proteins or variant proteins, for purification.
  • the present disclosure further pertains to methods of producing the subject bifunctional antagonist molecules.
  • a host cell transfected with an expression vector encoding a bifunctional antagonist molecule can be cultured under appropriate conditions to allow expression of the bifunctional antagonist molecule to occur.
  • the bifunctional antagonist molecule may be secreted and isolated from a mixture of cells and medium containing the bifunctional antagonist molecule.
  • the bifunctional antagonist molecule 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 are 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 non- proteinaceous 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 this designation 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 pharmaceutically acceptable carrier Such 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-HCI, 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 bifunctional antagonist molecule 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.
  • oral administration of the pharmaceutical compositions is contemplated. Pharmaceutical compositions that are administered in this fashion can be formulated with or without those carriers customarily used in the compounding of solid dosage forms such as tablets and capsules.
  • 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, alginic acid, certain silicates, and sodium carbonate; (5) solution retarding agents, such as paraffin; (6) absorption accelerators, such as quaternary ammonium compounds; (7) wetting agents,
  • pharmaceutically acceptable carriers such as sodium citrate or dicalcium phosphate, and/or any of the following: (1 ) fillers or
  • 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. Examples are salicylic acid and sulfur.
  • 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 bifunctional antagonist molecule), 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 0.1 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; 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 a method of treating or preventing various complex disease conditions whose pathogenesis involve the activation of both RANKL-NFKB and TGF-p/Activin-mediated Smad2/3 signaling pathway.
  • the novel bifunctional antagonist molecules of the present invention may have broad applications for the treatment of various disorders which include, but are not limited to, the following conditions: Metastasis: bone metastasis, lung metastasis, liver metastasis, and brain metastasis; Bone cancers: multiple myeloma, osteosarcoma, chondrosarcoma and Ewing's sarcoma; Bone disorders: osteolytic lesions and skeletal-related event in cancer, bone fragility, osteogenesis imperfecta, fracture, osteopenia, and osteoporosis.
  • the present disclosure provides methods of treating bone 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 bone disease is selected from osteomalacia, osteoporosis, osteogenesis imperfecta, fibrodysplasia ossificans progressive, corticosteroid-induced bone loss, bone loss associated with androgen-deprivation therapy, bone fracture, bone loss in cancer, bone metastasis and osteolytic lesions.
  • the present disclosure provides for a method of inhibiting loss of muscle mass and/or muscle function in a subject comprising administering an effective amount of a bifunctional antagonist molecule into the subject.
  • the modulation may attenuate the loss of the muscle mass and/or function of said subject by at least 5%, 10%, at least 25%, at least 50%, at least 75%, or at least 90%.
  • the inhibition of loss of muscle mass and function can be evaluated by using imaging techniques and physical strength tests.
  • imaging techniques for muscle mass evaluation include Dual-Energy X-Ray Absorptiometry (DEXA), Magnetic Resonance Imaging (MRI), and Computed Tomography (CT).
  • Examples of muscle function tests include grip strength test, stair climbing test, short physical performance battery (SPPB) and 6-minute walk, as well as maximal inspiratory pressure (MIP) and maximal expiratory pressure (MEP) that are used to measure respiratory muscle strength.
  • the present disclosure provides for a method of treating cancer cells as well as cancer cell metastasis in a subject, comprising administering to said subject a therapeutically effective amount (either as monotherapy or in a combination therapy regimen) of a bifunctional antagonist molecule of the present disclosure in pharmaceutically acceptable carrier, wherein such administration inhibits the growth and/or proliferation of a cancer cell.
  • a bifunctional antagonist molecule of the present disclosure is useful in treating disorders characterized as cancer.
  • Such disorders include, but are not limited to solid tumors, such as cancers of the breast, respiratory tract, brain, reproductive organs, digestive tract, urinary tract, eye, liver, skin, head and neck, thyroid, parathyroid and their distant metastases, lymphomas, sarcomas, multiple myeloma and leukemia.
