Classifications

• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K16/00—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies
  • C07K16/18—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies against material from animals or humans
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P37/00—Drugs for immunological or allergic disorders
  • A61P37/02—Immunomodulators
  • A61P37/06—Immunosuppressants, e.g. drugs for graft rejection
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K16/00—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies
  • C07K16/42—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies against immunoglobulins
  • C07K16/4208—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies against immunoglobulins against an idiotypic determinant on Ig
• • 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
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K2317/00—Immunoglobulins specific features
  • C07K2317/20—Immunoglobulins specific features characterized by taxonomic origin
  • C07K2317/24—Immunoglobulins specific features characterized by taxonomic origin containing regions, domains or residues from different species, e.g. chimeric, humanized or veneered
• • 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
  • C07K2317/30—Immunoglobulins specific features characterized by aspects of specificity or valency
  • C07K2317/33—Crossreactivity, e.g. for species or epitope, or lack of said crossreactivity
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K2317/00—Immunoglobulins specific features
  • C07K2317/50—Immunoglobulins specific features characterized by immunoglobulin fragments
  • C07K2317/52—Constant or Fc region; Isotype
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K2317/00—Immunoglobulins specific features
  • C07K2317/50—Immunoglobulins specific features characterized by immunoglobulin fragments
  • C07K2317/56—Immunoglobulins specific features characterized by immunoglobulin fragments variable (Fv) region, i.e. VH and/or VL
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K2317/00—Immunoglobulins specific features
  • C07K2317/50—Immunoglobulins specific features characterized by immunoglobulin fragments
  • C07K2317/56—Immunoglobulins specific features characterized by immunoglobulin fragments variable (Fv) region, i.e. VH and/or VL
  • C07K2317/565—Complementarity determining region [CDR]
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K2317/00—Immunoglobulins specific features
  • C07K2317/50—Immunoglobulins specific features characterized by immunoglobulin fragments
  • C07K2317/56—Immunoglobulins specific features characterized by immunoglobulin fragments variable (Fv) region, i.e. VH and/or VL
  • C07K2317/567—Framework region [FR]
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K2317/00—Immunoglobulins specific features
  • C07K2317/50—Immunoglobulins specific features characterized by immunoglobulin fragments
  • C07K2317/56—Immunoglobulins specific features characterized by immunoglobulin fragments variable (Fv) region, i.e. VH and/or VL
  • C07K2317/569—Single domain, e.g. dAb, sdAb, VHH, VNAR or nanobody®
• • 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
  • C07K2317/72—Increased effector function due to an Fc-modification
• • 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
• • 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
  • C07K2317/94—Stability, e.g. half-life, pH, temperature or enzyme-resistance
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K2319/00—Fusion polypeptide
  • C07K2319/31—Fusion polypeptide fusions, other than Fc, for prolonged plasma life, e.g. albumin

Definitions

• the present invention relates to albumin-binding polypeptides, and methods of using albumin-binding polypeptides, for example, to improve the half-life of other molecules.
• Plasma proteins are eliminated from circulation by two primary mechanisms: renal filtration of molecules below 60 kDa, and micropinocytosis by endothelial cells. Proteins below the renal threshold are rapidly cleared from circulation resulting in a half-life of 1 day or less, while proteins larger than the renal threshold are primarily cleared through micropinocytosis with half-lives around 3-5 days.
• Albumin and immunoglobulin G are proteins with long plasma half-lives of around 15-30 days due to their large size (66 and 150 kDa respectively) and their ability to recycle from endothelial micropinocytosis through pH dependent binding to the neonatal Fc receptor (FcRn).
• Single-domain antibody VHH domains are ideal albumin binding entities because they are small domains about 12-15 kDa in size, they are single domains composed of a single polypeptide that can be easily fused to another protein or peptide by recombinant means, they are readily humanized to reduce the potential for immunogenicity, and many naturally bind protein A for affinity purification.
• Embodiment 1 A polypeptide comprising at least one VHH domain that binds albumin, wherein at least one VHH domain that binds albumin comprises a CDR1 sequence selected from SEQ ID NOs: 5-8, a CDR2 sequence selected from SEQ ID NOs: 9-21, and a CDR3 sequence of SEQ ID NO: 22.
• Embodiment 2 The polypeptide of embodiment 1, wherein each VHH domain that binds albumin comprises, independently, a CDR1 sequence selected from SEQ ID NOs: 5- 8, a CDR2 sequence selected from SEQ ID NOs: 9-21, and a CDR3 sequence of SEQ ID NO: 22.
• Embodiment 3 The polypeptide of embodiment 1 or embodiment 2, wherein at least one VHH domain that binds albumin comprises CDR1, CDR2, and CDR3 sequences selected from: SEQ ID NOs: 5, 9, and 22; SEQ ID NOs: 5, 10, and 22; SEQ ID NOs: 5, 11, and 22; SEQ ID NOs: 5, 12, and 22; SEQ ID NOs: 5, 13, and 22; SEQ ID NOs: 5, 14, and 22; SEQ ID NOs: 5, 15, and 22; SEQ ID NOs: 6, 15, and 22; SEQ ID NOs: 7, 15, and 22; SEQ ID NOs: 8, 15, and 22; SEQ ID NOs: 6, 16, and 22; SEQ ID NOs: 6, 17, and 22; SEQ ID NOs: 6, 18, and 22; SEQ ID NOs: 6, 19, and 22; SEQ ID NOs: 6, 20, and 22; and SEQ ID NOs: 6, 21, and 22.
• Embodiment 4 The polypeptide of embodiment 3, wherein each VHH domain that binds albumin comprises, independently, CDR1, CDR2, and CDR3 sequences selected from: SEQ ID NOs: 5, 9, and 22; SEQ ID NOs: 5, 10, and 22; SEQ ID NOs: 5, 11, and 22; SEQ ID NOs: 5, 12, and 22; SEQ ID NOs: 5, 13, and 22; SEQ ID NOs: 5, 14, and 22; SEQ ID NOs: 5, 15, and 22; SEQ ID NOs: 6, 15, and 22; SEQ ID NOs: 7, 15, and 22; SEQ ID NOs: 8, 15, and 22; SEQ ID NOs: 6, 16, and 22; SEQ ID NOs: 6, 17, and 22; SEQ ID NOs: 6, 18, and 22; SEQ ID NOs: 6, 19, and 22; SEQ ID NOs: 6, 20, and 22; and SEQ ID NOs: 6, 21, and 22.
• Embodiment 5 The polypeptide of any one of embodiments 1-4, wherein at least one VHH domain that binds albumin is humanized.
• Embodiment 6 The polypeptide of embodiment 5, wherein each VHH domain that binds albumin is humanized.
• Embodiment 7 The polypeptide of any one of embodiments 1-6, wherein at least one VHH domain that binds albumin comprises a sequence at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99% identical to a sequence selected from SEQ ID NOs: 23-43 and 71-74.
• Embodiment 8 The polypeptide of embodiment 7, wherein each VHH domain that binds albumin comprises a sequence at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99% identical to a sequence selected from SEQ ID NOs: 23- 43 and 71-74.
• Embodiment 9. The polypeptide of any one of embodiments 1-7, wherein at least one VHH domain that binds albumin comprises a sequence selected from SEQ ID NOs: 23-43 and 71-74.
• Embodiment 10 The polypeptide of any one of embodiments 1-9, wherein each VHH domain that binds albumin comprises a sequence selected from SEQ ID NOs: 23-43 and 71-74.
• Embodiment 11 The polypeptide of any one of embodiments 1-10, wherein at least one VHH domain that binds albumin binds human albumin and at least one albumin selected from cynomolgus monkey, mouse, and rat albumin.
• Embodiment 12 The polypeptide of any one of embodiments 1-11, wherein each VHH domain that binds albumin binds human albumin and at least one albumin selected from cynomolgus monkey, mouse, and rat albumin.
• Embodiment 13 The polypeptide of any one of embodiments 1-12, wherein at least one VHH domain that binds albumin binds human, cynomolgus monkey, mouse, and rat albumin.
• Embodiment 14 The polypeptide of any one of embodiments 1-13, wherein each VHH domain that binds albumin binds human, cynomolgus monkey, mouse, and rat albumin.
• Embodiment 15 The polypeptide of any one of embodiments 1-14, wherein at least one VHH domain that binds albumin binds human albumin with an affinity of less than 5 nM, less than 2 nM, less than 1 nM, or less than 0.5 nM.
• Embodiment 16 The polypeptide of any one of embodiments 1-15, wherein at least one VHH domain that binds albumin binds each of human, cynomolgus monkey, mouse, and rat albumin with an affinity of less than 5 nM, less than 2 nM, less than 1 nM, or less than 0.5 nM.
• Embodiment 17 The polypeptide of any one of embodiments 1-16, wherein each VHH domain that binds albumin binds human albumin with an affinity of less than 5 nM, less than 2 nM, less than 1 nM, or less than 0.5 nM.
• Embodiment 18 The polypeptide of any one of embodiments 1-17, wherein each VHH domain that binds albumin binds each of human, cynomolgus monkey, mouse, and rat albumin with an affinity of less than 5 nM, less than 2 nM, less than 1 nM, or less than 0.5 nM.
• Embodiment 19 The polypeptide of any one of embodiments 1-18, wherein the each VHH domain that binds albumin does not bind albumin domain 3.
• Embodiment 20 The polypeptide of any one of embodiments 1-19, wherein the each VHH domain that binds albumin does not interfere with binding of albumin to FcRn.
• Embodiment 21 The polypeptide of any one of embodiments 1-20, wherein the polypeptide comprises at least one binding domain that binds a protein other than albumin.
• Embodiment 22 The polypeptide of embodiment 21, wherein at least one binding domain that binds a protein other than albumin is a VHH.
• Embodiment 23 The polypeptide of embodiment 22, wherein each binding domain that binds a protein other than albumin is a VHH.
• Embodiment 24 The polypeptide of embodiment 21, wherein at least one binding domain that binds a protein other than albumin comprises a heavy chain variable region and a light chain variable region.
• Embodiment 25 The polypeptide of embodiment 24, wherein each binding domain that binds a protein other than albumin comprises a heavy chain variable region and a light chain variable region.
• Embodiment 26 The polypeptide of any one of embodiments 21-25, wherein at least one binding domain that binds a protein other than albumin is a binding domain of a therapeutic antibody.
• Embodiment 27 The polypeptide of embodiment 26, wherein each binding domain that binds a protein other than albumin is a binding domain of a therapeutic antibody.
• Embodiment 28 The polypeptide of embodiment 26 or embodiment 27, wherein the therapeutic antibody is useful for treating a disease or disorder selected from an autoimmune disease or disorder, an inflammatory disease or disorder, an infection, and cancer.
• Embodiment 29 The polypeptide of any one of embodiment 1-28, wherein the polypeptide comprises an amino acid sequence of a therapeutic protein.
• Embodiment 30 The polypeptide of embodiment 29, wherein the therapeutic protein is useful for treating a disease or disorder selected from an autoimmune disease or disorder, an inflammatory disease or disorder, an infection, and cancer.
• Embodiment 31 The polypeptide of any one of embodiments 1-30, wherein the polypeptide comprises an Fc region.
• Embodiment 32 The polypeptide of embodiment 31, wherein the Fc region binds FcRn.
• Embodiment 33 The polypeptide of embodiment 31 or embodiment 32, wherein the Fc region is an IgGl Fc region.
• Embodiment 34 The polypeptide of any one of embodiments 31-33, wherein the Fc region comprises one or more substitutions that enhance half-life.
