WO2013106485A2 - Ultralong complementarity determining regions and uses thereof - Google Patents

Ultralong complementarity determining regions and uses thereof Download PDF

Info

Publication number
WO2013106485A2
WO2013106485A2 PCT/US2013/020903 US2013020903W WO2013106485A2 WO 2013106485 A2 WO2013106485 A2 WO 2013106485A2 US 2013020903 W US2013020903 W US 2013020903W WO 2013106485 A2 WO2013106485 A2 WO 2013106485A2
Authority
WO
WIPO (PCT)
Prior art keywords
antibody
sequence
ultralong cdr3
derived
seq
Prior art date
Application number
PCT/US2013/020903
Other languages
French (fr)
Other versions
WO2013106485A3 (en
Inventor
Omar A. BAZIRGAN
Hongyuan Helen MAO
Vaughn Smider
Dan EKIERT
Peter Schultz
Feng Wang
Ian Wilson
Yong Zhang
Original Assignee
The Scripps Research Institute
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by The Scripps Research Institute filed Critical The Scripps Research Institute
Priority to JP2014552273A priority Critical patent/JP6684490B2/en
Priority to EP13735853.7A priority patent/EP2802603A4/en
Priority to AU2013208003A priority patent/AU2013208003B2/en
Priority to CA2863224A priority patent/CA2863224A1/en
Priority to CN201380013323.8A priority patent/CN104520321A/en
Publication of WO2013106485A2 publication Critical patent/WO2013106485A2/en
Publication of WO2013106485A3 publication Critical patent/WO2013106485A3/en
Priority to AU2018201832A priority patent/AU2018201832A1/en

Links

Classifications

    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/52—Cytokines; Lymphokines; Interferons
    • C07K14/53—Colony-stimulating factor [CSF]
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/46—Hybrid immunoglobulins
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/20—Immunoglobulins specific features characterized by taxonomic origin
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/50—Immunoglobulins specific features characterized by immunoglobulin fragments
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/50—Immunoglobulins specific features characterized by immunoglobulin fragments
    • C07K2317/55—Fab or Fab'
    • 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
    • C07K2317/569—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
    • C07K2317/73—Inducing cell death, e.g. apoptosis, necrosis or inhibition of cell proliferation
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/70—Immunoglobulins specific features characterized by effect upon binding to a cell or to an antigen
    • C07K2317/76—Antagonist effect on antigen, e.g. neutralization or inhibition of binding
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/90—Immunoglobulins specific features characterized by (pharmaco)kinetic aspects or by stability of the immunoglobulin
    • C07K2317/94—Stability, e.g. half-life, pH, temperature or enzyme-resistance
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2318/00—Antibody mimetics or scaffolds
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • C07K2319/30—Non-immunoglobulin-derived peptide or protein having an immunoglobulin constant or Fc region, or a fragment thereof, attached thereto
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • C07K2319/50—Fusion polypeptide containing protease site
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • C07K2319/55—Fusion polypeptide containing a fusion with a toxin, e.g. diphteria toxin
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/62—DNA sequences coding for fusion proteins
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N5/00—Undifferentiated human, animal or plant cells, e.g. cell lines; Tissues; Cultivation or maintenance thereof; Culture media therefor

Definitions

  • immunoglobulin constructs comprising at least a portion of an ultralong CDR3, methods of making such constructs, pharmaceutical compositions and
  • medicaments comprising such constructs, and methods of using such constructs and compositions to prevent, inhibit, and/or treat a disease or condition in a subject.
  • Antibodies are natural proteins that the vertebrate immune system forms in response to foreign substances (antigens), primarily for defense against infection.
  • antibodies have been induced in animals under artificial conditions and harvested for use in therapy or diagnosis of disease conditions, or for biological research.
  • Each individual antibody producing cell produces a single type of antibody with a chemically defined composition, however, antibodies obtained directly from animal serum in response to antigen inoculation actually comprise an ensemble of non- identical molecules (e.g., polyclonal antibodies) made from an ensemble of individual antibody producing cells.
  • Some bovine antibodies have unusually long VH CDR3 sequences compared to other vertebrates. For example, about 10% of IgM contains "ultralong" CDR3 sequences, which can be up to 61 amino acids long. These unusual CDR3s often have multiple cysteines. Functional VH genes form through a process called V(D)J recombination, wherein the D-region encodes a significant proportion of CDR3. A unique D-region encoding an ultralong sequence has been identified in cattle. Ultralong CDR3s are partially encoded in the cattle genome, and provide a unique characteristic of their antibody repertoire in comparison to humans. Kaushik et al. (U.S. Patent Nos. 6,740,747 and 7,196,185) disclose several bovine germline D-gene sequences unique to cattle stated to be useful as probes and a bovine VDJ cassette stated to be useful as a vaccine vector. SUMMARY
  • the present disclosure provides antibodies that comprise an utralong CDR3 including, libraries that comprise an ultralong CDR3, and uses thereof.
  • the present disclosure also provides a library of antibodies or binding fragments thereof, wherein the antibodies or binding fragments thereof comprise an ultralong CDR3.
  • the ultralong CDR3 is 35 amino acids in length or longer, 40 amino acids in length or longer, 45 amino acids in length or longer, 50 amino acids in length or longer, 55 amino acids in length or longer, or 60 amino acids in length or longer.
  • the ultralong CDR3 is 35 amino acids in length or longer.
  • the ultralong CDR3 comprises 3 or more cysteine residues, 4 or more cysteine residues, 5 or more cysteine residues, 6 or more cysteine residues, 7 or more cysteine residues, 8 or more cysteine residues, 9 or more cysteine residues, 10 or more cysteine residues, 11 or more cysteine residues, or 12 or more cysteine residues.
  • the ultralong CDR3 comprises 3 or more cysteine residues.
  • the antibodies or binding fragments thereof comprise a cysteine motif.
  • the cysteine motif is selected from the group consisting of SEQ ID NOS: 45-156. In some embodiments of each or any of the above or below mentioned embodiments, the cysteine motif is selected from the group consisting of SEQ ID NOS: 45-156. In some embodiments of each or any of the above or below mentioned embodiments, the cysteine motif is selected from the group consisting of SEQ ID NOS: 45-156. In some embodiments of each or any of the above or below mentioned embodiments, the cysteine motif is selected from the group consisting of SEQ ID NOS: 45-156. In some embodiments of each or any of the above or below mentioned embodiments, the cysteine motif is selected from the group consisting of SEQ ID NOS: 45-156. In some embodiments of each or any of the above or below mentioned embodiments, the cysteine motif is selected from the group consisting of SEQ ID NOS: 45-156.