  • solid tumors such as cancers of the breast, respiratory tract, brain, reproductive organs, digestive tract, urinary tract, eye, liver, skin, head and neck, thyroid, parathyroid and their distant metastases, lymphomas, sarcomas, multiple myeloma and leukemia.
  • breast cancer include, but are not limited to invasive ductal carcinoma, invasive lobular carcinoma, ductal carcinoma in situ, and lobular carcinoma in situ.
  • cancers of the respiratory tract include, but are not limited to, small-cell and non-small-cell lung carcinoma, as well as bronchial adenoma and pleuropulmonary blastoma.
  • brain cancers include, but are not limited to, brain stem and hypophthalmic glioma, cerebellar and cerebral astrocytoma, medulloblastoma, ependymoma, as well as neuroectodermal and pineal tumor.
  • Tumors of the male reproductive organs include, but are not limited to, prostate and testicular cancer.
  • Tumors of the female reproductive organs include, but are not limited to endometrial, cervical, ovarian, vaginal, and vulvar cancer, as well as sarcoma of the uterus.
  • Tumors of the digestive tract include, but are not limited to anal, colon, colorectal, esophageal, gallbladder, gastric, pancreatic, rectal, smallintestine, and salivary gland cancers.
  • Tumors of the urinary tract include, but are not limited to bladder, penile, kidney, renal pelvis, ureter, and urethral cancers.
  • Eye cancers include, but are not limited to, intraocular melanoma and retinoblastoma.
  • liver cancers include, but are not limited to, hepatocellular carcinoma (liver cell carcinomas with or without fibrolamellar variant), cholangiocarcinoma (intrahepatic bile duct carcinoma), and mixed hepatocellular cholangiocarcinoma.
  • Skin cancers include, but are not limited to squamous cell carcinoma, Kaposi's sarcoma, malignant melanoma, Merkel cell skin cancer, and non-melanoma skin cancer.
  • Head-and-neck cancers include, but are not limited to nasopharyngeal cancer, and lip and oral cavity cancer.
  • Lymphomas include, but are not limited to AIDS-related lymphoma, nonHodgkin's lymphoma, cutaneous T-cell lymphoma, Hodgkin's disease, and lymphoma of the central nervous system.
  • Sarcomas include, but are not limited to, sarcoma of the soft tissue, osteosarcoma, malignant fibrous histiocytoma, lymphosarcoma, and rhabdomyosarcoma.
  • Leukemias include, but are not limited to acute myeloid leukemia, acute lymphoblastic leukemia, chronic lymphocytic leukemia, chronic myelogenous leukemia, and hairy cell leukemia.
  • the cancer will be a cancer with high expression of TNF-a and TGF-p, e.g., pancreatic cancer, gastric cancer, ovarian cancer, colorectal cancer, melanoma, leukemia, lung cancer, prostate cancer, brain cancer, bladder cancer, and head-neck cancer.
  • “Therapeutically effective amount” or “therapeutically effective dose” refers to that amount of the therapeutic agent being administered which will relieve to some extent one or more of the symptoms of the disorder being treated.
  • a therapeutically effective dose can be estimated initially from cell culture assays by determining an IC 5 o-
  • a dose can then be formulated in animal models to achieve a circulating plasma concentration range that includes the IC 5 o 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 a bifunctional antagonist molecule of the disclosure can be 0.001 to 100 mg/kg, 0.001 to 90 mg/kg, 0.001 to 80 mg/kg, 0.001 to 70 mg/kg, 0.001 to 60 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, 0.010 to 30 mg/kg, 0.010 to 20 mg/kg, 0.010 to 10 mg/kg, 0.010 to 5 mg/kg, 0.010 to 4 mg/kg, 0.010 to 3 mg/kg, 0.010 to 2 mg/kg,
  • dosage values may vary with the type and severity of the conditions to be alleviated. 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.