• Embodiment 35 The polypeptide of embodiment 34, wherein the Fc region comprises one or more substitutions that enhance FcRn binding at at least one pH and/or reduce dissociation rate of Fc and FcRn.
• Embodiment 36 The polypeptide of any one of embodiments 31-35, wherein the Fc region comprises substitutions at one or more amino acid positions selected from 252, 254, 256,
• Embodiment 37 The polypeptide of embodiment 36, wherein the Fc region comprises substitutions at amino acid positions 252, 254, and 256; or amino acid positions 252 and 428; or amino acid positions 428 and 434.
• Embodiment 38 The polypeptide of embodiment 37, wherein the Fc region comprises substitutions M252Y, S254T, and T256E; M252Y and M428V; or M428L and N434S.
• Embodiment 39 The polypeptide of any one of embodiments 31-38, wherein the Fc region comprises a sequence selected from SEQ ID NOs: 47-68 and 85-87.
• Embodiment 40 The polypeptide of any one of embodiments 1-39, wherein the half-life of the polypeptide is greater than the half-life of the same polypeptide lacking a VHH domain that binds albumin.
• Embodiment 41 A pharmaceutical composition comprising the polypeptide of any one of embodiments 1-40 and a pharmaceutically acceptable carrier.
• Embodiment 42 An isolated nucleic acid that encodes the polypeptide of any one of embodiments 1-40.
• Embodiment 43 A vector comprising the nucleic acid of embodiment 42.
• Embodiment 44 A host cell comprising the nucleic acid of embodiment 42 or the vector of embodiment 43.
• Embodiment 45 A host cell that expresses the polypeptide of any one of embodiments 1-40.
• Embodiment 46 A method of producing the polypeptide of any one of embodiments 1-40, comprising incubating the host cell of embodiment 44 or embodiment 45 under conditions suitable for expression of the polypeptide.
• Embodiment 47 The method of embodiment 46, further comprising isolating the polypeptide.
• Embodiment 48 A method comprising administering to a subject the polypeptide of any one of embodiments 1-40, or the pharmaceutical composition of embodiment 41.
• Embodiment 49 A method of treating a disease or disorder comprising administering to a subject with the disease or disorder a pharmaceutically effective amount of the polypeptide of any one of embodiments 1-40, or the pharmaceutical composition of embodiment 41.
• Embodiment 50 The method of embodiment 49, wherein the disease or disorder is selected from an autoimmune disease or disorder, an inflammatory disease or disorder, an infection, and cancer.
• FIG. 1A-1C is a schematic of a monomeric single-domain antibody that binds albumin comprising an Fc with S364N, Y407N, and K409T mutations (sdAb-NNT-Fc).
• FIG. 1B-1C shows monovalent binding of 4A01-NNT-hFc (SEQ ID NOs: 23 and 68) to human serum albumin (HSA; IB) and murine serum albumin (MSA; 1C).
• FIG. 2A-2B FIG. 2A is a schematic showing the experimental design for biolayer interferometry assessing binding to albumin domain 3.
• FIG. 2B shows a biolayer interferometry trace showing 4A01-NNT-hFc (SEQ ID NOs: 23 and 68) does not bind to albumin domain 3, while 1C04 does.
• FIG. 3 A-3B FIG. 3 A is a schematic showing the experimental design for biolayer interferometry assessing B2M-FcRn binding to albumin.
• FIG. 3B is a biolayer interferometry trace showing 4A01-NNT-hFc (SEQ ID NOs: 23 and 68) and humanized 4A01v51-NNT-hFc do not block B2m-FcRn binding to albumin, while 1C04 does.
• FIG. 4A-4I shows an alignment of certain 4A01 humanized variants (SEQ ID NOs: 24-43).
• FIG. 4B-4C show human albumin (HSA) binding ELISA of certain 4A01 humanized variants.
• FIG. 4D-4E show cynomolgus monkey albumin (CSA) binding ELISA of certain 4A01 humanized variants.
• FIG. 4F-4G show murine albumin (MSA) binding ELISA of certain 4A01 humanized variants.
• FIG. 4H-4I show rat albumin (RS A) binding ELISA of certain 4A01 humanized variants.
• FIG. 5 A-5D show human albumin (HSA; FIG. 5 A), cynomolgus monkey albumin (CSA; FIG. 5B), murine albumin (MSA; FIG. 5C), and rat albumin (RS A; FIG. 5D) binding ELISA of humanized hz4A01v51.
• FIG. 6 shows various monospecific and multispecific single-domain antibody formats.
• Format (i) comprises two albumin-specific VHH domains (black) formatted as VHH-hlgG Fc (hlgG Fc is shown in grey).
• Format (ii) is a monovalent, albumin-specific VHH domain (black) formatted as VHH-hlgG -NNT-Fc (monomeric Fc, grey).
• Format (iii) is a bispecific polypeptide consisting of an albumin-binding VHH domain (black) and a non-albumin targeted VHH domain (grey) connected via glycine-serine linker.
• Format (iv) comprises two albuminspecific VHH domains (black) formatted as hlgGl Fc-VHH (hlgG Fc is shown in grey).
• Format (v) is a bispecific polypeptide, bivalent for each target, comprising albumin-specific VHH domains (black) fused to the C-terminus of the heavy chain of a non-albumin antibody (comprising a light chain and a heavy chain shown in grey), the heavy chain of such polypeptides may be formatted as VH-CHl-hlgG Fc-VHH.
• Format (vi) is a bispecific polypeptide, bivalent for each target, comprising albumin-specific VHH domains (black) fused to the N-terminus of the heavy chain of a non-albumin antibody (comprising a light chain and a heavy chain shown in grey), the heavy chain of such polypeptides may be formatted as VHH- VH-CHl-hlgG Fc.
• Format (vii) is a bispecific polypeptide, bivalent for each target, comprising albumin-specific VHH domains (black) fused to the between the CHI and Fc region of a nonalbumin antibody (comprising a light chain and a heavy chain shown in grey), the heavy chain of such polypeptides may be formatted as VH-CHl-VHH-hlgG Fc.
• Format (viii) is a bispecific polypeptide, bivalent for each target, comprising albumin-specific VHH domains (black) fused to the N-terminus of the light chain of a non-albumin antibody (comprising a light chain and a heavy chain shown in grey), the light chain of such polypeptides may be formatted as VHH-VL- CL.
• Format (ix) is a bispecific polypeptide, bivalent for each target, comprising albumin-specific VHH domains (black) fused to the C-terminus of the light chain of a non-albumin antibody (comprising a light chain and a heavy chain shown in grey), the light chain of such polypeptides may be formatted as VL-CL-VHH.
• FIG. 7A-7B shows binding of albumin-binding and non-albumin binding sdAb polypeptides to human albumin by ELISA.
• FIG. 7A shows binding at pH 7.4, while FIG. 7B shows binding at pH 6.
• Constructs in FIG. 7A-7B are formatted as described in FIG. 6(iii).
• FIG. 8 shows binding of a monovalent sdAb polypeptide (cx5009) to albumin of human, cynomolgus, mouse, or rat by ELISA at pH 7.4.
• Constructs in FIG. 9 are formatted as described in FIG. 6(ii).
• FIG. 9A-9D shows the in vivo pharmacokinetic (PK) profile of an albumin-binding bivalent VHH-hlgGl-xELL-Fc polypeptide (cxl 1956) compared to a non-targeted bivalent VHH-hlgGl-xELL-Fc polypeptide (cxl 1851).
• FIG. 9A and FIG. 9B show the serum PK profile in BALB/c mice dosed with 30 mg/kg of the test articles as determined by ELISA
• FIG. 9C and FIG. 9D show the serum PK profile in mice dosed with 0.3 mg/kg of the test articles.
• FIG. 9A and FIG. 9C show the absolute serum concentration in pg/mL
• FIG. 9B and FIG. 9D show the data normalized to the concentration 30 min post dosing (cMax). Constructs in FIG. 9A-9D are formatted as described in FIG. 6(i).
• FIG. 10 shows binding of human IgGl and human IgGl-xELL to recombinant biotinylated human FCGRT (FcRn)/B2M heterodimers by Bio-Layer Interferometry (BLI). Association and dissociation to FcRn was detected at pH 6 and pH 8.
• FIG. 11 A-l IB show binding of different monospecific and bispecific albumin-binding single domain antibodies formats to bind recombinant human albumin at neutral (7.4) pH (FIG. 11 A), and IL-4R (FIG. 1 IB) by ELISA.
• Monospecific molecules cxl2583 and cxl2584
• bispecific molecules are formatted at described in FIG. 6(v) (cxl2587 and cxl2594) or FIG 6(vii) (cxl2595 and cxl2596).
• FIG. 12A-12D show human albumin (HSA) binding ELISA of certain 4A01 humanized variants formatted as monovalent VHH-hlgGl-NNT-Fc polypeptides (FIG. 11 A- 1 IB) and bivalent VHH-hlgGl-xELL-Fc polypeptides (FIG. 12C-12D) at pH 6 (FIG. 12A and FIG. 12C) and pH 7.4 (FIG. 12B and 12D).
• HSA human albumin
• Embodiments provided herein relate to albumin-binding polypeptides and uses thereof.
• reference sample denotes a sample with at least one known characteristic that can be used as a comparison to a sample with at least one unknown characteristic.
• a reference sample can be used as a positive or negative indicator.
• a reference sample can be used to establish a level of protein and/or mRNA that is present in, for example, healthy tissue, in contrast to a level of protein and/or mRNA present in the sample with unknown characteristics.
• the reference sample comes from the same subject, but is from a different part of the subject than that being tested.
• the reference sample is from a tissue area surrounding or adjacent to the cancer.
• the reference sample is not from the subject being tested, but is a sample from a subject known to have, or not to have, a disorder in question. In some embodiments, the reference sample is from the same subject, but from a point in time before the subject developed cancer. In some embodiments, the reference sample is from a benign cancer sample, from the same or a different subject.
• a negative reference sample is used for comparison, the level of expression or amount of the molecule in question in the negative reference sample will indicate a level at which one of skill in the art will appreciate, given the present disclosure, that there is no and/or a low level of the molecule.
• a positive reference sample is used for comparison, the level of expression or amount of the molecule in question in the positive reference sample will indicate a level at which one of skill in the art will appreciate, given the present disclosure, that there is a level of the molecule.
• the terms “benefit”, “clinical benefit”, “responsiveness”, and “therapeutic responsiveness” as used herein in the context of benefiting from or responding to administration of a therapeutic agent, can be measured by assessing various endpoints, e.g., inhibition, to some extent, of disease progression, including slowing down and complete arrest; reduction in the number of disease episodes and/or symptoms; reduction in lesion size; inhibition (that is, reduction, slowing down or complete stopping) of disease cell infiltration into adjacent peripheral organs and/or tissues; inhibition (that is, reduction, slowing down or complete stopping) of disease spread; relief, to some extent, of one or more symptoms associated with the disorder; increase in the length of disease-free presentation following treatment, for example, progression-free survival; increased overall survival; higher response rate; and/or decreased mortality at a given point of time following treatment.
• a subject or cancer that is “non- responsive” or “fails to respond” is one that has failed to meet the above noted qualifications to be “responsive”.
• nucleic acid molecule refers to a polymer of nucleotides.
• polymers of nucleotides may contain natural and/or non-natural nucleotides, and include, but are not limited to, DNA, RNA, and PNA.
• Nucleic acid sequence refers to the linear sequence of nucleotides comprised in the nucleic acid molecule or polynucleotide.