  • the cysteine motif is selected from the group consisting of SEQ ID NOS: 45-99. In some embodiments of each or any of the above or below mentioned embodiments, the cysteine motif is selected from the group consisting of SEQ ID NOS: 45-135. In some embodiments of each or any of the above or below mentioned embodiments, the cysteine motif is selected from the group consisting of SEQ ID NOS: 100-135. In some embodiments of each or any of the above or below mentioned embodiments, the cysteine motif is selected from the group consisting of SEQ ID NOS: 136-156.
  • the ultralong CDR3 comprises a non-human DH or a derivative thereof.
  • the ultralong CDR3 comprises a JH sequence or a derivative thereof.
  • the ultralong CDR3 comprises: a non-human VH sequence or a derivative thereof, a non-human DH sequence or a derivative thereof; and/or a JH sequence or derivative thereof.
  • the ultralong CDR3 comprises an additional amino acid sequence comprising two to six amino acid residues or more positioned between the VH sequence and the DH sequence.
  • the ultralong CDR3 comprises a non-bovine sequence.
  • the non-bovine sequence is a non-antibody or a human sequence.
  • the non-bovine sequence replaces at least a portion of the ultralong CDR3.
  • the non-bovine sequence is a hormone, lymphokine, interleukin, chemokine, cytokine, toxin, or combination thereof.
  • the non-bovine sequence is a cytokine.
  • the cytokine is granulocyte colony- stimulating factor (G-CSF).
  • the ultralong CDR3 comprises an additional sequence that is a linker.
  • the linker is linked to a C-terminus, a N-terminus, or both C-terminus and N-terminus of the non- antibody sequence.
  • the linker is (GGGGS) n (SEQ ID NO: 339), where n is an integer between 0 and 5.
  • the linker is (GSG)n (SEQ ID NO: 342), GGGSGGGGS (SEQ ID NO: 337) or GGGGSGGGS (SEQ ID NO: 338)
  • the ultralong CDR3 comprises a X 1 X 2 X 3 X 4 X 5 X n motif, wherein Xi is threonine (T), glycine (G), alanine (A), serine (S), or valine (V), wherein X 2 is serine (S), threonine (T), proline (P), isoleucine (I), alanine (A), valine (V), or asparagine (N), wherein X 3 is valine (V), alanine (A), threonine (T), or aspartic acid (D), wherein X 4 is histidine (H), threonine (T), arginine (R), tyrosine (Y), phenylalanine (F), or leucine (L), wherein X 5 is glutamine (Q), and wherein n is 27 - 54.
  • Xi is threonine (T), glycine (G), alanine (
  • the ultralong CDR3 further comprises a (X a X b ) z motif, wherein X a is any amino acid residue, X b is an aromatic amino acid selected from the group consisting of: tyrosine (Y), phenylalanine (F), tryptophan (W), and histidine (H), and wherein z is 1 - 4.
  • the (X a X b ) z motif is YXYXYX.
  • the ultralong CDR3 comprises a X 1 X 2 X 3 X 4 X 5 X n (X a X b ) z motif, wherein X 1 is threonine (T), glycine (G), alanine (A), serine (S), or valine (V), wherein X 2 is serine (S), threonine (T), proline (P), isoleucine (I), alanine (A), valine (V), or asparagine (N), wherein X 3 is valine (V), alanine (A), threonine (T), or aspartic acid (D), wherein X 4 is histidine (H), threonine (T), arginine (R), tyrosine (Y), phenylalanine (F), or leucine (L), and wherein X 5 is glutamine (Q), wherein X 1 is threonine (T), glycine (G), alan
  • the X ! X 2 X 3 X 4 X 5 motif is TTVHQ (SEQ ID NO: 159) or TSVHQ (SEQ ID NO: 160), and wherein the (X a X b ) z motif is YXYXYX.
  • the ultralong CDR3 comprises TSVHQETKKYQ (SEQ ID NO.157).
  • the ultralong CDR3 comprises VHQETKKYQ (SEQ ID NO: 158).
  • the ultralong CDR3 comprises CTTVHQX n (SEQ ID NO. 223).
  • the ultralong CDR3 comprises CTSVHQX n (SEQ ID NO. 223), wherein n is 1-8.
  • the ultralong CDR3 comprises TTVHQ (SEQ ID NO. 159).
  • the ultralong CDR3 comprises TSVHQ (SEQ ID NO. 160).
  • the ultralong CDR3 comprises VHQ. [0039] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 comprises K Q.
  • the ultralong CDR3 comprises VYQ.
  • the ultralong CDR3 comprises CX 1 X 2 X 3 X 4 Q (SEQ ID NO: 228), wherein X 1 is T, S, A, or G, wherein X 2 is T, S, A, P, or I, wherein X 3 is V or K, and wherein X 4 is H, K, or Y.
  • the ultralong CDR3 comprises CX 1 X 2 VHQ (SEQ ID NO: 230), wherein X 1 is T, S, A, or G, and wherein X 2 is T, S, A, P, or I.
  • the ultralong CDR3 comprises CX 1 X 2 VX 3 Q (SEQ ID NO: 232), wherein X 1 is T, S, A, or G, wherein X 2 is T, S, A, P, or I, and wherein X 3 is H, Y, or K.
  • the ultralong CDR3 comprises CX 1 X 2 K Q (SEQ ID NO: 234), wherein X 1 is T, S, A, or G, and wherein X 2 is T, S, A, P, or I.
  • the ultralong CDR3 comprises YTYNYEW (SEQ ID NO: 235).
  • the ultralong CDR3 comprises YX ! YX 2 (SEQ ID NO: 296), wherein X 2 is E or D.
  • the ultralong CDR3 comprises YX ! YX 2 Y (SEQ ID NO: 297).
  • the ultralong CDR3 comprises YEX, wherein X is H, W, N, F, I or Y.
  • the ultralong CDR3 comprises YDX, wherein X is H, W, N, F, I or Y.
  • the ultralong CDR3 comprises XYE, wherein X is T, S, N or I.
  • the ultralong CDR3 comprises XYD, wherein X is T, S, N or I.
  • the ultralong CDR3 comprises Y(E/D)X 1 X n W (SEQ ID NOS: 304-305), wherein X 1 is H,W, N, F, I or Y, and wherein n is 1-4.
  • the antibodies or binding fragments thereof are chimeric, human engineered, or humanized.
  • the ultralong CDR3 is a ruminant CDR3.
  • the ruminant is a cow.
  • the present disclosure also provides a library of polynucleotides encoding for antibodies or binding fragments thereof, wherein the encoded antibodies or binding fragments thereof comprise an ultralong CDR3.
  • the ultralong CDR3 is 35 amino acids in length or longer, 40 amino acids in length or longer, 45 amino acids in length or longer, 50 amino acids in length or longer, 55 amino acids in length or longer, or 60 amino acids in length or longer.
  • the ultralong CDR3 is 35 amino acids in length or longer.
  • the ultralong CDR3 comprises 3 or more cysteine residues, 4 or more cysteine residues, 5 or more cysteine residues, 6 or more cysteine residues, 7 or more cysteine residues, 8 or more cysteine residues, 9 or more cysteine residues, 10 or more cysteine residues, 11 or more cysteine residues, or 12 or more cysteine residues.