  • the total dose administered will achieve a plasma antibody concentration in the range of, e.g., about 1 to 1000 pg/ml, about 1 to 750 pg/ml, about 1 to 500 pg/ml, about 1 to 250 pg/ml, about 10 to 1000 pg/ml, about 10 to 750 pg/ml, about 10 to 500 pg/ml, about 10 to 250 pg/ml, about 20 to 1000 pg/ml, about 20 to 750 pg/ml, about 20 to 500 pg/ml, about 20 to 250 pg/ml, about 30 to 1000 pg/ml, about 30 to 750 pg/ml, about 30 to 500 pg/ml, about 30 to 250 pg/ml.
  • 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 5 o (the dose lethal to 50% of the population) and the ED 5 o (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 LD50/ED50.
  • Compositions that exhibit large therapeutic indices are generally preferred.
  • the dosing frequency of the administration of the bifunctional antagonist molecule 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 weekly or monthly, until a desired therapeutic result is achieved.
  • Exemplary dosing frequencies include, but are not limited to: once weekly without break; once weekly, every other week; 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; 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 bifunctional antagonist molecule 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 bifunctional antagonist molecule 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 bifunctional antagonist molecule 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 bifunctional antagonist molecule 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 consecutive times by said subject
  • the present disclosure provides a method for treating cancer or cancer metastasis in a subject, comprising administering a therapeutically effective amount of the pharmaceutical compositions of the invention in combination with a second therapy selected from the group consisting of: cytotoxic chemotherapy, immunotherapy, small molecule kinase inhibitor targeted therapy, surgery, radiation therapy, and stem cell transplantation.
  • a second therapy selected from the group consisting of: cytotoxic chemotherapy, immunotherapy, small molecule kinase inhibitor targeted therapy, surgery, radiation therapy, and stem cell transplantation.
  • the combination therapy may comprise administering to the subject a therapeutically effective amount of immunotherapy, including, but are not limited to, treatment using depleting antibodies to specific tumor antigens; treatment using antibody-drug conjugates; treatment using agonistic, antagonistic, or blocking antibodies to co-stimulatory or co-inhibitory molecules (immune checkpoints) such as CTLA-4, RANKL, PD-L1 , OX-40, CD137, TIGIT, GITR, LAG3, TIM-3, CD47, SIRPa, ICOS, and VISTA; treatment using bispecific T cell engaging antibodies (BiTE®) such as blinatumomab: treatment involving administration of biological response modifiers such as TNF family, IL-1 , IL-4, IL-7, IL-12, IL-15, IL-17, IL-21 , IL-22, GM- CSF, IFN-a, IFN-p and IFN-y; treatment using therapeutic vaccines such as sipuleucel-T; treatment
  • immunotherapy
  • the combination therapy comprises administering a bifunctional antagonist molecule and the second agent composition simultaneously, either in the same pharmaceutical composition or in separate pharmaceutical composition.
  • a bifunctional antagonist molecule composition and the second agent composition are administered sequentially, i.e., a bifunctional antagonist molecule composition is administered either prior to or after the administration of the second agent composition.
  • the administrations of a bifunctional antagonist molecule composition and the second agent composition are concurrent, i.e., the administration period of a bifunctional antagonist molecule composition and the second agent composition overlap with each other.
  • the administrations of a bifunctional antagonist molecule composition and the second agent composition are non-concurrent.
  • the administration of a bifunctional antagonist molecule composition is terminated before the second agent composition is administered.
  • the administration second agent composition is terminated before a bifunctional antagonist molecule composition is administered.
  • Example 1 The bifunctional antagonist molecules of the present disclosure can be prepared according to recombinant DNA techniques that are well known to those of skill in the art. In this example, the preparation of the bifunctional antagonist molecules is generally described.
  • cDNAs encoding various novel bifunctional antagonist polypeptides were generated via gene synthesis and subcloned into mammalian expression plasmids.