• polypeptide and “protein” are used interchangeably to refer to a polymer of amino acid residues, and are not limited to a minimum length. Such polymers of amino acid residues may contain natural or non-natural amino acid residues, and include, but are not limited to, peptides, oligopeptides, dimers, trimers, and multimers of amino acid residues. Both full- length proteins and fragments thereof are encompassed by the definition.
• the terms also include post-expression modifications of the polypeptide, for example, glycosylation, sialylation, acetylation, phosphorylation, and the like.
• polypeptide refers to a protein which includes modifications, such as deletions, additions, and substitutions (generally conservative in nature), to the native sequence, as long as the protein maintains the desired activity. These modifications may be deliberate, as through site-directed mutagenesis, or may be accidental, such as through mutations of hosts which produce the proteins or errors due to PCR amplification.
• albumin refers to any native, mature albumin that results from processing of an albumin precursor in a cell.
• the term includes albumin from any vertebrate source, including mammals such as primates (e.g., humans and cynomolgus or rhesus monkeys) and rodents (e.g., mice and rats), unless otherwise indicated.
• the term also includes naturally- occurring variants of albumin, such as splice variants or allelic variants.
• a nonlimiting exemplary mature human albumin amino acid sequence is shown, e.g., in UniProt Accession No. P02768.2. See SEQ ID NO. 1.
• Nonlimiting exemplary murine, cynomolgus monkey, and rat albumin amino acid sequences are shown in SEQ ID NOs: 2-4.
• the term “specifically binds” to an antigen or epitope is a term that is well understood in the art, and methods to determine such specific binding are also well known in the art.
• a molecule is said to exhibit “specific binding” or “preferential binding” if it reacts or associates more frequently, more rapidly, with greater duration and/or with greater affinity with a particular cell or substance than it does with alternative cells or substances.
• a single-domain antibody (sdAb) or VHH-containing polypeptide “specifically binds” or “preferentially binds” to a target if it binds with greater affinity, avidity, more readily, and/or with greater duration than it binds to other substances.
• a sdAb or VHH-containing polypeptide that specifically or preferentially binds to an albumin epitope is a sdAb or VHH-containing polypeptide that binds this epitope with greater affinity, avidity, more readily, and/or with greater duration than it binds to other albumin epitopes or non-albumin epitopes. It is also understood by reading this definition that; for example, a sdAb or VHH-containing polypeptide that specifically or preferentially binds to a first target may or may not specifically or preferentially bind to a second target. As such, “specific binding” or “preferential binding” does not necessarily require (although it can include) exclusive binding. Generally, but not necessarily, reference to binding means preferential binding. “Specificity” refers to the ability of a binding protein to selectively bind an antigen.
• the term “inhibit” with regard to the activity of a target protein refers to a decrease in the activity of the protein. In some embodiments, “inhibit” refers to a decrease in activity compared to the protein in the absence of the modulator.
• epitope refers to a site on a target molecule (for example, an antigen, such as a protein, nucleic acid, carbohydrate or lipid) to which an antigen-binding molecule (for example, a sdAb or VHH-containing polypeptide) binds.
• a target molecule for example, an antigen, such as a protein, nucleic acid, carbohydrate or lipid
• an antigen-binding molecule for example, a sdAb or VHH-containing polypeptide
• Epitopes often include a chemically active surface grouping of molecules such as amino acids, polypeptides or sugar side chains and have specific three-dimensional structural characteristics as well as specific charge characteristics. Epitopes can be formed both from contiguous and/or juxtaposed noncontiguous residues (for example, amino acids, nucleotides, sugars, lipid moiety) of the target molecule.
• Epitopes formed from contiguous residues typically are retained on exposure to denaturing solvents whereas epitopes formed by tertiary folding typically are lost on treatment with denaturing solvents.
• An epitope may include but is not limited to at least 3, at least 5 or 8-10 residues (for example, amino acids or nucleotides). In some embodiments, an epitope is less than 20 residues (for example, amino acids or nucleotides) in length, less than 15 residues or less than 12 residues. Two antibodies may bind the same epitope within an antigen if they exhibit competitive binding for the antigen.
• an epitope can be identified by a certain minimal distance to a CDR residue on the antigen-binding molecule. In some embodiments, an epitope can be identified by the above distance, and further limited to those residues involved in a bond (for example, a hydrogen bond) between a residue of the antigen-binding molecule and an antigen residue.
• An epitope can be identified by various scans as well, for example an alanine or arginine scan can indicate one or more residues that the antigen-binding molecule can interact with. Unless explicitly denoted, a set of residues as an epitope does not exclude other residues from being part of the epitope for a particular antigen-binding molecule.
• a set of residues identified as an epitope designates a minimal epitope of relevance for the antigen, rather than an exclusive list of residues for an epitope on an antigen.
• a “nonlinear epitope” or “conformational epitope” comprises noncontiguous polypeptides, amino acids and/or sugars within the antigenic protein to which an antigen-binding molecule specific to the epitope binds.
• at least one of the residues will be noncontiguous with the other noted residues of the epitope; however, one or more of the residues can also be contiguous with the other residues.
• a “linear epitope” comprises contiguous polypeptides, amino acids and/or sugars within the antigenic protein to which an antigen-binding molecule specific to the epitope binds. It is noted that, in some embodiments, not every one of the residues within the linear epitope need be directly bound (or involved in a bond) by the antigen-binding molecule. In some embodiments, linear epitopes can be from immunizations with a peptide that effectively consisted of the sequence of the linear epitope, or from structural sections of a protein that are relatively isolated from the remainder of the protein (such that the antigen-binding molecule can interact, at least primarily), just with that sequence section.
• an antibody is used in the broadest sense and encompass various polypeptides that comprise antibody-like antigen-binding domains, including but not limited to conventional antibodies (typically comprising at least one heavy chain and at least one light chain) and fragments thereof (e.g., scFv, Fab), single-domain antibodies (sdAbs, comprising at least one VHH domain and an Fc region), VHH-containing polypeptides (polypeptides comprising at least one VHH domain), and fragments of any of the foregoing so long as they exhibit the desired antigen-binding activity.
• an antibody comprises a dimerization domain.
• dimerization domains include, but are not limited to, heavy chain constant domains (comprising CHI, hinge, CH2, and CH3, where CHI typically pairs with a light chain constant domain, CL, while the hinge mediates dimerization) and Fc regions (comprising hinge, CH2, and CH3, where the hinge mediates dimerization).
• antibody also includes, but is not limited to, chimeric antibodies, humanized antibodies, and antibodies of various species such as camelid (including llama), shark, mouse, human, cynomolgus monkey, etc.
• an antigen binding domain refers to a portion of an antibody sufficient to bind antigen.
• an antigen binding domain of a conventional antibody comprises three heavy chain CDRs and three light chain CDRs.
• an antigen binding domain comprises a heavy chain variable region comprising CDR1-FR2-CDR2-FR3-CDR3, and any portions of FR1 and/or FR4 required to maintain binding to antigen, and a light chain variable region comprising CDR1-FR2-CDR2-FR3-CDR3, and any portions of FR1 and/or FR4 required to maintain binding to antigen.
• an antigen-binding domain of an sdAb or VHH-containing polypeptide comprises three CDRs of a VHH domain.
• an antigen binding domain of an sdAb or VHH-containing polypeptide comprises a VHH domain comprising CDR1-FR2-CDR2- FR3-CDR3, and any portions of FR1 and/or FR4 required to maintain binding to antigen.
• VHH refers to the antigen-binding portion of a single-domain antibody, such as a camelid antibody or shark antibody.
• a VHH comprises three CDRs and four framework regions, designated FR1, CDR1, FR2, CDR2, FR3, CDR3, and FR4.
• a VHH may be truncated at the N-terminus or C-terminus such that it comprises only a partial FR1 and/or FR4, or lacks one or both of those framework regions, so long as the VHH substantially maintains antigen binding and specificity.
• single domain antibody and “sdAb” are used interchangeably herein to refer to an antibody comprising at least one monomeric domain, such as a VHH domain, without a light chain, and an Fc region.
• an sdAb is a dimer of two polypeptides wherein each polypeptide comprises at least one VHH domain and an Fc region.
• the terms “single domain antibody” and “sdAb” encompass polypeptides that comprise multiple VHH domains, such as a polypeptide having the structure VHH1-VHH2-FC or VHHi- VHH2-VHH3-FC, wherein VHHi, VHH2, and VHH3 may be the same or different.
• VHH-containing polypeptide refers to a polypeptide that comprises at least one VHH domain.
• a VHH polypeptide comprises two, three, or four or more VHH domains, wherein each VHH domain may be the same or different.
• a VHH-containing polypeptide comprises an Fc region.
• the VHH-containing polypeptide may be referred to as an sdAb. Further, in some such embodiments, the VHH polypeptide may form a dimer.
• Nonlimiting structures of VHH- containing polypeptides include VHHi-Fc, VHH1-VHH2-FC, and VHHi- VHH2-VHH3-FC, wherein VHHi, VHH2, and VHH3 may be the same or different.
• one VHH may be connected to another VHH by a linker, or one VHH may be connected to the Fc by a linker.
• the linker comprises 1-20 amino acids, preferably 1-20 amino acids predominantly composed of glycine and, optionally, serine.
• Non-limiting linkers are presented in SEQ ID NOs: 88-93.
• a VHH-containing polypeptide comprises an Fc
• it forms a dimer when a VHH-containing polypeptide comprises an Fc, it forms a dimer.
• the structure VHH1-VHH2-FC if it forms a dimer, is considered to be tetravalent (i.e., the dimer has four VHH domains).
• the structure VHH1-VHH2-VHH3-FC if it forms a dimer, is considered to be hexavalent (i.e., the dimer has six VHH domains).
• the term “monoclonal antibody” refers to an antibody (including an sdAb or VHH- containing polypeptide) of a substantially homogeneous population of antibodies, that is, the individual antibodies comprising the population are identical except for possible naturally- occurring mutations that may be present in minor amounts. Monoclonal antibodies are highly specific, being directed against a single antigenic site. Furthermore, in contrast to polyclonal antibody preparations, which typically include different antibodies directed against different determinants (epitopes), each monoclonal antibody is directed against a single determinant on the antigen. Thus, a sample of monoclonal antibodies can bind to the same epitope on the antigen.
• the modifier “monoclonal” indicates the character of the antibody as being obtained from a substantially homogeneous population of antibodies, and is not to be construed as requiring production of the antibody by any particular method.
• the monoclonal antibodies may be made by the hybridoma method first described by Kohler and Milstein, 1975, Nature 256:495, or may be made by recombinant DNA methods such as described in U.S. Pat. No. 4,816,567.
• the monoclonal antibodies may also be isolated from phage libraries generated using the techniques described in McCafferty et al., 1990, Nature 348:552-554, for example.
• CDR denotes a complementarity determining region as defined by at least one manner of identification to one of skill in the art.
• CDRs can be defined in accordance with any of the Chothia numbering schemes, the Kabat numbering scheme, a combination of Kabat and Chothia, the AbM definition, and/or the contact definition.
• a VHH comprises three CDRs, designated CDR1, CDR2, and CDR3.
• heavy chain constant region refers to a region comprising at least three heavy chain constant domains, CHI, hinge, CH2, and CH3.
• Nonlimiting exemplary heavy chain constant regions include y, 6, and a.
• Nonlimiting exemplary heavy chain constant regions also include 8 and p.
• Each heavy constant region corresponds to an antibody isotype.
• an antibody comprising a y constant region is an IgG antibody
• an antibody comprising a 6 constant region is an IgD antibody
• an antibody comprising an a constant region is an IgA antibody.
• an antibody comprising a p constant region is an IgM antibody
• an antibody comprising an 8 constant region is an IgE antibody.