  • the ultralong CDR3 comprises 3 or more cysteine residues.
  • the antibodies or binding fragments thereof comprise a cysteine motif.
  • the cysteine motif is selected from the group consisting of SEQ ID NOS: 45-156. In some embodiments of each or any of the above or below mentioned embodiments, the cysteine motif is selected from the group consisting of SEQ ID NOS: 45-156. In some embodiments of each or any of the above or below mentioned embodiments, the cysteine motif is selected from the group consisting of SEQ ID NOS: 45-156. In some embodiments of each or any of the above or below mentioned embodiments, the cysteine motif is selected from the group consisting of SEQ ID NOS: 45-156. In some embodiments of each or any of the above or below mentioned embodiments, the cysteine motif is selected from the group consisting of SEQ ID NOS: 45-156. In some embodiments of each or any of the above or below mentioned embodiments, the cysteine motif is selected from the group consisting of SEQ ID NOS: 45-156.
  • the cysteine motif is selected from the group consisting of SEQ ID NOS: 45-99. In some embodiments of each or any of the above or below mentioned embodiments, the cysteine motif is selected from the group consisting of SEQ ID NOS: 45-135. In some embodiments of each or any of the above or below mentioned embodiments, the cysteine motif is selected from the group consisting of SEQ ID NOS: 100-135. In some embodiments of each or any of the above or below mentioned embodiments, the cysteine motif is selected from the group consisting of SEQ ID NOS: 136-156. [0063] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 comprises a non-human DH or a derivative thereof.
  • the ultralong CDR3 comprises a JH sequence or a derivative thereof.
  • the ultralong CDR3 comprises: a non-human VH sequence or a derivative thereof, a non-human DH sequence or a derivative thereof; and/or a JH sequence or derivative thereof.
  • the ultralong CDR3 comprises an additional amino acid sequence comprising two to six amino acid residues or more positioned between the VH sequence and the DH sequence.
  • the ultralong CDR3 comprises a non-bovine sequence.
  • the non-bovine sequence is a non-antibody or a human sequence.
  • the non-bovine sequence replaces at least a portion of the ultralong CDR3.
  • the non-antibody sequence is a hormone, lymphokine, interleukin, chemokine, cytokine, toxin, or combination thereof.
  • the non-bovine sequence is a cytokine.
  • the cytokine is granulocyte colony- stimulating factor (G-CSF).
  • the ultralong CDR3 comprises an additional sequence that is a linker.
  • the linker is linked to a C-terminus, a N-terminus, or both C-terminus and N-terminus of the non- antibody sequence.
  • the linker is (GGGGS) n (SEQ ID NO: 339), where n is an integer between 0 and 5.
  • the linker is (GSG)n (SEQ ID NO: 342), GGGSGGGGS (SEQ ID NO: 337) or GGGGSGGGS (SEQ ID NO: 338).
  • the ultralong CDR3 comprises a X 1 -X 2 -X 3 -X 4 -X 5 motif, wherein X 1 is threonine (T), glycine (G), alanine (A), serine (S), or valine (V), wherein X 2 is serine (S), threonine (T), proline (P), isoleucine (I), alanine (A), valine (V), or asparagine (N), wherein X 3 is valine (V), alanine (A), threonine (T), or aspartic acid (D), wherein X 4 is histidine (H), threonine (T), arginine (R), tyrosine (Y), phenylalanine (F), or leucine (L), and wherein X5 is glutamine (Q).
  • X 1 is threonine (T), glycine (G), alanine (A), serine (S), or valine
  • the X ! X 2 X 3 X 4 X 5 motif is TTVHQ (SEQ ID NO: 159) or TSVHQ (SEQ ID NO: 160).
  • the ultralong CDR3 further comprises a (X a X b ) z motif, wherein X a is an aromatic amino acid selected from the group consisting of: tyrosine (Y), phenylalanine (F), tryptophan (W), and histidine (H), wherein X b is any amino acid residue, and wherein z is 1 -4.
  • X a is an aromatic amino acid selected from the group consisting of: tyrosine (Y), phenylalanine (F), tryptophan (W), and histidine (H), wherein X b is any amino acid residue, and wherein z is 1 -4.
  • the (X a X b ) z motif is YXYXYX.
  • the ultralong CDR3 comprises a X 1 X 2 X 3 X 4 X 5 X n (X 6 X 7 ) z motif, wherein X 1 is threonine (T), glycine (G), alanine (A), serine (S), or valine (V), wherein X 2 is serine (S), threonine (T), proline (P), isoleucine (I), alanine (A), valine (V), or asparagine (N), wherein X 3 is valine (V), alanine (A), threonine (T), or aspartic acid (D), wherein X 4 is histidine (H), threonine (T), arginine (R), tyrosine (Y), phenylalanine (F), or leucine (L), and wherein X 5 is glutamine (Q), wherein X a
  • the X ! X 2 X 3 X 4 X 5 motif is TTVHQ (SEQ ID NO: 159) or TSVHQ (SEQ ID NO: 160), and wherein the (X a -X b ) z motif is YXYXYX.
  • the ultralong CDR3 comprises TSVHQETKKYQ (SEQ ID NO. 157).
  • the ultralong CDR3 comprises VHQETKKYQ (SEQ ID NO: 158).
  • the ultralong CDR3 comprises CTTVHQXn (SEQ ID NO. 223).
  • the ultralong CDR3 comprises CTSVHQXn (SEQ ID NO. 224), wherein n is 1-8.
  • the ultralong CDR3 comprises TTVHQ (SEQ ID NO. 159). [0087] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 comprises TSVHQ (SEQ ID NO. 160).
  • the ultralong CDR3 comprises VHQ.
  • the ultralong CDR3 comprises K Q.
  • the ultralong CDR3 comprises VYQ.
  • the ultralong CDR3 comprises CX 1 X 2 X 3 X 4 Q, wherein X 1 is T, S, A, or G, wherein X 2 is T, S, A, P, or I, wherein X 3 is V or K, and wherein X 4 is H, K, or Y.
  • the ultralong CDR3 comprises CX 1 X 2 VHQ, wherein X 1 is T, S, A, or G, and wherein X 2 is T, S, A, P, or I.
  • the ultralong CDR3 comprises CX 1 X 2 VX 3 Q, wherein X 1 is T, S, A, or G, wherein X 2 is T, S, A, P, or I, and wherein X 3 is H, Y, or K.
  • the ultralong CDR3 comprises CX 1 X 2 K Q, wherein X 1 is T, S, A, or G, and wherein X 2 is T, S, A, P, or I.
  • the ultralong CDR3 comprises YTYNYEW (SEQ ID NO: 235).
  • the ultralong CDR3 comprises YX 1 YX 2 , wherein X 2 is E or D.