  • CHO cells were transiently or stably transfected with the mammalian expression plasmids encoding the individual bifunctional polypeptide antagonists.
  • Transiently transfected CHO cells or stably transfected CHO pools were grown in high-density suspension cultures in a CO 2 shaking incubator at 32°C for 5-8 days. The culture media were collected after passing through a 0.22pm filter unit (Millipore Corporation, MA).
  • the recombinantly expressed bifunctional polypeptides were purified from the culture media via Protein A affinity chromatography using an AKTA PFLC system (GE Healthcare).
  • Binding activities of individual bifunctional antagonists to human ligands or target proteins were measured by biolayer interferometry (BLI) using Octet RED96 (ForteBIO, Pall Corporation, USA). Binding analysis was performed by first capturing the polypeptide bifunctional antagonists to biosensors followed by two baseline steps in 1x kinetic buffer. The bifunctional antagonists-captured biosensors were then submerged in wells containing different concentrations of specific individual ligand, such as RANKL, Activin A, activin B, Activin AB, myostatin, TGF-pi , TGF-P2 or TGF-P3, for 6 min association followed by 6 min of dissociation time in 1x kinetic buffer.
  • specific individual ligand such as RANKL, Activin A, activin B, Activin AB, myostatin, TGF-pi , TGF-P2 or TGF-P3, for 6 min association followed by 6 min of dissociation time in 1x kinetic buffer.
  • the bifunctional antagonists-captured sensors were also dipped in wells containing 1x kinetic buffer to allow single reference subtraction in order to compensate for the natural dissociation of captured bifunctional antagonists.
  • the binding sensorgrams were collected using the 8-channel detection mode on the Octet RED96 biosensor. Data were acquired and analyzed using the data acquisition software v11 .1 (ForteBIO, Pall Corporation, USA).
  • bifunctional antagonist molecules A112, A113 and A114 were examined using BLI analysis. As depicted in Table 9, bifunctional polypeptide antagonists A112, A113 and A114 were able to selectively bind to RANKL, Activin A, Activin B, Activin AB and myostatin with high affinity.
  • A239 and A240 were examined using BLI analysis. As shown in Table 10, A239 and A240 are able to bind RANKL, TGF-pi and TGF-P3 with high affinity.
  • Smad2/3 signaling assay An engineered luciferase reporter cell line, C2C12- CAGA-luc, capable of sensing Smad2/3 signaling was used to measure activin A, activin B, Activin AB, myostatin and GDF-1 1 signaling activities in cell cultures.
  • bifunctional antagonists To measure neutralizing activities of bifunctional antagonists, 2 nM of human ligand (i.e., human activin A, activin B, Activin AB, myostatin, and GDF-1 1 , respectively) was preincubated with increasing concentrations of each bifunctional antagonist at 0.00004 nM, 0.0004 nM, 0.004 nM, 0.04 nM, 0.4 nM, 4 nM, 40 nM and 400 nM for 1 hour at room temperature. Subsequently, the reaction mixtures were added to the C2C12-CAGA-luc cell cultures.
  • human activin A i.e., human activin A, activin B, Activin AB, myostatin, and GDF-1 1 , respectively
  • bifunctional antagonist A1 12 strongly neutralize Activin A, Activin B, Activin AB and myostatin in cell-based assays.
  • A1 12 a representative bifunctional antagonist capable of simultaneously sequestering RANKL and activin was evaluated in comparison to anti-RANKL antibody and ActRIIA-Fc, respectively, for its ability to inhibit osteoclastogenesis mediated by RANKL and activin A in RAW 246.7 cells.
  • A240 a representative bifunctional antagonist capable of simultaneously neutralizing RANKL and TGF-p was examined in comparison to anti-RANKL antibody and TGFRII-Fc, respectively, for its ability to suppress osteoclastogenesis induced by RANKL and TGF-p in RAW 246.7 cells.