• Certain isotypes can be further subdivided into subclasses.
• IgG antibodies include, but are not limited to, IgGl (comprising a yi constant region), IgG2 (comprising a y2 constant region), IgG3 (comprising a y3 constant region), and IgG4 (comprising a y4 constant region) antibodies
• IgA antibodies include, but are not limited to, IgAl (comprising an on constant region) and IgA2 (comprising an 012 constant region) antibodies
• IgM antibodies include, but are not limited to, IgMl and IgM2.
• a “Fc region” as used herein refers to a portion of a heavy chain constant region comprising CH2 and CH3.
• an Fc region comprises a hinge, CH2, and CH3.
• the hinge mediates dimerization between two Fc-containing polypeptides.
• An Fc region may be of any antibody heavy chain constant region isotype discussed herein.
• an Fc region is an IgGl, IgG2, IgG3, or IgG4.
• the Fc region is derived from a human Fc region and lacks the C-terminal lysine residue.
• the Fc region is derived from a human Fc region and comprises the C-terminal lysine residue.
• the C-terminal amino acid of the Fc region is an amino acid other than lysine.
• the Fc region is derived from a human Fc region and lacks the C-terminal glycine and lysine residues.
• an “acceptor human framework” as used herein is a framework comprising the amino acid sequence of a heavy chain variable domain (VH) framework derived from a human immunoglobulin framework or a human consensus framework, as discussed herein.
• An acceptor human framework derived from a human immunoglobulin framework or a human consensus framework can comprise the same amino acid sequence thereof, or it can contain amino acid sequence changes.
• the number of amino acid changes are fewer than 10, or fewer than 9, or fewer than 8, or fewer than 7, or fewer than 6, or fewer than 5, or fewer than 4, or fewer than 3, across all of the human frameworks in a single antigen binding domain, such as a VHH.
• Affinity refers to the strength of the sum total of noncovalent interactions between a single binding site of a molecule (for example, an antibody, such as an sdAb, or VHH- containing polypeptide) and its binding partner (for example, an antigen).
• the affinity or the apparent affinity of a molecule X for its partner Y can generally be represented by the dissociation constant (KD) or the Ko-apparent, respectively.
• KD dissociation constant
• Affinity can be measured by common methods known in the art (such as, for example, ELISA KD, KinExA, flow cytometry, and/or surface plasmon resonance devices), including those described herein. Such methods include, but are not limited to, methods involving BIAcore®, Octet®, or flow cytometry.
• KD refers to the equilibrium dissociation constant of an antigen-binding molecule/antigen interaction.
• KD refers to the equilibrium dissociation constant of an antigen-binding molecule/antigen interaction.
• the KD of the antigen-binding molecule is measured by flow cytometry using an antigen-expressing cell line and fitting the mean fluorescence measured at each antibody concentration to a non-linear one-site binding equation (Prism Software graphpad).
• the KD is KD -apparent-
• biological activity refers to any one or more biological properties of a molecule (whether present naturally as found in vivo, or provided or enabled by recombinant means). Biological properties include, but are not limited to, binding a ligand, inducing or increasing cell proliferation, and inducing or increasing expression of cytokines.
• An “agonist” or “activating” antibody is one that increases and/or activates a biological activity of the target antigen.
• the agonist antibody binds to an antigen and increases its biologically activity by at least about 20%, 40%, 60%, 80%, 85% or more.
• an “antagonist”, a “blocking” or “neutralizing” antibody is one that inhibits, decreases and/or inactivates a biological activity of the target antigen.
• the neutralizing antibody binds to an antigen and reduces its biologically activity by at least about 20%, 40%, 60%, 80%, 85% 90%, 95%, 99% or more.
• An “affinity matured” sdAb or VHH-containing polypeptide refers to a sdAb or VHH- containing polypeptide with one or more alterations in one or more CDRs compared to a parent sdAb or VHH-containing polypeptide that does not possess such alterations, such alterations resulting in an improvement in the affinity of the sdAb or VHH-containing polypeptide for antigen.
• a “humanized VHH” as used herein refers to a VHH in which one or more framework regions have been substantially replaced with human framework regions. In some instances, certain framework region (FR) residues of the human immunoglobulin are replaced by corresponding non-human residues. Furthermore, the humanized VHH can comprise residues that are found neither in the original VHH nor in the human framework sequences, but are included to further refine and optimize sdAb VHH-containing polypeptide performance. In some embodiments, a humanized sdAb or VHH-containing polypeptide comprises a human Fc region. As will be appreciated, a humanized sequence can be identified by its primary sequence and does not necessarily denote the process by which the antibody was created.
• effector-positive Fc region possesses an “effector function” of a native sequence Fc region.
• effector functions include Fc receptor binding; Clq binding and complement dependent cytotoxicity (CDC); Fc receptor binding; antibody-dependent cell- mediated cytotoxicity (ADCC); phagocytosis; down regulation of cell surface receptors (for example B-cell receptor); and B-cell activation, etc.
• Such effector functions generally require the Fc region to be combined with a binding domain (for example, an antibody variable domain) and can be assessed using various assays.
• a “native sequence Fc region” comprises an amino acid sequence identical to the amino acid sequence of an Fc region found in nature.
• Native sequence human Fc regions include a native sequence human IgGl Fc region (non- A and A allotypes); native sequence human IgG2 Fc region; native sequence human IgG3 Fc region; and native sequence human IgG4 Fc region as well as naturally occurring variants thereof.
• a “variant Fc region” comprises an amino acid sequence which differs from that of a native sequence Fc region by virtue of at least one amino acid modification.
• a “variant Fc region” comprises an amino acid sequence which differs from that of a native sequence Fc region by virtue of at least one amino acid modification, yet retains at least one effector function of the native sequence Fc region.
• the variant Fc region has at least one amino acid substitution compared to a native sequence Fc region or to the Fc region of a parent polypeptide, for example, from about one to about ten amino acid substitutions, and preferably, from about one to about five amino acid substitutions in a native sequence Fc region or in the Fc region of the parent polypeptide.
• the variant Fc region herein will possess at least about 80% sequence identity with a native sequence Fc region and/or with an Fc region of a parent polypeptide, at least about 90% sequence identity therewith, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity therewith.
• Fc receptor or “FcR” describes a receptor that binds to the Fc region of an antibody.
• an FcyR is a native human FcR.
• an FcR is one which binds an IgG antibody (a gamma receptor) and includes receptors of the FcyRI, FcyRII, and FcyRIII subclasses, including allelic variants and alternatively spliced forms of those receptors.
• FcyRII receptors include FcyRIIA (an “activating receptor”) and FcyRIIB (an “inhibiting receptor”), which have similar amino acid sequences that differ primarily in the cytoplasmic domains thereof.
• Activating receptor FcyRIIA contains an immunoreceptor tyrosine-based activation motif (IT AM) in its cytoplasmic domain
• Inhibiting receptor FcyRIIB contains an immunoreceptor tyrosine-based inhibition motif (ITEM) in its cytoplasmic domain.
• IT AM immunoreceptor tyrosine-based activation motif
• ITEM immunoreceptor tyrosine-based inhibition motif
• FcR Fc receptor
• FcRn neonatal receptor
• substantially similar denotes a sufficiently high degree of similarity between two or more numeric values such that one of skill in the art would consider the difference between the two or more values to be of little or no biological and/or statistical significance within the context of the biological characteristic measured by said value.
• the two or more substantially similar values differ by no more than about any one of 5%, 10%, 15%, 20%, 25%, or 50%.
• a polypeptide “variant” means a biologically active polypeptide having at least about 80% amino acid sequence identity with the native sequence polypeptide after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity, and not considering any conservative substitutions as part of the sequence identity.
• Such variants include, for instance, polypeptides wherein one or more amino acid residues are added, or deleted, at the N- or C-terminus of the polypeptide.
• a variant will have at least about 80% amino acid sequence identity.
• a variant will have at least about 90% amino acid sequence identity.
• a variant will have at least about 95% amino acid sequence identity with the native sequence polypeptide.
• percent (%) amino acid sequence identity and “homology” with respect to a peptide, polypeptide or antibody sequence are defined as the percentage of amino acid residues in a candidate sequence that are identical with the amino acid residues in the specific peptide or polypeptide sequence, after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity, and not considering any conservative substitutions as part of the sequence identity. Alignment for purposes of determining percent amino acid sequence identity can be achieved in various ways that are within the skill in the art, for instance, using publicly available computer software such as BLAST, BLAST-2, ALIGN or MEGALIGNTM (DNASTAR) software. Those skilled in the art can determine appropriate parameters for measuring alignment, including any algorithms needed to achieve maximal alignment over the full length of the sequences being compared.
• An amino acid substitution may include but are not limited to the replacement of one amino acid in a polypeptide with another amino acid. Exemplary substitutions are shown in Table 1. Amino acid substitutions may be introduced into an antibody of interest and the products screened for a desired activity, for example, retained/improved antigen binding, decreased immunogenicity, or improved ADCC or CDC.
• Amino acids may be grouped according to common side-chain properties:
• Non-conservative substitutions will entail exchanging a member of one of these classes for another class.
• vector is used to describe a polynucleotide that can be engineered to contain a cloned polynucleotide or polynucleotides that can be propagated in a host cell.
• a vector can include one or more of the following elements: an origin of replication, one or more regulatory sequences (such as, for example, promoters and/or enhancers) that regulate the expression of the polypeptide of interest, and/or one or more selectable marker genes (such as, for example, antibiotic resistance genes and genes that can be used in colorimetric assays, for example, P-galactosidase).
• expression vector refers to a vector that is used to express a polypeptide of interest in a host cell.
• a “host cell” refers to a cell that may be or has been a recipient of a vector or isolated polynucleotide.
• Host cells may be prokaryotic cells or eukaryotic cells.
• Exemplary eukaryotic cells include mammalian cells, such as primate or non-primate animal cells; fungal cells, such as yeast; plant cells; and insect cells.
• Nonlimiting exemplary mammalian cells include, but are not limited to, NSO cells, PER.C6® cells (Crucell), and 293 and CHO cells, and their derivatives, such as 293-6E, CHO-DG44, CH0-K1, CHO-S, and CHO-DS cells.
• Host cells include progeny of a single host cell, and the progeny may not necessarily be completely identical (in morphology or in genomic DNA complement) to the original parent cell due to natural, accidental, or deliberate mutation.
• a host cell includes cells transfected in vivo with a polynucleotide(s) a provided herein.
• isolated refers to a molecule that has been separated from at least some of the components with which it is typically found in nature or produced.
• a polypeptide is referred to as “isolated” when it is separated from at least some of the components of the cell in which it was produced.
• a polypeptide is secreted by a cell after expression, physically separating the supernatant containing the polypeptide from the cell that produced it is considered to be “isolating” the polypeptide.
• a polynucleotide is referred to as “isolated” when it is not part of the larger polynucleotide (such as, for example, genomic DNA or mitochondrial DNA, in the case of a DNA polynucleotide) in which it is typically found in nature, or is separated from at least some of the components of the cell in which it was produced, for example, in the case of an RNA polynucleotide.
• a DNA polynucleotide that is contained in a vector inside a host cell may be referred to as “isolated”.
• the terms “individual” and “subject” are used interchangeably herein to refer to an animal; for example a mammal.
• mammals including, but not limited to, humans, rodents, simians, felines, canines, equines, bovines, porcines, ovines, caprines, mammalian laboratory animals, mammalian farm animals, mammalian sport animals, and mammalian pets.
• an “individual” or “subject” refers to an individual or subject in need of treatment for a disease or disorder.