  • the ultralong CDR3 comprises YX ! YX 2 Y.
  • the ultralong CDR3 comprises YEX, wherein X is H, W, N, F, I or Y.
  • the ultralong CDR3 comprises YDX, wherein X is H, W, N, F, I or Y.
  • the ultralong CDR3 comprises XYE, wherein X is T, S, N or I.
  • the ultralong CDR3 comprises XYD, wherein X is T, S, N or I. [00102] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 comprises Y(E/D)X 1 X n W, wherein X 1 is H,W, N, F, I or Y, and wherein n is 1-4.
  • the antibodies or binding fragments thereof are chimeric, human engineered, or humanized.
  • the ultralong CDR3 is a ruminant CDR3.
  • the ruminant is a cow.
  • the antibodies or binding fragments thereof are present in a spatially addressed format.
  • the polynucleotides coding for the antibodies or binding fragments thereof are present in a spatially addressed format.
  • the present disclosure also provides a library of vectors comprising any of the library of polynucleotides disclosed herein.
  • the present disclosure also provides a library of host cells comprising the any library of vectors disclosed herein.
  • the cell is a bacteria, virus, or bacteriophage.
  • the antibodies or binding fragments thereof are displayed on the cell surface.
  • the antibodies or binding fragments thereof are secreted from the cell.
  • the antibodies or binding fragments thereof are present in a spatially addressed format.
  • the present disclosure also provides an antibody or binding fragment thereof comprising an ultralong CDR3, wherein the ultralong CDR3 comprises a non-bovine sequence.
  • the ultralong CDR3 is 35 amino acids in length or longer, 40 amino acids in length or longer, 45 amino acids in length or longer, 50 amino acids in length or longer, 55 amino acids in length or longer, or 60 amino acids in length or longer.
  • the ultralong CDR3 is 35 amino acids in length or longer.
  • the ultralong CDR3 comprises 3 or more cysteine residues, 4 or more cysteine residues, 5 or more cysteine residues, 6 or more cysteine residues, 7 or more cysteine residues, 8 or more cysteine residues, 9 or more cysteine residues, 10 or more cysteine residues, 11 or more cysteine residues, or 12 or more cysteine residues.
  • the ultralong CDR3 comprises 3 or more cysteine residues.
  • the antibodies or binding fragments thereof comprise a cysteine motif.
  • the cysteine motif is selected from the group consisting of SEQ ID NOS: 45-156. In some embodiments of each or any of the above or below mentioned embodiments, the cysteine motif is selected from the group consisting of SEQ ID NOS: 45-99. In some embodiments of each or any of the above or below mentioned embodiments, the cysteine motif is selected from the group consisting of SEQ ID NOS: 45-135. In some embodiments of each or any of the above or below mentioned embodiments, the cysteine motif is selected from the group consisting of SEQ ID NOS: 100-135. In some embodiments of each or any of the above or below mentioned embodiments, the cysteine motif is selected from the group consisting of SEQ ID NOS: 136-156.
  • the non-bovine sequence is a non-antibody sequence or a human sequence.
  • the ultralong CDR3 comprises a non-human DH or a derivative thereof.
  • the ultralong CDR3 comprises a JH sequence or a derivative thereof.
  • the ultralong CDR3 comprises: a non-human VH sequence or a derivative thereof, a non-human DH sequence or a derivative thereof; and/or a JH sequence or derivative thereof.
  • the ultralong CDR3 comprises an additional amino acid sequence comprising two to six amino acid residues or more positioned between the VH sequence and the DH sequence.
  • the non-bovine sequence replaces at least a portion of the ultralong CDR3.
  • the non-bovine sequence is a hormone, lymphokine, interleukin, chemokine, cytokine, toxin, or combination thereof.
  • the non-bovine sequence is a cytokine.
  • the cytokine is granulocyte colony- stimulating factor (G-CSF).
  • the antibodies or binding fragments thereof are chimeric, human engineered, or humanized.
  • the ultralong CDR3 is a ruminant CDR3.
  • the ruminant is a cow.
  • the present disclosure also provides a polynucleotide encoding for any antibody or binding fragment thereof disclosed herein.
  • the present disclosure also provides a vector comprising any polynucleotide encoding for the antibody or binding fragment thereof disclosed herein.
  • the present disclosure also provides a host cell comprising any vector disclosed herein.
  • the cell is a bacteria, virus, or bacteriophage.
  • the antibody or binding fragment thereof is displayed on the surface of the cell.
  • the antibody or binding fragment thereof is secreted from the cell.
  • the present disclosure also provides a method of producing an antibody or binding fragment thereof comprising an ultralong CDR3 or fragment thereof comprising culturing a host cell comprising a polynucleotide encoding any of the antibodies disclosed herein under conditions wherein the polynucleotide sequence is expressed and the antibody or binding fragment thereof comprising an ultralong CDR3 or fragment thereof is produced.
  • the methods further comprise recovering the antibody or binding fragment thereof comprising an ultralong CDR3 or fragment thereof from the host cell culture.
  • the present disclosure also provides a pharmaceutical composition comprising any antibody or binding fragment thereof disclosed herein.
  • the present disclosure also provides a method of treating a mammal in need thereof comprising administering to the mammal an amount of any antibody disclosed herein.
  • the mammal is a human.
  • a recombinant antibody or fragment thereof wherein at least a portion of the recombinant antibody or fragment thereof is based on or derived from at least a portion of an ultralong CDR3.
  • an antibody or fragment thereof comprising at least a portion of an ultralong CDR3 sequence and at least a portion of a non-bovine sequence.
  • an antibody or fragment thereof comprising (a) a first antibody sequence, wherein at least a portion of the first antibody sequence is derived from at least a portion of an ultralong CDR3; (b) a non-antibody sequence; and (c) optionally, a second antibody sequence, wherein at least a portion of the second antibody sequence is derived from at least a portion of an ultralong CDR3.
  • the antibodies disclosed herein may be a chimeric, human engineered, or humanized antibody.
  • the antibodies disclosed herein may be a bovine engineered, bovinized, or fully bovine antibody.
  • the antibodies disclosed herein may comprise a Fab, a scFv, dsFv, diabody, (dsFv) 2 , minibody, flex minibody or bi-specific fragment.
  • the antibodies disclosed herein may be an isolated antibody.
  • the antibodies disclosed herein may further comprise a non-antibody sequence.
  • the non-antibody sequence may be derived from a mammal.
  • the mammal may be a bovine, human, or non-bovine mammal.
  • the antibodies disclosed herein may comprise a non-antibody sequence derived from a non-bovine animal.
  • the non-bovine animal may be a scorpion.
  • the non-bovine animal may be a lizard.
  • the lizard may be a gila monster.
  • the non-antibody sequence may be a derived from a growth factor.
  • the growth factor may be a GCSF, GMCSF or FGF21.
  • the GCSF may be a bovine GCSF.
  • the GCSF may be a human GCSF.