  • RAW 246.7 cell-based osteoclast formation assay was examined in comparison to anti-RANKL antibody and ActRIIA-Fc, respectively, for its ability to inhibit osteoclastogenesis mediated by RANKL and activin A in RAW 246.7 cells.
  • RAW 246.7 cells were grown in RPMI-1640 medium supplemented with 10% FBS in 6-well culture plates and were maintained in a CO2 incubator at 37°C. To evaluate the effect of A112, RAW 246.7 cultures were incubated in the presence or absence of exogenously added agents as follows: (1 ) (1 ) No addition (control), (2) 100 ng/mL RANKL, (3) 100 ng/mL activin A, (4) 100 ng/mL RANKL and 100 ng/mL activin A, (5) 100 ng/mL RANKL, 100 ng/mL activin A and 2.5 ug/mL anti-RANKL antibody, (6) 100 ng/mL RANKL, 100 ng/mL activin A and 2.5 ug/mL TGFRII-Fc, and (7) 100 ng/mL RANKL, 100 ng/mL activin A and 2.5 ug/mL A1 12.
  • RAW 246.7 cultures were incubated in the presence or absence of various exogenously added agents as follows: (1 ) No addition (control), (2) 100 ng/mL RANKL, (3) 5 ng/mL TGF-pi , (4) 100 ng/mL RANKL and 5 ng/mL TGF- 1 , (5) 100 ng/mL RANKL, 5 ng/mL TGF- 1 and 2.5 ug/mL anti- RANKL antibody, (6) 100 ng/mL RANKL, 5 ng/mL TGF- 1 and 2.5 ug/mL TGFRII-Fc, and (7) 100 ng/mL RANKL, 5 ng/mL TGF-pi and 2.5 ug/mL A240.
  • the RAW 246.7 cultures were subjected to TRAP staining using a trap staning kit (Sigma) by following the Manufacturer’s instructions.
  • Osteoclast formation defined as TRAP staning-positve multinucleated cells containg 3 or more cell nuclei and the number of osteoclasts were counted. Representative osteoclast formation images were photographed with a inverted microscope quipped with digital camera.
  • FIG. 7 depicts the photograph images of the control RAW 246.7 cell culture and RAW 246.7 cell cultures treated with different conditions with arrows pointing to the osteoclast formations.
  • no osteoclast formation was detected in the RAW 246.7 culture (FIG. 7, panel A).
  • osteoclasts were detected in the RAW 246.7 cultures as TRAP-positive multinucleated cells (FIG. 7, panels B and C).
  • TRAP-positive multinucleated cells FIG. 7, panels B and C.
  • multinucleated TRAP-positive cells were detected in higher density in the RAW 246.7 culture (FIG.
  • FIG. 9 depicts the photograph images of the control RAW 246.7 cell culture and RAW 246.7 cell cultures treated with different conditions with arrows pointing to the osteoclast formations. Under control condition, no osteoclast formation was detected in the RAW 246.7 culture (FIG. 9, panel A). After 5-day treatment with RANKL or TGF-pi , osteoclasts were appeared in the RAW 246.7 cultures as TRAP-positive multinucleated cells (FIG. 9, panels B and C).
  • a mouse model of glucocorticoid-induced bone loss was used to evaluate the effectiveness of parallel inhibition of activin and RANKL in preventing bone loss.
  • co-admisnistration of ActRIIA-Fc and anti-murine antibody was used as a surrogate treatment to mimic the action of bifunctional antagonist A112. It is important note that due to the lack of high homology between human RANKL and rodent RANKL, the bifunctional anatgonists of the present invention designed to bind human RANKL do not interact with the endogenous RANKL in rodents.
  • Anti-murine RANKL antibody was purchased from BioxCelL Recombinant ActRIIA-Fc with >98% purity was purified from medium of transiently transfected CHO cultures with protein A chromatography followed by size exclusion chromatography.
  • Ten-week-old female CD1 mice were purchased from Envigo. The mice were fed with dexamethasone (DEX) via drinking water at a dose of 2.4 mg/kg/day (DEX-fed mice).