• the subject to receive the treatment can be a patient, designating the fact that the subject has been identified as having a disorder of relevance to the treatment, or being at adequate risk of contracting the disorder.
• a “disease” or “disorder” as used herein refers to a condition where treatment is needed and/or desired.
• autoimmune disorder refers to a disease or disorder typically associated with the nonanaphylactic hypersensitivity reactions (Type II, Type III and/or Type IV hypersensitivity reactions) that generally results from a subject’s own humoral and/or cell- mediated immune response to one or more immunogenic substances of endogenous exogenous origin.
• inflammatory disorder refers to disorders associated with inflammation, including, but not limited to, chronic or acute inflammatory diseases, and expressly includes inflammatory autoimmune diseases and inflammatory allergic conditions.
• infectious disease and infectious disease or disorder refer to a disease or disorder caused by an exogenous infectious agent, such as, but not limited to, bacteria, viruses, fungi, protozoa, and parasites.
• cancer encompass solid and hematological/lymphatic cancers and also encompass malignant, pre-malignant, and benign growth, such as dysplasia.
• Exemplary cancers include, but are not limited to: basal cell carcinoma, biliary tract cancer; bladder cancer; bone cancer; brain and central nervous system cancer; breast cancer; cancer of the peritoneum; cervical cancer; choriocarcinoma; colon and rectum cancer; connective tissue cancer; cancer of the digestive system; endometrial cancer; esophageal cancer; eye cancer; cancer of the head and neck; gastric cancer (including gastrointestinal cancer); glioblastoma; hepatic carcinoma; hepatoma; intra-epithelial neoplasm; kidney or renal cancer; larynx cancer; leukemia; liver cancer; lung cancer (e.g., small-cell lung cancer, non-small cell lung cancer, adenocarcinoma of the lung, and squamous carcinoma of the lung
• an “increase” or “decrease” refers to a statistically significant increase or decrease, respectively.
• “modulating” can also involve effecting a change (which can either be an increase or a decrease) in affinity, avidity, specificity and/or selectivity of a target or antigen, for one or more of its ligands, binding partners, partners for association into a homomultimeric or heteromultimeric form, or substrates; effecting a change (which can either be an increase or a decrease) in the sensitivity of the target or antigen for one or more conditions in the medium or surroundings in which the target or antigen is present (such as pH, ion strength, the presence of co-factors, etc.); and/or cellular proliferation or cytokine production, compared to the same conditions but without the presence of a test agent.
• This can be determined in any suitable manner and/or using any suitable assay known per se or described herein, depending on the target involved.
• treatment is an approach for obtaining beneficial or desired clinical results.
• Treatment covers any administration or application of a therapeutic for disease in a mammal, including a human.
• beneficial or desired clinical results include, but are not limited to, any one or more of: alleviation of one or more symptoms, diminishment of extent of disease, preventing or delaying spread (for example, metastasis, for example metastasis to the lung or to the lymph node) of disease, preventing or delaying recurrence of disease, delay or slowing of disease progression, amelioration of the disease state, inhibiting the disease or progression of the disease, inhibiting or slowing the disease or its progression, arresting its development, and remission (whether partial or total).
• treatment is a reduction of pathological consequence of a proliferative disease.
• the methods provided herein contemplate any one or more of these aspects of treatment. In-line with the above, the term treatment does not require one-hundred percent removal of all aspects of the disorder.
• “Ameliorating” means a lessening or improvement of one or more symptoms as compared to not administering a therapeutic agent. “Ameliorating” also includes shortening or reduction in duration of a symptom.
• anti -cancer agent is used herein in its broadest sense to refer to agents that are used in the treatment of one or more cancers.
• exemplary classes of such agents in include, but are not limited to, chemotherapeutic agents, anti-cancer biologies (such as cytokines, receptor extracellular domain-Fc fusions, and antibodies), radiation therapy, CAR-T therapy, therapeutic oligonucleotides (such as antisense oligonucleotides and siRNAs) and oncolytic viruses.
• biological sample means a quantity of a substance from a living thing or formerly living thing.
• substances include, but are not limited to, blood, (for example, whole blood), plasma, serum, urine, amniotic fluid, synovial fluid, endothelial cells, leukocytes, monocytes, other cells, organs, tissues, bone marrow, lymph nodes and spleen.
• control refers to a composition known to not contain an analyte (“negative control”) or to contain an analyte (“positive control”).
• positive control can comprise a known concentration of analyte.
• inhibitors refer to a decrease or cessation of any phenotypic characteristic or to the decrease or cessation in the incidence, degree, or likelihood of that characteristic.
• To “reduce” or “inhibit” is to decrease, reduce or arrest an activity, function, and/or amount as compared to a reference.
• by “reduce” or “inhibit” is meant the ability to cause an overall decrease of 10% or greater.
• by “reduce” or “inhibit” is meant the ability to cause an overall decrease of 50% or greater.
• by “reduce” or “inhibit” is meant the ability to cause an overall decrease of 75%, 85%, 90%, 95%, or greater.
• the amount noted above is inhibited or decreased over a period of time, relative to a control over the same period of time.
• “delaying development of a disease” means to defer, hinder, slow, retard, stabilize, suppress and/or postpone development of the disease (such as cancer). This delay can be of varying lengths of time, depending on the history of the disease and/or individual being treated. As is evident to one skilled in the art, a sufficient or significant delay can, in effect, encompass prevention, in that the individual does not develop the disease. For example, a late stage cancer, such as development of metastasis, may be delayed.
• Preventing includes providing prophylaxis with respect to the occurrence or recurrence of a disease in a subject that may be predisposed to the disease but has not yet been diagnosed with the disease. Unless otherwise specified, the terms “reduce”, “inhibit”, or “prevent” do not denote or require complete prevention over all time, but just over the time period being measured.
• a “therapeutically effective amount” of a substance/molecule, agonist or antagonist may vary according to factors such as the disease state, age, sex, and weight of the individual, and the ability of the substance/molecule, agonist or antagonist to elicit a desired response in the individual.
• a therapeutically effective amount is also one in which any toxic or detrimental effects of the substance/molecule, agonist or antagonist are outweighed by the therapeutically beneficial effects.
• a therapeutically effective amount may be delivered in one or more administrations.
• a therapeutically effective amount refers to an amount effective, at dosages and for periods of time necessary, to achieve the desired therapeutic and/or prophylactic result.
• composition refers to a preparation which is in such form as to permit the biological activity of the active ingredient(s) to be effective, and which contains no additional components which are unacceptably toxic to a subject to which the formulation would be administered.
• Such formulations may be sterile.
• a “pharmaceutically acceptable carrier” refers to a non-toxic solid, semisolid, or liquid filler, diluent, encapsulating material, formulation auxiliary, or carrier conventional in the art for use with a therapeutic agent that together comprise a “pharmaceutical composition” for administration to a subject.
• a pharmaceutically acceptable carrier is non-toxic to recipients at the dosages and concentrations employed and are compatible with other ingredients of the formulation.
• the pharmaceutically acceptable carrier is appropriate for the formulation employed.
• Administration “in combination with” one or more further therapeutic agents includes simultaneous (concurrent) and sequential administration in any order.
• the term “concurrently” is used herein to refer to administration of two or more therapeutic agents, where at least part of the administration overlaps in time, or where the administration of one therapeutic agent falls within a short period of time relative to administration of the other therapeutic agent, or wherein the therapeutic effect of both agents overlap for at least a period of time.
• conjunction with refers to administration of one treatment modality in addition to another treatment modality.
• in conjunction with refers to administration of one treatment modality before, during, or after administration of the other treatment modality to the individual.
• package insert is used to refer to instructions customarily included in commercial packages of therapeutic products, that contain information about the indications, usage, dosage, administration, combination therapy, contraindications and/or warnings concerning the use of such therapeutic products.
• An “article of manufacture” is any manufacture (for example, a package or container) or kit comprising at least one reagent, for example, a medicament for treatment of a disease or disorder (for example, cancer), or a probe for specifically detecting a biomarker described herein.
• the manufacture or kit is promoted, distributed, or sold as a unit for performing the methods described herein.
• label and “detectable label” mean a moiety attached, for example, to an antibody or antigen to render a reaction (for example, binding) between the members of the specific binding pair, detectable.
• the labeled member of the specific binding pair is referred to as “detectably labeled.”
• label binding protein refers to a protein with a label incorporated that provides for the identification of the binding protein.
• the label is a detectable marker that can produce a signal that is detectable by visual or instrumental means, for example, incorporation of a radiolabeled amino acid or attachment to a polypeptide of biotinyl moi eties that can be detected by marked avidin (for example, streptavidin containing a fluorescent marker or enzymatic activity that can be detected by optical or colorimetric methods).
• marked avidin for example, streptavidin containing a fluorescent marker or enzymatic activity that can be detected by optical or colorimetric methods.
• labels for polypeptides include, but are not limited to, the following: radioisotopes or radionuclides (for example, 3 H, 14 C, 35 S, 90 Y, "Tc, in In, 125 I, 131 I, 177 LU, 166 HO, or 153 Sm); chromogens, fluorescent labels (for example, FITC, rhodamine, lanthanide phosphors), enzymatic labels (for example, horseradish peroxidase, luciferase, alkaline phosphatase); chemiluminescent markers; biotinyl groups; predetermined polypeptide epitopes recognized by a secondary reporter (for example, leucine zipper pair sequences, binding sites for secondary antibodies, metal binding domains, epitope tags); and magnetic agents, such as gadolinium chelates.
• radioisotopes or radionuclides for example, 3 H, 14 C, 35 S, 90 Y, "Tc, in In, 125
• labels commonly employed for immunoassays include moieties that produce light, for example, acridinium compounds, and moieties that produce fluorescence, for example, fluorescein.
• the moiety itself may not be detectably labeled but may become detectable upon reaction with yet another moiety.
• Single-domain antibodies including VHH domains that bind albumin are provided herein.
• a VHH domain that binds albumin does not interfere with albumin binding to FcRn.
• a VHH domain that binds albumin does not bind domain 3 of albumin.
• a VHH domain that binds albumin binds with an affinity (KD) between 0.01 nM and 5 nM, or between 0.01 nM at 2 nM, or between 0.01 nM and 1 nM, between 0.01 nM and 0.5 nM, 0.05 nM and 5 nM, or between 0.05 nM at 2 nM, or between 0.05 nM and 1 nM, or between 0.05 nM and 0.5 nM.
• KD affinity
• a polypeptide comprising at least one VHH domain that binds albumin is provided.
• a polypeptide comprising one, two, three, four, five, six, seven, or eight VHH domains that bind albumin is provided.
• a polypeptide provided herein comprises one, two, three, or four VHH domains that bind albumin.
• Such polypeptides may comprise one or more additional VHH domains that bind one or more target proteins other than albumin.
• a polypeptide that comprises one or more VHH domains that bind albumin also comprises a therapeutic antigen-binding domain and/or a therapeutic polypeptide.
• therapeutic antigen-binding domains include, but are not limited to, traditional antibody antigen-binding domains, which comprise a heavy chain variable region and a light chain variable region, and single-domain antibody antigen-binding domains, such as VHH domains.
• Nonlimiting formats of polypeptides comprising one or more VHH domains that bind albumin and one or more traditional antibody domains are provided in FIG. 6(v)-(ix).
• Other non-limiting exemplary therapeutic polypeptides include, for example, receptor extracellular domains, enzymes, and ligands.
• the polypeptide comprising at least one VHH domain that binds albumin has a longer half-life in vivo than the same polypeptide without the at least one VHH domain that binds albumin.
• the half-life is at least 1.5x, at least 2x, at least 3x, at least 4x, or at least 5x longer than the half-life of the polypeptide without the VHH domain that binds albumin.