  • the GMCSF and/or the FGF21 may be from a human.
  • the non-antibody sequence may be a derived from a cytokine.
  • the cytokine may be a beta-interferon.
  • the non-antibody sequence may be a derived from a hormone.
  • the hormone may be an exendin-4, GLP-1, somatostatin, or erythropoietin.
  • the GLP-1 and/or erythropoietin may be from a human.
  • the non-antibody sequence may be a derived from a toxin.
  • the toxin may be a Mokal, VM-24, ziconotide, chlorotoxin, or protoxin2 (ProTxII).
  • the non- antibody sequence may be IL8, ziconotide, somatostatin, chlorotoxin, SDFl(alpha), or IL21.
  • the non-antibody sequence may comprise an amino acid sequence based on or derived from any of SEQ ID NOS: 317-332.
  • the non-antibody sequence may replace at least a portion of the ultralong CDR3.
  • the non-antibody sequence may be inserted into the sequence of the ultralong CDR3.
  • the non-antibody sequence may be conjugated to at least a portion of the antibody (e.g., ultralong CDR3, variable region, heavy chain, light chain).
  • the non-antibody sequence may be attached to the ultralong CDR3, linker, cleavage site, non-bovine sequence, non-ultralong CDR3 antibody sequence, or combination thereof.
  • the non-antibody sequence may be adjacent to the ultralong CDR3, linker, cleavage site, non-bovine sequence, non-ultralong CDR3 antibody sequence, or combination thereof.
  • the antibodies disclosed herein may comprise an ultralong CDR3 may be based on or derived from a cow ultralong CDR3. At least a portion of the antibodies disclosed herein may be from a mammal. At least a portion of the first antibody sequence and/or at least a portion of the second antibody sequence of the antibodies disclosed herein may be from a mammal. The mammal may be a bovine, human or non-bovine mammal.
  • the antibodies disclosed herein may comprise 3 or more amino acids in length.
  • the antibodies disclosed herein may comprise a sequence that may be based on or derived from an ultralong CDR3 disclosed herein.
  • the antibodies disclosed herein may comprise 1 or more amino acid residues based on or derived from a stalk domain of the ultralong CDR3.
  • the antibodies disclosed herein may comprise 1 or more amino acid residues based on or derived from a knob domain of the ultralong CDR3.
  • At least a portion of the antibodies disclosed herein may be based on or derived from at least a portion of an ultralong CDR3 disclosed herein.
  • the portion of the antibody based on or derived from at least a portion of the ultralong CDR3 may be 20 or fewer amino acids in length.
  • the portion of the antibody based on or derived from at least a portion of the ultralong CDR3 may be 3 or more amino acids in length
  • the antibodies disclosed herein may comprise 1 or more conserved motifs derived from a stalk domain of the ultralong CDR3.
  • the 1 or more conserved motifs derived from the stalk domain of the ultralong CDR3 may comprise any of the stalk domain conserved motifs disclosed herein.
  • the portion of the ultralong CDR3s disclosed herein may comprise at least a portion of a stalk domain of the ultralong CDR3, at least a portion of the knob domain of the ultralong CDR3, or a combination thereof.
  • the antibodies disclosed herein may comprise a sequence selected from any one of
  • the antibodies disclosed herein may comprise a sequence that may be 50% or more homologous to a sequence selected from any one of SEQ ID NOS: 157-224 and 235-295.
  • a portion of any of the antibodies disclosed herein may be based on or derived from at least a portion of a single ultralong CDR3 sequence.
  • a portion of the antibodies disclosed herein may be based on or derived from at least a portion of two or more different ultralong CDR3 sequences.
  • the portion of the ultralong CDR3 is based on or derived from a BLV1H12 ultralong CDR3 sequence.
  • the portion of the ultralong CDR3 may be based on or derived from a sequence that may be 50% or more homologous to a BLV1H12 ultralong CDR3 sequence.
  • the portion of the ultralong CDR3 may be based on or derived from a BLV5B8, BLVCV1, BLV5D3, BLV8C11, BF1H1, or F18 ultralong CDR3 sequence.
  • the portion of the ultralong CDR3 may be based on or derived from a sequence that may be 50% or more homologous to a BLV5B8, BLVCV1, BLV5D3, BLV8C11, BF1H1, or F18 ultralong CDR3 sequence.
  • the antibodies disclosed herein may comprise a first and/or second antibody sequence that comprises 3 or more amino acids in length.
  • a portion of the first antibody sequence derived from at least a portion of the ultralong CDR3 and/or the portion of the second antibody sequence derived from at least a portion of the ultralong CDR3 may be 20 or fewer amino acids in length.
  • a portion of the first antibody sequence derived from at least a portion of the ultralong CDR3 and/or the portion of the second antibody sequence derived from at least a portion of the ultralong CDR3 may be 3 or more amino acids in length.
  • the first and/or second antibody sequences comprise one or more amino acid residues based on or derived from a stalk domain of the ultralong CDR3.
  • the first and/or second antibody sequences may comprise one or more amino acid residues based on or derived from a knob domain of the ultralong CDR3.
  • the one or more amino acid residues derived from the knob domain of the ultralong CDR3 may be a serine and/or cysteine residue.
  • the first and/or second antibody sequences may comprise one or more conserved motifs derived from a stalk domain of the ultralong CDR3.
  • the one or more conserved motifs derived from the stalk domain of the ultralong CDR3 may comprise a sequence selected from any one of SEQ ID NOS: 157-307 and SEQ ID NOS: 333-336.
  • the portion of the first antibody sequence derived from at least a portion of the ultralong CDR3 and/or the portion of the second antibody sequence derived from at least a portion of the ultralong CDR3 comprises a sequence selected from any one of SEQ ID NOS: 157-307 and SEQ ID NOS: 333-336.
  • the portion of the first antibody sequence derived from at least a portion of the ultralong CDR3 and/or the portion of the second antibody sequence derived from at least a portion of the ultralong CDR3 may comprise a sequence that may be 50% or more homologous to a sequence selected from any one of SEQ ID NOS: 157-224 and 235-295.
  • the portion of the first antibody sequence derived from at least a portion of the ultralong CDR3 may comprise a sequence selected from any one of SEQ ID NOS: 157-234.
  • the portion of the first antibody sequence derived from at least a portion of the ultralong CDR3 may comprise a sequence that may be 50% or more homologous to a sequence selected from any one of SEQ ID NOS: 157-224.
  • the portion of the second antibody sequence derived from at least a portion of the ultralong CDR3 comprises a sequence selected from any one of SEQ ID NOS: 235-307 and SEQ ID NOS: 333-336.
  • the portion of the second antibody sequence derived from at least a portion of the ultralong CDR3 may comprise a sequence that may be 50%) or more homologous to a sequence selected from any one of SEQ ID NOS: 235-295.