  • DEX dexamethasone
  • the DEX-fed mice were treated once per week for a period of 4 weeks.
  • Aged- matched female CD1 mice that did not receive dexamethasone (DEX) in the drinking water served as the control group (n 8).
  • FIG. 11 shows the representative microCT images of bone volume of the distal femurs in the different mouse groups: (A) Control, (B) DEX (Dexamethasome fed), (C) DEX plus ActRIIA-Fc treatment, (D) DEX plus anti-murine RANKL antibody treatment, and (E) DEX plus the combination treatment with ActRIIA-Fc and anti-murine RANKL antibody. Note the marked bone loss resulting from dexamethasone (panel B vs. panel A).
  • FIG. 12 shows the microCT imaging analysis on the average trabecular bone thickness of the distal femurs in the different mouse groups as illustrated in the figure.
  • the data indicate that compared to normal control, there was a dramatic bone loss in the dexamethasome-fed mice.
  • the combination treatment with with ActRIIA-Fc and anti-murine RANKL antibody more effectively compared to treatment with ActRIIA-Fc alone or anti-murine RANKL antibody alone, as the combination treatment not only fully ameliorated bone loss but its effect in countering bone loss was statistically greater than that of ActRIIA-Fc or anti-murine RANKL antibody.
  • the data suggest that the combination treatment enhanced the bone mass in the dexamethasome-fed mice to a level that was statistically greater than normal control.
  • bifunctional antagonist A112 as well as other novel bifunctional antagonists of activin and RANKL as disclosed in the present invention may represent a more efficacious approach to treating bone loss and fragility conditions in human patients.
  • SEQ ID NOs: 1 -9 are amino acid sequences of various Activin or Activin-related ligands.
  • SEQ ID NOs: 10 and 14 are amino acid sequences of a heavy chain of various antibodies which specifically binds to Activin or Activin-related ligand.
  • SEQ ID NOs: 1 1 and 15 are amino acid sequences of a light chain of various antibodies which specifically binds to Activin or Activin-related ligand.
  • SEQ ID NOs: 12 and 16 are amino acid sequences of a heavy chain variable region of various antibodies which specifically binds to Activin or Activin-related ligand.
  • SEQ ID NOs: 13 and 17 are amino acid sequences of a light chain variable region of various antibodies which specifically binds to Activin or Activin-related ligand.
  • SEQ ID NOs: 18-19 are amino acid sequences of various TGF-p ligands.
  • SEQ ID NO: 20 is an amino acid sequence of a heavy chain of an antibody which specifically binds to TGF-p ligand.
  • SEQ ID NO: 21 is an amino acid sequences of a light chain of an antibody which specifically binds to TGF-p ligand.
  • SEQ ID NO: 22 is an amino acid sequence of a heavy chain variable region of an antibody which specifically binds to TGF-p ligand.
  • SEQ ID NO: 23 is an amino acid sequences of a light chain variable region of an antibody which specifically binds to TGF-p ligand.
  • SEQ ID NO: 24 is an amino acid sequence of a heavy chain of an antibody which specifically binds to RANKL ligand.
  • SEQ ID NO: 25 is an amino acid sequences of a light chain of an antibody which specifically binds to RANKL ligand.
  • SEQ ID NO: 26 is an amino acid sequence of a heavy chain variable region of an antibody which specifically binds to RANKL ligand.
  • SEQ ID NO: 27 is an amino acid sequences of a light chain variable region of an antibody which specifically binds to RANKL ligand.
  • SEQ ID NO: 28 is an amino acid sequence of Human Osteoprotegerin (OPG).
  • SEQ ID NOs: 29-37 are the amino acid sequences of a heavy chain of a bifunctional antagonist molecule that specifically binds to Activin or Activin-related ligand and RANKL.