• a polypeptide that comprises at least one VHH domain that binds albumin comprises an Fc region.
• a polypeptide provided herein comprises one, two, three, or four VHH domains that bind albumin and an Fc region.
• an Fc region mediates dimerization of the polypeptide at physiological conditions.
• a VHH domain that binds albumin comprises a CDR1 sequence selected from SEQ ID NOs: 5-8, a CDR2 sequence selected from SEQ ID NOs: 9-21, and a CDR3 sequence of SEQ ID NO: 22.
• a VHH domain that binds albumin comprises CDR1, CDR2, and CDR3 sequences selected from: SEQ ID NOs: 5, 9, and 22; SEQ ID NOs: 5, 10, and 22; SEQ ID NOs: 5, 11, and 22; SEQ ID NOs: 5, 12, and 22; SEQ ID NOs: 5, 13, and 22; SEQ ID NOs: 5, 14, and 22; SEQ ID NOs: 5, 15, and 22; SEQ ID NOs: 6, 15, and 22; SEQ ID NOs: 7, 15, and 22; SEQ ID NOs: 8, 15, and 22; SEQ ID NOs: 6, 16, and 22; SEQ ID NOs: 6, 17, and 22; SEQ ID NOs: 6, 18, and 22; SEQ ID NOs: 6, 19, and 22; SEQ ID NOs: 6, 20, and 22; and SEQ ID NOs: 6, 21, and 22.
• a VHH domain that binds albumin comprises an amino acid sequence that is a sequence at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99% identical to a sequence selected from SEQ ID NOs: 23-43 and 71-74.
• a VHH domain that binds albumin comprises an amino acid sequence selected from SEQ ID NOs: 23-43 and 71-74.
• a VHH domain that binds albumin which competes for binding to albumin with a VHH domain comprising an amino acid sequence selected from SEQ ID NOs: 23-43 and 71-74.
• a VHH domain that binds albumin may be humanized.
• Humanized antibodies (such as sdAbs or VHH-containing polypeptides) are useful as therapeutic molecules because humanized antibodies reduce or eliminate the human immune response to non-human antibodies, which can result in an immune response to an antibody therapeutic, and decreased effectiveness of the therapeutic.
• a humanized antibody comprises one or more variable domains in which CDRs, (or portions thereof) are derived from a non-human antibody, and FRs (or portions thereof) are derived from human antibody sequences.
• a humanized antibody optionally will also comprise at least a portion of a human constant region.
• some FR residues in a humanized antibody are substituted with corresponding residues from a non-human antibody (for example, the antibody from which the CDR residues are derived), for example, to restore or improve antibody specificity or affinity.
• Human framework regions that can be used for humanization include but are not limited to: framework regions selected using the “best-fit” method (see, for example, Sims et al. (1993) J. Immunol. 151 :2296); framework regions derived from the consensus sequence of human antibodies of a particular subgroup of heavy chain variable regions (see, for example, Carter et al. (1992) roc. Natl. Acad. Set. USA, 89:4285; and Presta et al. (1993) J. Immunol, 151 :2623); human mature (somatically mutated) framework regions or human germline framework regions (see, for example, Almagro and Fransson, (2008) Front. Biosci.
• FR regions of a VHH are replaced with human FR regions to make a humanized VHH.
• certain FR residues of the human FR are replaced in order to improve one or more properties of the humanized VHH.
• VHH domains with such replaced residues are still referred to herein as “humanized.”
• sdAbs including VHH domains that bind albumin can slow the clearance of molecules they are linked to, including molecules comprising a human Fc region.
• an Fc region included in an albumin-binding polypeptide is a human Fc region, or is derived from a human Fc region.
• Non-limiting sdAb formats comprising an Fc region are shown in FIG. 6.
• an Fc region included in an albumin-binding polypeptide is derived from a human Fc region, and comprises a three amino acid deletion in the lower hinge corresponding to IgGl E233, L234, and L235, herein referred to as “Fc xELL.”
• Fc xELL polypeptides do not engage FcyRs and thus are referred to as “effector silent” or “effector null”, however in some embodiments, xELL Fc regions bind FcRn and therefore have extended halflife and transcytosis associated with FcRn mediated recycling.
• the Fc region included in an albumin-binding polypeptide is derived from a human Fc region and comprises mutations M252Y and M428V, which may be referred to as “YV”.
• mutations enhance binding to FcRn at the acidic pH of the endosome (near 6.5), while losing detectable binding at neutral pH (about 7.2), allowing for enhanced FcRn mediated recycling and extended half-life.
• the Fc region included in an albumin-binding polypeptide is derived from a human Fc region and comprises mutations M252Y, S254T, and T256E, which may be referred to as “YTE”.
• such mutations extend serum half-life in humans by significantly reducing the dissociation rate of Fc and FcRn.
• the Fc region included in an albumin-binding polypeptide is derived from a human Fc region and comprises mutations M428L and N434S, which may be referred to as “LS”.
• such mutations extend serum half-life in humans by increasing the binding affinity of Fc for FcRn at pH6 and reducing the dissociation rate.
• Various Fc mutations that enhance circulating half-life are described, for example, in Saunders, Front. Immunol, doi.org/10.3389/fimmu.2019.01296 (2019).
• the Fc region included in an albumin-binding polypeptide is derived from a human Fc region and comprises mutations designed for heterodimerization, herein referred to as “knob” and “hole”.
• the “knob” Fc region comprises the mutation T366W.
• the “hole” Fc region comprises mutations T366S, L368A, and Y407V.
• Fc regions used for heterodimerization comprise additional mutations, such as the mutation S354C on a first member of a heterodimeric Fc pair that forms an asymmetric disulfide with a corresponding mutation Y349C on the second member of a heterodimeric Fc pair.
• one member of a heterodimeric Fc pair comprises the modification H435R or H435K to prevent protein A binding while maintaining FcRn binding.
• one member of a heterodimeric Fc pair comprises the modification H435R or H435K, while the second member of the heterodimeric Fc pair is not modified at H435.
• the hold Fc region comprises the modification H435R or H435K (referred to as “hole-R” in some instances when the modification is H435R), while the knob Fc region does not.
• the hole-R mutation improves purification of the heterodimer over homodimeric hole Fc regions that may be present.
• Nonlimiting exemplary Fc regions that may be used in an albumin-binding polypeptide include Fc regions comprising the amino acid sequences of SEQ ID NOs: 47-68 and 85-87.
• albumin-binding polypeptides bind to an epitope of albumin outside of domain 3.
• the albumin-binding polypeptides provided herein do not interfere with (i.e., does not inhibit) albumin binding to FcRn.
• Methods of determining whether an albumin-binding polypeptide interferes with albumin binding to FcRn are known in the art; nonlimiting exemplary methods are also provided herein.
• a polypeptide comprising an albumin binding domain provided herein has a longer half-life in vivo than the polypeptide lacking the albumin binding domain.
• a polypeptide comprising an albumin binding domain provided herein has a half-life that is at least 1.5x, at least 2x, at least 3x, at least 4x, or at least 5x longer than the half-life of the polypeptide without the albumin binding domain.
• Nucleic acid molecules comprising polynucleotides that encode a polypeptide comprising an albumin-binding domain are provided.
• the nucleic acid molecule may also encode a leader sequence that directs secretion of the polypeptide comprising an albumin-binding domain, which leader sequence is typically cleaved such that it is not present in the secreted polypeptide.
• the leader sequence may be a native heavy chain (or VHH) leader sequence, or may be another heterologous leader sequence.
• Nucleic acid molecules can be constructed using recombinant DNA techniques conventional in the art.
• a nucleic acid molecule is an expression vector that is suitable for expression in a selected host cell.
• Vectors comprising nucleic acids that encode a polypeptide comprising an albumin-binding domain are provided.
• Such vectors include, but are not limited to, DNA vectors, phage vectors, viral vectors, retroviral vectors, etc.
• a vector is selected that is optimized for expression of polypeptides in a desired cell type, such as CHO or CHO-derived cells, or in NSO cells. Exemplary such vectors are described, for example, in Running Deer et al., Biotechnol. Prog. 20:880-889 (2004).
• a polypeptide comprising an albumin-binding domain may be expressed in prokaryotic cells, such as bacterial cells; or in eukaryotic cells, such as fungal cells (such as yeast), plant cells, insect cells, and mammalian cells. Such expression may be carried out, for example, according to procedures known in the art.
• exemplary eukaryotic cells that may be used to express polypeptides include, but are not limited to, COS cells, including COS 7 cells; 293 cells, including 293-6E cells; CHO cells, including CHO-S, DG44. Lecl3 CHO cells, and FUT8 CHO cells; PER.C6® cells (Crucell); and NSO cells.
• the polypeptides may be expressed in yeast. See, e.g., U.S. Publication No. US 2006/0270045 Al.
• a particular eukaryotic host cell is selected based on its ability to make desired post-translational modifications to the polypeptide. For example, in some embodiments, CHO cells produce polypeptides that have a higher level of sialylation than the same polypeptide produced in 293 cells.
• nucleic acids such as vectors
• Introduction of one or more nucleic acids into a desired host cell may be accomplished by any method, including but not limited to, calcium phosphate transfection, DEAE-dextran mediated transfection, cationic lipid-mediated transfection, electroporation, transduction, infection, etc.
• Nonlimiting exemplary methods are described, for example, in Sambrook et al., Molecular Cloning, A Laboratory Manual, 3 rd ed. Cold Spring Harbor Laboratory Press (2001).
• Nucleic acids may be transiently or stably transfected in the desired host cells, according to any suitable method.
• Host cells comprising any of the nucleic acids or vectors described herein are also provided.
• a host cell that expresses a polypeptide comprising an albumin-binding domain described herein is provided.
• the polypeptides expressed in host cells can be purified by any suitable method. Such methods include, but are not limited to, the use of affinity matrices or hydrophobic interaction chromatography.
• Suitable affinity ligands include the R0R1 ECD and agents that bind Fc regions.
• a Protein A, Protein G, Protein A/G, or an antibody affinity column may be used to bind the Fc region and to purify a polypeptide that comprises an Fc region.
• Hydrophobic interactive chromatography for example, a butyl or phenyl column, may also suitable for purifying some polypeptides such as antibodies.
• Ion exchange chromatography for example anion exchange chromatography and/or cation exchange chromatography
• Mixed-mode chromatography for example reversed phase/anion exchange, reversed phase/cation exchange, hydrophilic interaction/anion exchange, hydrophilic interaction/cation exchange, efc.
• Many methods of purifying polypeptides are known in the art.
• the polypeptide is produced in a cell-free system.
• a cell-free system Nonlimiting exemplary cell-free systems are described, for example, in Sitaraman et al., Methods Mol. Biol. 498: 229-44 (2009); Spirin, Trends Biotechnol. 22: 538-45 (2004); Endo et al., Biotechnol. Adv. 21 : 695-713 (2003).
• a polypeptide comprising an albumin-binding domain prepared by the methods described above are provided.
• the polypeptide is prepared in a host cell.
• the polypeptide is prepared in a cell-free system.
• the polypeptide is purified.
• a cell culture media comprising a polypeptide is provided.
• compositions comprising antibodies prepared by the methods described above are provided.
• the composition comprises a polypeptide comprising an albumin-binding domain prepared in a host cell.
• the composition comprises a polypeptide prepared in a cell-free system.
• the composition comprises a purified polypeptide.
• Exemplary methods of treating diseases using albumin-binding polypeptides comprising administering a therapeutic polypeptide comprising an albumin-binding domain provided herein.