  • the portion of the first antibody sequence derived from at least a portion of the ultralong CDR3 and the portion of the second antibody sequence derived from at least a portion of the ultralong CDR3 may be derived from the same ultralong CDR3 sequence.
  • the portion of the first antibody sequence derived from at least a portion of the ultralong CDR3 and the portion of the second antibody sequence derived from at least a portion of the ultralong CDR3 is derived from two or more different ultralong CDR3 sequences.
  • the portions of the ultralong CDR3 of the first and/or second antibody sequences may be based on or derived from a BLV1H12 ultralong CDR3 sequence.
  • the portions of the ultralong CDR3 of the first and/or second antibody sequences may be based on or derived from a sequence that may be 50% or more homologous to a BLV1H12 ultralong CDR3 sequence.
  • the portions of the ultralong CDR3 of the first and/or second antibody sequences may be based on or derived from a BLV5B8, BLVCV1, BLV5D3, BLV8C11, BF1H1, or F18 ultralong CDR3 sequence.
  • the portions of the ultralong CDR3 of the first and/or second antibody sequences may be based on or derived from a sequence that may be 50%> or more homologous to a BLV5B8, BLVCV1, BLV5D3, BLV8C11, BF1H1, or F18 ultralong CDR3 sequence.
  • the ultralong CDR3 is based on or derived from an ultralong CDR3 that may be 35 or more amino acids in length.
  • the ultralong CDR3 may be based on or derived from an ultralong CDR3 comprising 3 or more cysteine residues.
  • the ultralong CDR3 is based on or derived from an ultralong CDR3 may comprise one or more cysteine motifs.
  • the one or more cysteine motifs may be selected from the group consisting of SEQ ID NOS: 45-156.
  • the cysteine motif is selected from the group consisting of SEQ ID NOS: 45-99.
  • the cysteine motif is selected from the group consisting of SEQ ID NOS: 45-135.
  • the cysteine motif is selected from the group consisting of SEQ ID NOS: 100-135.
  • the cysteine motif is selected from the group consisting of SEQ ID NOS: 136-156.
  • the antibodies disclosed herein may be based on or derived from an ultralong CDR3 that may be 35 or more amino acids in length.
  • the antibodies disclosed herein may be based on or derived from an ultralong CDR3 comprising 3 or more cysteine residues.
  • the antibodies disclosed herein may be based on or derived from an ultralong CDR3 may comprise 1 or more cysteine motifs.
  • the antibodies disclosed herein may comprise an ultralong CDR3 that is 35 or more amino acids in length.
  • the antibodies disclosed herein may comprise an ultralong CDR3 comprising 3 or more cysteine residues.
  • the antibodies disclosed herein may comprise an ultralong CDR3 comprising one or more cysteine motifs.
  • the ultralong CDR3 may be a heavy chain CDR3.
  • the ultralong CDR3 may comprise an amino acid sequence derived from or based on a non-human DH sequence.
  • the ultralong CDR3 may comprise an amino acid sequence derived from or based on a JH sequence.
  • the ultralong CDR3 may comprise an amino acid sequence derived from or based on a non-human VH sequence; an amino acid sequence derived from or based on a non-human DH sequence; and/or an amino acid sequence derived from or based on a JH sequence.
  • the ultralong CDR3 may comprise an additional amino acid sequence comprising at least about two amino acid residues positioned between the VH derived amino acid sequence and the DH derived amino acid sequence.
  • Any of the antibodies disclosed herein may comprise a sequence based on or derived from a sequence selected from SEQ ID NOS: 24-44, the antibody or binding fragment thereof encoded by a DNA sequence based on or derived from the DNA of SEQ ID NOS: 2-22.
  • Any of the antibodies disclosed herein may comprise a sequence based on or derived from a sequence selected from SEQ ID NO: 23, the antibody or binding fragment thereof encoded by a DNA sequence based on or derived from the DNA of SEQ ID NO: 1.
  • any of the ultralong CDR3s disclosed herein may comprise a sequence based on or derived from a sequence selected from SEQ ID NOS: 24-44. Any of the antibodies disclosed herein may comprise a sequence based on or derived from a sequence selected from SEQ ID NO: 23. Any of the ultralong CDR3s disclosed herein may be encoded by a DNA sequence that may be derived from or based on SEQ ID NOS: 2-22. Any of the antibodies disclosed herein may comprise a portion encoded by a DNA sequence that may be derived from or based on SEQ ID NO: 1.
  • Any of the antibodies disclosed herein may comprise one or more linkers. Any of the antibodies disclosed herein may comprise a first linker sequence. Any of the antibodies disclosed herein may comprise a second linker sequence. The first and second linker sequences may comprise the same sequence. The first and second linker sequences may comprise different sequences. The first and/or second linker sequences may be the same length. The first and/or second linker sequences may be different lengths. The first and/or second linker sequences may be 3 or more amino acids in length.
  • the first and/or second linker sequence may attach the non-antibody sequence to the portion based on or derived from the portion of the ultralong CDR3.
  • the first and/or second linker sequences may attach the non-antibody sequence to the first antibody sequence.
  • the first and/or second linker sequences may attach the non-antibody sequence to the second antibody sequence.
  • the first and/or second linker sequences may be adjacent to a non-antibody sequence, a portion of an ultralong CDR3 sequence, a cleavage site sequence, a non-bovine sequence, an antibody sequence, or a combination thereof.
  • the first and/or second linker sequences may comprise one or more glycine residues.
  • the first and/or second linker sequences may comprise two or more consecutive glycine residues.
  • the first and/or second linker sequences may comprise one or more serine residues.
  • the first and/or second linker sequence may comprise one or more polar amino acid residues.
  • the one or more polar amino acid residues may be selected from serine, threonine, asparagine, or glutamine.
  • the the polar amino acid residues may comprise uncharged side chains.
  • Any of the antibodies disclosed herein may comprise one or more cleavage sites.
  • the one or more cleavage sites may comprise a recognition site for a protease.
  • the protease may be a Factor Xa or thrombin.
  • the one or more cleavage sites may comprise an amino acid sequence of IEGR.
  • the one or more cleavage site may be between a first antibody sequence and the non-antibody sequence.
  • the one or more cleavage sites may be between a second antibody sequence and the non-antibody sequence.
  • the one or more cleavage sites may be between the one or more linkers and the non-antibody sequence.
  • the one or more cleavage sites may be between a first antibody sequence and the one or more linkers.
  • the one or more cleavage sites may be between a second antibody sequence and the one or more linkers.
  • the one or more cleavage sites may be adjacent to a non-antibody sequence, a portion of an ultralong CDR3 sequence, a linker sequence, an antibody sequence, or a combination thereof.
  • [00175] is library of antibodies or binding fragments thereof, wherein the antibodies or binding fragments thereof may comprise any of the antibodies disclosed herein.
  • nucleic acid library comprising a plurality of
  • polynucleotides comprising sequences coding for antibodies or binding fragments thereof, wherein the antibodies or binding fragments thereof may comprise an ultralong CDR3.