  • SEQ ID NOs: 38-39 are the amino acid sequences of a heavy chain of a bifunctional antagonist molecule that specifically binds to TGF-p ligand and RANKL.
  • SEQ ID NOs: 40-48 are the amino acid sequences of various bifunctional antagonist molecules that specifically binds to Activin or Activin-related ligand and that specifically binds to OPG.
  • SEQ ID NOs: 49-50 are the amino acid sequences of a heavy chain of a bifunctional antagonist molecule that specifically binds to Activin or Activin-related ligand and OPG.
  • SEQ ID NOs: 51-52 are the amino acid sequences of various bifunctional antagonist molecules that specifically binds to TGF-p ligand and that specifically binds to OPG.
  • SEQ ID NO: 53 is the amino acid sequences of a heavy chain of a bifunctional antagonist molecule that specifically binds to TGF-p ligand and OPG.
  • SEQ ID NO: 54 is the amino acid sequence of a heavy chain of a bifunctional antagonist molecule that specifically binds to Activin or Activin-related ligand and RANKL.
  • SEQ ID NO: 55 is the amino acid sequence of a light chain of a bifunctional antagonist molecule that specifically binds to Activin or Activin-related ligand and RANKL.
  • SEQ ID NO: 56 is the amino acid sequence of a heavy chain of a bifunctional antagonist molecule that specifically binds to Activin or Activin-related ligand and RANKL.
  • SEQ ID NO: 57 is the amino acid sequence of a light chain of a bifunctional antagonist molecule that specifically binds to Activin or Activin-related ligand and RANKL.
  • SEQ ID NO: 58 is the amino acid sequence of a heavy chain of a bifunctional antagonist molecule that specifically binds to TGF-p ligand and RANKL.
  • SEQ ID NO: 59 is the amino acid sequence of a light chain of a bifunctional antagonist molecule that specifically binds to TGF-p ligand and RANKL.
  • SEQ ID NOs: 60-79 are the amino acid sequences of various peptide linker sequences.
  • KSDEPVCASDNATYASECAMKEAACSSGVLLEVKHSGSCN (SEQ ID NO: 5)
  • RQECVATKENPQVYFCCCEGNFCNERFTHLPEAGGPEVTYEPPPTAPT SEQ ID NO: 6
  • RQECVATEENPQVYFCCCEGNFCNERFTHLPEAGGPEVTYEPPPTAPT SEQ ID NO: 7
  • Anti-Activin A antibody light chain amino acid sequence SYEVTQAPSVSVSPGQTASITCSGDKLGDKYACWYQQKPGQSPVLVIYQDSKRPSGIPERFSG SNSGNTATLTISGTQAMDEADYYCQAWDSSTAVFGGGTKLTVLRTVAAPSVFIFPPSDEQLKS GTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKH
  • Anti-Activin A antibody heavy chain variable region amino acid sequence
  • Anti-Activin A antibody light chain variable region amino acid sequence
  • Anti-Activin A antibody heavy chain amino acid sequence
  • Anti-Activin A antibody light chain amino acid sequence
  • Anti-Activin A antibody heavy chain variable region amino acid sequence
  • Anti-Activin A antibody light chain variable region amino acid sequence
  • TGF-8 Receptor ll-ECD isoform 1 TGF-8 RIIB-ECD
  • TGF-B Receptor ll-ECD isoform 2 TGF-B RIIA-ECD
  • Anti-RANKL antibody heavy chain variable region amino acid sequence EVQLLESGGGLVQPGGSLRLSCAASGFTFSSYAMSWVRQAPGKGLEWVSGITGSGGSTYYA
  • VFSCSVMHEALHNHYTQKSLSLSPGK (SEQ ID NO: 54)
  • VFSCSVMHEALHNHYTQKSLSLSPGK (SEQ ID NO: 56)
EP21892613.7A 2020-11-11 2021-11-05 Bifunktionelle antagonisten von activin/tgf-beta und rankl und verwendungen davon Pending EP4243931A1 (de)

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