• diseases include any disease that would benefit from treatment with the therapeutic polypeptide.
• Nonlimiting exemplary diseases that may be treated with therapeutic polypeptides comprising an albumin-binding domain provided herein include infectious diseases, autoimmune diseases or disorders, inflammatory diseases or disorders, and cancer.
• the method comprises administering to the individual an effective amount of a therapeutic polypeptide comprising an albumin-binding domain provided herein.
• Such methods of treatment may be in humans or animals. In some embodiments, methods of treating humans are provided.
• the therapeutic polypeptides comprising an albumin-binding domain provided herein can be administered as needed to subjects. Determination of the frequency of administration can be made by persons skilled in the art, such as an attending physician based on considerations of the condition being treated, age of the subject being treated, severity of the condition being treated, general state of health of the subject being treated and the like.
• an effective dose of a therapeutic polypeptide is administered to a subject one or more times.
• an effective dose of a therapeutic polypeptide is administered to the subject daily, semiweekly, weekly, every two weeks, once a month, etc.
• An effective dose of a therapeutic polypeptide is administered to the subject at least once.
• the effective dose of a therapeutic polypeptide may be administered multiple times, including multiple times over the course of at least a month, at least six months, or at least a year.
• compositions are administered in an amount effective for treating disease.
• the therapeutically effective amount is typically dependent on the weight of the subject being treated, his or her physical or health condition, the extensiveness of the condition to be treated, or the age of the subject being treated.
• antibodies may be administered in an amount in the range of about 0.05 mg/kg body weight to about 100 mg/kg body weight per dose. In some embodiments, antibodies may be administered in an amount in the range of about 10 pg/kg body weight to about 100 mg/kg body weight per dose. In some embodiments, antibodies may be administered in an amount in the range of about 50 pg/kg body weight to about 5 mg/kg body weight per dose.
• antibodies may be administered in an amount in the range of about 100 pg/kg body weight to about 10 mg/kg body weight per dose. In some embodiments, antibodies may be administered in an amount in the range of about 100 pg/kg body weight to about 20 mg/kg body weight per dose. In some embodiments, antibodies may be administered in an amount in the range of about 0.5 mg/kg body weight to about 20 mg/kg body weight per dose. In some embodiments, antibodies may be administered in an amount in the range of about 0.5 mg/kg body weight to about 10 mg/kg body weight per dose. In some embodiments, antibodies may be administered in an amount in the range of about 0.05 mg/kg body weight to about 20 mg/kg body weight per dose.
• antibodies may be administered in an amount in the range of about 0.05 mg/kg body weight to about 10 mg/kg body weight per dose. In some embodiments, antibodies may be administered in an amount in the range of about 5 mg/kg body weight or lower, for example less than 4, less than 3, less than 2, or less than 1 mg/kg of the antibody.
• therapeutic polypeptides can be administered in vivo by various routes, including, but not limited to, intravenous, intra-arterial, parenteral, intraperitoneal or subcutaneous.
• routes including, but not limited to, intravenous, intra-arterial, parenteral, intraperitoneal or subcutaneous.
• the appropriate formulation and route of administration may be selected according to the intended application.
• compositions comprising polypeptides comprising albumin-binding domains are provided in formulations with a wide variety of pharmaceutically acceptable carriers (see, for example, Gennaro, Remington: The Science and Practice of Pharmacy with Facts and Comparisons: Drugfacts Plus, 20th ed. (2003); Ansel et al., Pharmaceutical Dosage Forms and Drug Delivery Systems, 7 th ed., Lippencott Williams and Wilkins (2004); Kibbe et al., Handbook of Pharmaceutical Excipients, 3 rd ed., Pharmaceutical Press (2000)).
• Various pharmaceutically acceptable carriers which include vehicles, adjuvants, and diluents, are available.
• Non-limiting exemplary carriers include saline, buffered saline, dextrose, water, glycerol, ethanol, and combinations thereof.
• a pharmaceutical composition comprises a polypeptide comprising an albumin-binding domain at a concentration of at least 10 mg/mL, 20 mg/mL, 30 mg/mL, 40 mg/mL, 50 mg/mL, 60 mg/mL, 70 mg/mL, 80 mg/mL, 90 mg/mL, 100 mg/mL, 125 mg/mL, 150 mg/mL, 175 mg/mL, 200 mg/mL, 225 mg/mL, or 250 mg/mL.
• Nonlimiting exemplary methods of diagnosis and treatment are useful for evaluating a subject and/or a specimen from a subject (e.g. a cancer patient).
• evaluation is one or more of diagnosis, prognosis, and/or response to treatment.
• the methods described herein comprise evaluating a presence, absence, or level of a protein. In some embodiments, the methods described herein comprise evaluating a presence, absence, or level of expression of a nucleic acid.
• the compositions described herein may be used for these measurements. In some embodiments, the evaluation may direct treatment (including treatment with the polypeptides described herein). Kits
• kits that include any of the polypeptides comprising an albumin-binding domain as described herein, and suitable packaging.
• the invention includes a kit with (i) a polypeptide comprising an albumin-binding domain, and (ii) instructions for using the kit to administer the polypeptide to an individual.
• Suitable packaging for compositions described herein are known in the art, and include, for example, vials (e.g, sealed vials), vessels, ampules, bottles, jars, flexible packaging (e.g, sealed Mylar or plastic bags), and the like. These articles of manufacture may further be sterilized and/or sealed. Also provided are unit dosage forms comprising the compositions described herein. These unit dosage forms can be stored in a suitable packaging in single or multiple unit dosages and may also be further sterilized and sealed. Instructions supplied in the kits of the invention are typically written instructions on a label or package insert (e.g., a paper sheet included in the kit), but machine-readable instructions (e.g., instructions carried on a magnetic or optical storage disk) are also acceptable. The instructions relating to the use of the antibodies generally include information as to dosage, dosing schedule, and route of administration for the intended treatment or industrial use. The kit may further comprise a description of selecting an individual suitable or treatment.
• vials e.g, sealed vials
• vessels
• kits may be unit doses, bulk packages (e.g., multi-dose packages) or sub-unit doses.
• kits may also be provided that contain sufficient dosages of molecules disclosed herein to provide effective treatment for an individual for an extended period, such as about any of a week, 2 weeks, 3 weeks, 4 weeks, 6 weeks, 8 weeks, 3 months, 4 months, 5 months, 6 months, 7 months, 8 months, 9 months, or more.
• Kits may also include multiple unit doses of molecules and instructions for use and packaged in quantities sufficient for storage and use in pharmacies, for example, hospital pharmacies and compounding pharmacies.
• the kit includes a dry (e.g., lyophilized) composition that can be reconstituted, resuspended, or rehydrated to form generally a stable aqueous suspension of antibody.
• Example 1 Development of anti-albumin single domain antibodies (sdAbs) [00132] Single domain antibodies targeting human albumin were generated via immunization of llamas and alpaca with a recombinant version of human serum albumin (SEQ ID NO: 1).
• PBMCs peripheral blood mononuclear cells
• Yeast libraries displaying the VHH-Fc-AGA2 fusion proteins were enriched using recombinant forms of human albumin via magnetic bead isolation followed by fluorescence activated cell sorting (FACS). Sorted yeast were plated out and isolated colonies were picked into 96-well blocks and an induction of yeast cell surface expression of VHH-Fc- AGA2 fusion protein was conducted. Biotinylated recombinant human albumin or irrelevant biotinylated protein (albumin negative) were directly applied to induced yeast, washed, treated with fluorophore labelled streptavidin, and analyzed by 96-well flow cytometry.
• FACS fluorescence activated cell sorting
• Nucleic acid sequences encoding VHHs that bound to biotinylated recombinant human albumin and not to irrelevant biotinylated protein were cloned in-frame with a human Fc xELL encoding region into mammalian expression vectors, and expressed by transient transfection in HEK293 Freestyle cells (293F cells) or CHO cells using polyethylenimine. Supernatant was collected after 3-7 days, secreted recombinant protein was purified by protein A chromatography, and concentration was calculated from the absorbance at 280 nm and extinction coefficient.
• Anti-albumin sdAb 4A01 was selected for humanization.
• Example 2 Monovalent binding of anti-albumin sdAb 4A01 to human and mouse albumin
• Monomeric anti -albumin sdAb 4A01 was made by fusing the 4A01 VHH to a human Fc comprising S364N, Y407N, and K409T mutations (4A01-NNT-hFc; SEQ ID NOs: 23 and 68; FIG. 1 A). Binding of monomeric anti -albumin sdAb 4A01 was assessed by ELISA by titrating monomeric sdAb onto immobilized albumin protein from the indicated species (Medisorp plate), and detecting using anti-human Fc (HRP), as follows.
• HRP anti-human Fc
• Plates were coated with the albumin protein of the indicated species (Sigma) at 2 pg/ml, 50pl/well, 4°C overnight, lx Fish Gelatin (blocking agent, Biotium) was added to the coated wells and incubated for 1 hour at RT. Titrations of 4A01-NNT-hFc (starting at lOOnM, 1 :3 dilutions, last well blank) were added and then incubated for 1 hour at RT. Plates were then washed 3 times with 0.1% D-PBST before adding of anti-human Fc HRP antibody (1 :2000 in 0.1% D-PBST, Jackson).
• anti-albumin sdAb 4A01 bound to both human and mouse albumin with comparable affinity.
• the KD for human albumin was 0.23 nM and the KD for mouse albumin was 0.20 nM.
• Albumin binds to the beta-2 microglobulin FcRn complex primarily through domain 3, and that binding is believed to be involved in the improved half-life of proteins fused to anti -albumin antibodies, or fused to albumin itself.
• binding of 4A01-NNT-hFc was assayed by biolayer interferometry, as follows.
• Albumin domain 3 (mouse Fc tagged) was immobilized on anti-mouse IgG Fc capture biosensor. All buffers/protein formulations were in MBST5 (50nM MES pH5, 150mM NaCl, 0.025% Tween)). A baseline was established with buffer only. Mouse Fc-tagged human albumin domain III (lOpg/ml) was loaded onto the anti-mouse IgG Fc capture biosensors (ForteBio). Anti-albumin sdAbs 4A01 (4A01-NNT-hFc) and 1C04 (similar format) were then loaded and allowed to associate with the captured biotin domain 3, followed by dissociation with MBST5. sdAb 1C04 is known to bind to albumin domain 3, and was used as a positive control. See FIG. 2A.
• Anti-albumin sdAb 4A01 (4A01-NNT-hFc), hz4A01v51, and 1C04 were then tested for interference with albumin-FcRn binding, as follows. Binding was assessed by biolayer interferometry using biotinylated recombinant FcRn-B2M immobilized on a streptavidin biosensor. The immobilized FcRn-B2M was then complexed with recombinant human albumin. All buffers/protein formulations were in MBST5 (50mM MES pH5, 150mM NaCl, 0.025% Tween). A baseline was established with buffer only.
• Biotinylated FcRn-B2M (lOpg/ml, Aero Biosystems) was loaded onto the streptavidin biosensors (ForteBio), and a further baseline determined. 50pM recombinant human albumin (Sigma) was then added and allowed to associate with the immobilized FcRn-B2M. Anti -albumin sdAbs 4A01 and 4A01v51, and sdAb 1C04 were then loaded and allowed to associate with the captured biotin domain 3, followed by dissociation with MBST5. See FIG. 3A
• Example 4 Humanization of anti-albumin sdAb 4A01 and species cross-reactivity
• Various humanized forms of sdAb 4A01 were made based on the human heavy chain frameworks VH3-23*04. Certain amino acids were back-mutated to the donor amino acid, and certain mutations were tested, for example, in CDR2.