  • nucleic acid library comprising a plurality of
  • polynucleotides comprising sequences coding for antibodies or binding fragments thereof, wherein the antibodies or binding fragments thereof may comprise any of the antibodies disclosed herein.
  • polynucleotide comprising a nucleic acid sequence that encodes a variable region, wherein the variable region may comprise an ultralong CDR3.
  • vector comprising a polynucleotide, wherein the polynucleotide comprises a nucleic acid sequence that encodes a variable region, wherein the variable region may comprise an ultralong CDR3.
  • host cell comprising a polynucleotide, wherein the polynucleotide comprises a nucleic acid sequence that encodes a variable region, wherein the variable region may comprise an ultralong CDR3.
  • polynucleotide comprising a nucleic acid sequence that encodes the antibody or binding fragment thereof of any of the antibodies disclosed herein.
  • vector comprising a polynucleotide, wherein the polynucleotide comprises a nucleic acid sequence that encodes the antibody or binding fragment thereof of any of the antibodies disclosed herein.
  • host cell comprising a polynucleotide, wherein the polynucleotide comprises a nucleic acid sequence that encodes the antibody or binding fragment thereof of any of the antibodies disclosed herein.
  • an antibody or binding fragment thereof comprising an ultralong CDR3 or fragment thereof comprising culturing a host cell comprising a polynucleotide, wherein the polynucleotide may comprise a nucleic acid sequence that encodes the antibody or binding fragment thereof of any of the antibodies disclosed herein under conditions wherein the polynucleotide sequence may be expressed and the antibody or binding fragment thereof comprising an ultralong CDR3 or fragment thereof may be produced.
  • the method may comprise recovering the antibody or binding fragment thereof comprising the ultralong CDR3 or fragment thereof from the host cell culture.
  • composition comprising any of the antibodies disclosed herein.
  • the pharmaceutical compostion may comprise two or more antibodies, wherein at least one of the two or more antibodies comprises at least a portion of an ultralong CDR3.
  • composition comprising (a) an antibody or fragment thereof comprising sequence based on or derived from at least a portion of an ultralong CDR3; and (b) a pharmaceutically acceptable excipient.
  • the antibodies disclosed herein comprise an ultralong CDR3 sequence and a non-antibody sequence.
  • the non-antibody sequence is selected from the group comprising Mokal, Vm24, human GLP-1, Exendin-4, beta- interferon, human EPO, human FGF21, human GMCSF, human interferon-beta, bovine GCSF, human GCSF, be IL8, ziconotide, somatostatin, chlorotoxin, SDFl(alpha), IL21 and a derivative or variant thereof.
  • the non-antibody sequence may comprise an amino acid sequence based on or derived from any of SEQ ID NOS: 317-332.
  • the disease or condition may be selected from the group comprising autoimmune disease, heteroimmune disease or condition, inflammatory disease, pathogenic infection, thromboembolic disorder, respiratory disease or condition, metabolic disease, central nervous system (CNS) disorder, bone disease, cancer, blood disorder, obesity, diabetes, osteoporosis, anemia, or pain.
  • autoimmune disease heteroimmune disease or condition
  • inflammatory disease pathogenic infection
  • thromboembolic disorder respiratory disease or condition
  • metabolic disease central nervous system (CNS) disorder
  • bone disease cancer
  • blood disorder obesity, diabetes, osteoporosis, anemia, or pain.
  • the disease or condition would benefit from the modulation of an ion channel.
  • the ion channel may be selected from the group comprising a potassium ion channel, sodium ion channel, or acid sensing ion channel.
  • the ion channel may be selected from the group comprising Kvl .3 ion channel, Navl .7 ion channel and acid sensing ion channel (ASIC).
  • the disease or condition would benefit from the modulation of a receptor.
  • the receptor may be selected from the group comprising GLP1R, GCGR, EPO receptor, FGFR, FGF21R, CSFR, GMCSFR, IL8R, IL21R and GCSFR.
  • the disease or condition may be mastitis.
  • the subject may be a mammal.
  • the mammal may be a bovine or human.
  • the crystals are crystals based on or derived from the antibodies disclosed herein.
  • the crystals may have a space group P2 1 2 1 2 1 .
  • the crystal has the unit cell dimensions of "a" between about 40 to 80 angstroms, between 45 to about 75 angstroms, or between about 50 to about 75 angstroms; "b" between about 40 to 140 angstroms, between about 50 to about 130 angstroms, between about 55 to about 130 angstroms; and "c” between 100 to about 350 angstroms, between 120 to about 340 angstroms, or between about 125 to about 330 angstroms.
  • the crystal may comprise a bovine antibody or portion thereof.
  • the crystal may comprise a Fab fragment based on or derived from a bovine antibody.
  • the crystal may be an isolated crystal.
  • any antibody comprising an ultralong CDR3 may be used including, for example, any of the above mentioned antibodies comprising an ultralong CDR3.
  • Figure 1A-C present the identification of a new structural domain in bovine antibodies.
  • Figure 1 A shows a comparison of CDR H3 length amongst murine, human, and bovine repertoires. An ultralong subset of over 60 amino acids is uniquely found in bovine heavy chains.
  • Figure IB shows sequences of representative CDR H3 from murine (mu), human (hu), or bovine sequences from the literature along with six bovine sequences (B-Sl to B-S4, and B-Ll and B-L2) from our deep sequencing results.
  • the conserved cysteine of framework 3 and tryptophan of framework 4 that define CDR H3 boundaries in all antibody variable regions are shaded in grey for reference..
  • the lengths of the CDR H3s are indicated at the right.
  • the murine antibodies include D44.1, an anti-HEL antibody, 93F3, an aldolase, and OKT3, a therapeutic antibody targeting human CD3. This antibody is unusual in having a free cysteine in CDR H3.
  • the human antibodies include Yvo, a cryoglobulin, CR6261, an anti- influenza A hemaglutinin, and PG9, an anti-HIV antibody which has one of the longest human CDR H3s.
  • the bovine antibodies represent the ultralong sequences in the literature, and short sequences for comparison. BLV5B8 and BLV1H12 (indicated in bold) were used in our structure determinations. Relatively conserved TTVHQ and CPDG motifs are in bold.
  • Figure 1C shows crystal structures of BLV1H12 (left) and BLV5B8 (middle) Fabs compared to the 93F3 Fab with a "normal" CDR H3 (right).
  • a superlong, two ⁇ - stranded stalk protrudes from each bovine V H immunoglobulin domain and terminates in an unusual three disulfide- linked knob domain.
  • Figure 2A-C present the structural diversity in ultralong bovine antibodies.
  • FIG. 2A shows a comparison of the structure of the two knobs showing differences in disulfide patterns. Close up views of the knobs of BLV1H12 (left) and BLV5H8 (right) are shown, in addition to a two-dimensional representation of the knob and its disulfide pattern. Disulfides are in numbered and circled. The sequences of the knob regions are shown below, with cysteines conserved with the D H 2 germline gene segment underlined. The disulfide pattern is indicated above each sequence.