• FIG. 4A shows an alignment of the human heavy chain acceptor sequence with the humanized forms of 4A01.
• Binding of monomeric anti-albumin sdAbs 4A01 (“lm4A01”) and its humanized versions to human serum albumin, cynomolgus serum albumin, murine serum albumin, and rat serum albumin was determined by ELISA as follows. Medisorp plates were coated with albumin protein at 2pg/ml, 50pl/well at 4°C overnight (human, murine, and rat albumin - Sigma, cynomolgus monkey albumin - Abeam), lx Fish Gelatin (blocking agent, Bethyl Laboratories) was added to albumin-coated wells followed by a 1 hour incubation at RT.
• Binding of 4A01 and humanized forms of 4A01 to human albumin is shown in FIG. 4B-4C. All of the sdAbs bound human albumin with a KD between 0.10 and 0.43 nM. Binding of 4A01 and humanized forms of 4A01 to cynomolgus monkey albumin is shown in FIG. 4D- 4E. All of the sdAbs bound cynomolgus monkey albumin with a KD between 0.11 and 0.34 nM. Binding of 4A01 and humanized forms of 4A01 to murine albumin is shown in FIG. 4F-4G. All of the sdAbs bound murine albumin with a KD between 0.11 and about 0.25 nM. Binding of 4A01 and humanized forms of 4A01 to rat albumin is shown in FIG. 4H-4I. All of the sdAbs bound rat albumin with a KD between 0.14 and about 0.33 nM.
• FIG. 5A-5D show binding of 4A01 and humanized hz4A01v51 to human (5 A), cynomolgus monkey (5B), murine (5C), and rat (5D) albumin.
• 4A01 and all of the humanized variants tested bound all four species of albumin with an affinity of less than 1 nM.
• Humanized hz4A01v51 bound all four species of albumin with an affinity of less than 0.3 nM, and achieved maximal binding of greater than 90%.
• Example 5 Binding of single domain antibody polypeptides to human albumin [00149] Binding of humanized single domain antibody (sdAb) polypeptides to human albumin at neutral (7.4) or endosomal (6) pH was tested by ELISA. 96-well ELISA plates were coated with 2 pg/mL recombinant albumin in PBS overnight at 4°C, washed with PBS/0.05% Tween- 20 (PBS-T) and then blocked with 5% milk powder in PBS-T for 2 h at room temperature. Serial dilutions of test articles were prepared in PBS pH 7.4 or a buffer containing 20mM His, 150 mM NaCl, pH 6 and added to the plates.
• sdAb humanized single domain antibody
• HRP horse radish peroxidase
• a bivalent bispecific sdAb polypeptide comprising an albumin binding domain of SEQ ID NO: 43 (hz4A01v51 VHH) and a non-mammalian targeted binding domain, formatted as shown in FIG. 6(iii) (cxl 1917) binds albumin with low nanomolar to sub-nanomolar affinity.
• the apparent affinity is only mildly affected by pH with a Kd of 0.7 nM at a neutral pH (7.4) compared to a Kd of 2 nM at pH 6.
• Binding is only mediated by the monovalent albumin-targeting sdAb subunit, as an sdAb polypeptide comprising two nonmammalian targeted binding domains formatted as described in FIG. 6(iii) (cxl 1916) did not bind albumin with appreciable affinity at any pH tested.
• sdAb humanized single domain antibody
• 96-well ELISA plates were coated with 2 pg/mL recombinant albumin in PBS overnight at 4°C, washed with PBS/0.05% Tween-20 (PBS-T) and then blocked with lx fish gelatin for 1 h at room temperature.
• Serial dilutions of test articles were prepared in PBS-T pH 7.4 and added to the plates. Plates were incubated for 1 h at room temperature. After the incubation cells were washed in PBS-T and then incubated for 30 min at room temperature with an HRP -conjugated secondary antibody specific to human IgGl. Plates were then washed before addition of a TMB substrate.
• the HRP- TMB reaction was allowed to develop and absorbance at 650 nm was measured with a 96 well plate reader. The data were plotted and analyzed using GraphPad Prism analysis software. The results are shown in FIG. 3.
• cx5009 a monovalent albumin-specific sdAb, hz4A01v51 VHH-hlgGl-xELL-NNT-Fc (SEQ ID NO: 69), formatted as shown in FIG. 6(ii), binds to albumin from human, cynomolgus, mouse, and rat.
• Apparent affinities at a neutral pH (7.4) are similar across species with Kas in the sub-nanomolar range ( ⁇ 0.2nM).
• Example 7 In vivo pharmacokinetic profile of albumin-binding single domain antibody polypeptides
• albumin-binding single domain antibodies to extend the serum exposure of human IgG was tested in healthy mice.
• the xELL variation of human IgGl reduces Fc gamma receptor binding but does not affect FcRn binding.
• mice were injected intravenously with either 30 mg/kg or 0.3 mg/kg single doses and serum samples were drawn 30 min, 6 h, 24 h, 96 h and 168 h after the test article injection. Test article concentrations in mouse serum were determined by ELISA.
• human FcRn/B2M heterodimeric protein (His-tag, Aero Biosystem) was immobilized on 96-well ELISA plates by incubating 4 pg/mL of a protein solution in PBS for 12h at 4°C. The next day plates were blocked with a 3% BSA TBS-T buffer for 2 h before incubation of the serum samples on these plates for 2 h. Binding of test article in the serum samples to the FcRn immobilized on the ELISA plates was detected using an HRP -conjugated secondary anti-idiotype detection antibody able to bind the sdAb.
• the secondary antibody was incubated on the plates for 1 h and binding was visualized using a TMB substrate solution followed by addition of stop solution (1 M H2SO4) and measuring the absorbance at 450 nm on an Emax spectrophotometer (Molecular Devices). Absorbance values were converted into test article concentrations in SoftMax Pro using standard curves from proteins with known concentrations. 4-parameter logistic regression was used to fit the standard curve. Data were exported and graphed using GraphPad Prism analysis software.
• the albumin-targeting sdAb polypeptide can slow the clearance of human IgGl and extend the serum exposure when attached to the IgGl.
• Absolute concentrations of anti-albumin hz4A01v51 VHH-IgGl xELL-Fc (cxl l956) in serum after single doses of 30 mg/kg (FIG. 9A) or 0.3 mg/kg (FIG. 9C) are significantly higher than concentrations of a nontargeted VHH-IgGl xELL-Fc of equivalent size that does not bind albumin (cxl 1851).
• cMax levels 30 min after the injection are already lower than those of cxl 1956.
• the more rapid clearance of the non-targeted construct (cxl 1851) continues within the first 6h after injection as shown in the normalized plots (FIG. 9B and FIG. 9D).
• non-targeted cxl 1851 concentrations drop by almost 60% in the 30 mg/kg dose level cohort by 6 hours, whereas albumin-binding cxl 1956 concentrations only drop by about 12% (FIG. 10B).
• concentration of albumin-binding cxl 1956 dropped to only about 87% of Cmax, compared to about 72% of cMax for non-albumin-binding cxl 1851.
• Test articles were diluted either in a buffer containing 50 mM MES, 150 mM NaCl and 0.025% Tween-20 at pH 6 or a buffer with 50 mM Tris, 150 mM NaCl and 0.025% Tween-20 at pH 8. Test article dissociation was followed for 300 seconds by dipping the sensor in the respective pH buffer without test articles. Association and dissociation curves were exported using the Forte Data Analysis software.
• Example 8 Binding of various single-domain antibody formats to human albumin [00159] The ability of different monospecific and bispecific albumin-binding single domain antibody formats to bind recombinant human albumin at neutral (7.4) pH, and a second target (IL-4R) was evaluated by ELISA.
• Monospecific antibodies comprising an albumin-targeting sdAb (hz4A01v51 VHH) linked to the C-terminal end of an xELL Fc region via a glycine-serine linker of 6 or 12 residues, bispecific antibodies comprising the Fab domains (VL-CL (SEQ ID NO: 77 and VH-CH1 (SEQ ID NO: 76) of an IL-4R-targeting antibody (dupilumab), an IgGl or IgG4 Fc region, and an albumin-targeting sdAb (hz4A01v51 VHH) positioned at different locations, and monospecific control IL-4R targeting molecules lacking the albumin-targeting sdAb were evaluated.
• test article designations and general structure of the polypeptides used in this study are summarized in Table 2.
• ELISA 96-well ELISA plates (MaxiSorb, Biolegend), were coated with human albumin or IL4R at 1 ug/mL (lOOuL/well) overnight at 4°C in PBS.
• the plates were washed 3x times in 0.05% PBST (150uL/well) and then blocked with Casein in 0.05% PBST (200uL/well) for 2 hours at RT.
• the plates were washed 3x times in 0.05% PBST, and lOOuL of titrated test articles in 0.05% PBST were added to the wells of the plate (starting lOOnM, 1 :3 dilutions, 11 -point titration) and incubated at 4°C for 1 hour. After another wash, plates were then incubated for 30 min at room temperature with an HRP- conjugated secondary antibody in 0.05% PBST (lOOuL/well) specific to human IgGl (Jackson ImmunoResearch). Plates were then washed again before addition of TMB substrate (lOOuL/well) that was allowed to reach RT before addition to the plate.
• Example 9 Modification of anti-albumin sdAb Hz4A01v51
• the framework regions of Hz4A01v51 were further modified, including by back- mutating certain residues to the donor amino acid and/or introducing alternative charged residues.
• the modified VHHs (Hz4A01v51.9, Hz4A01v51.11, Hz4A01v51.12, and Hz4A01v51.13), were used to generate monovalent (VHH-fused to Fc NTT) anti-albumin binding molecules having the general structure shown in FIG. 6(ii).
• Several (Hz4A01v51.9, Hz4A01v51.12, and Hz4A01v51.13) were also used to generate bivalent (VHH-fused to Fc xELL) anti-albumin binding molecules having the general structure shown in FIG.
• Binding of the monovalent and bivalent anti-albumin molecules and the monovalent Hz4A01v51-NNT- hFc to human serum albumin at pH 6.0 and at pH 7.0 was determined by ELISA as follows. Plates (Maxi Sorb, Biolegend) were coated with albumin at 2ug/mL (lOOuL) overnight at 4°C in PBS, or with albumin at 2ug/mL (lOOuL) overnight at 4°C in 20mM His-HCl, 150mM NaCl pH 6. The plates were washed 3x times in 0.05% PBST or with the pH 6 buffer and then blocked with 5% Milk PBST for 2 hours at RT.
• the plates were washed 3x times in 0.05% PBST or with the pH 6 buffer and titrations of the test articles in PBST or the pH 6 buffer were added to the plates (starting lOOnM, 1 :5 dilutions) and incubated at 4°C for 1 hour. After another wash, plates were then incubated for 30 min at room temperature with an HRP-conjugated secondary antibody specific to human IgGl. Plates were then washed before addition of a TMB substrate. The HRP-TMB reaction was allowed to develop for six minutes, TMB stop buffer was added and the absorbance was measured at 450nm on a plate reader (Molecular Devices). The data were plotted and analyzed using GraphPad Prism analysis software. The 0.16 nM titration point was not tested for the negative control and ELL samples.
• the modified anti-albumin antibodies exhibit similar binding profiles at pH 6 (FIG. 12A), and pH 7.4 (FIG. 12B) and all exhibited improved binding over that observed for Hz4A01v51, particularly at pH 6.
• Hz4A01v51.9 and Hz4A01v51.13 exhibited similar binding profiles that were improved over Hz4A01v51 at both pH 6 (FIG. 12C) and pH 7.4 (FIG. 12D).

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