  • Figure 2B shows an overlay of the variable regions of BLV1H12 and BLV5B8 shows structural homology in the variable regions except the upper part of the stalk and knob, which are
  • Figure 2C shows surface and charge density representation of BLV1H12 (left) and BLV5B8 (right) showing different shapes and charge in the knob region.
  • Figure 3A-C present the genetic basis for ultralong antibody formation.
  • Figure 3A shows the identification of V H BUL, a germline variable region used in ultralong antibodies.
  • the leader sequence is in light grey, coding sequence is indicated with the amino acid translation above, the intron is in italics, and the unique TTVHQ extension, which forms a portion of the ascending strand of the stalk is in bold.
  • the recombination signal sequence heptamer and nonamer are underlined.
  • Figure 3B shows the VHBUL region is found on chromosome 21.
  • FIG. 3C shows a schematic of the bovine immunoglobulin loci depicting VHBUL, D h 2, and ⁇ , which are preferentially used in ultralong antibodies.
  • the process of V(D)J recombination assembles the gene segments to form functional ultralong heavy and light chain genes, (bottom left) The V-D-J regions mapped onto the BLV1H12 Fab structure.
  • VHBUL is unique in encoding CDR HI and CDR H2 residues that interact with the stalk, as well as a TTVHQ motif that initiates the ascending ⁇ -strand.
  • the ⁇ light chain encodes CDR LI and CDR L2 residues that interact with the stalk.
  • Arrows indicate areas of potential junctional diversity. Relatively long V-D insertions are indicated in purple. It is unclear whether this sequence results from N-additions, gene conversion, or another mechanism, (bottom right) A detailed depiction of the interactions of CDR HI , H2, LI , and L2 with the stalk of BLV1H12, as well as the location of the YxYxY motif of the descending strand.
  • Figure 4A-C depict deep sequence diversity of bovine ultralong VH CDR H3s.
  • Figure 4A shows the distribution of the number of cysteines in bovine ultralong CDR H3s of IgM and IgG.
  • Figure 4B shows the length distribution of ultralong CDR H3s. Note that clonal sequences selected during an immune response can bias the proportion at any given length.
  • Figure 4C shows representative sequences of ultralong bovine VH CDR H3s. The terminal portion of the VHBUL region is shown, along with junctional diversity at the V-D joint, D H 2 and 1 ⁇ 2 (top). The sequences of BLVH12 and BLV5B8 are shown for comparison, followed by 20 ultralong CDR H3 sequences (bottom).
  • Cysteines conserved with D H 2 are underlined.
  • the conserved cysteine and tryptophan that define the CDR H3 boundaries in all antibody variable regions are highlighted in grey for reference.
  • the CPDG motif is underlined in grey and the region of the descending strand encoding a YxYxY motif is underlined in grey.
  • Figure 5A-C show that cysteine mutations contribute to ultralong CDR H3 diversity.
  • Figure 5A shows that the consensus of ultralong CDR H3 deep sequences aligns with D H 2.
  • a consensus sequence for three deep sequencing runs were determined, and aligned with one another and with DH2. The consensus aligns well except for some areas of insertions/deletions.
  • Figure 5B shows that the D H 2 gene region analysis showing residues that can readily mutate to cysteine, including SH hotspots.
  • the nucleotide sequence is above and translated amino-acid sequence below.
  • RGYW hotspots which are recognized by AID for SH and/or gene conversion, are boxed. Nucleotides at positions 3, 15, 19, 21, 25, 27, 31, 33, 39, 43, 45, 49, 51, 57, 60, 64, 73, 75, 79, 81, 84, 88, 90, 93, 97, 102, 106, 112, 117, 121, 123, 127, 129, 133, 139, and 145 in (B) can be altered in a single mutation to a cysteine- encoding codon.
  • Figure 5C shows affinity maturation groups show mutation to and from cysteine. Several groups of clonally related sequences were identified and analyzed for somatic
  • Figure 6A-D show bovine antibodies with ultralong CDR H3s bind antigen.
  • FIG. 6A shows immunization experimental scheme for identifying antigen-specific, ultralong CDR H3 antibodies.
  • Heavy chain variable region mRNA was isolated, amplified by RT PCR, and paired with the invariant light chain to produce a small library of IgG produced in HEK293 cells.
  • Figure 6B shows ELISA of 132 ultralong CDR H3 antibodies against BVDV (left), and binding activity of the "hits" B8, B9, and H12 in a titration assay (right).
  • Figure 6C shows the sequences of B8, H9, and H12 in comparison to BLV1H12 and the germline DR2 region. Lengths (L) of the CDR H3 are indicated at the right. Cysteines conserved with DR2 are underlined.
  • Figure 6D shows that H12 binds NS2-3 on cells. A flag-tagged BVDV NS2-3 protein construct was transfected into
  • HEK293A cells and stained with anti-Flag as a positive control (left), the H12 antibody (middle), and B8 (right). Binding assays with untransfected cells are shown on the bottom.
  • Figure 7A-B depict a model for ultralong CDR H3 diversification into novel minifolds.
  • Figure 7A shows a schematic of the DR2 knob with 4 cysteines is shown on the left, with SH and/or gene conversion leading to a multitude of new cysteine patterns and new loops on the right.
  • Figure 7B shows mechanisms for generating antibody diversity. In humans and mice (left), combinatorial diversity through V(D)J recombination and VH-VL pairing creates a multitude of different binding sites, which are further optimized following antigen exposure by somatic hypermutation.
  • Figure 8A-J depict schemes showing attachment of bovine G-CSF onto the knob domain of a heavy chain region of bovine BLV1H12 antibody to design an immunoglobulin construct described herein.
  • Figure 8A shows a ribbon diagram of a heavy chain region and light chain region of bovine BLV1H12 antibody. The boxed region highlights the extended region of the ultralong CDR3 comprising the stalk and knob domain.
  • Figure 8B shows a ribbon diagram of a growth factor (e.g., bovine G-CSF) inserted into or replacing a portion of the knob domain of a heavy chain region of a bovine BLV1H12 antibody.
  • a growth factor e.g., bovine G-CSF
  • Figure 8C shows a ribbon diagram of a toxin (e.g., Mokal, VM-24) inserted into or replacing a portion of the knob domain of a heavy chain region of a bovine BLV1H12 antibody.
  • Figure 8D shows a ribbon diagram of a receptor ligand (e.g., GLP-1, exendin-4) inserted into or replacing a portion of the knob domain of a heavy chain region of a bovine BLV1H12 antibody.
  • Figure 8E shows a ribbon diagram of a hormone (e.g., erythropoietin) inserted into or replacing a portion of the knob domain of a heavy chain region of a bovine BLV1H12 antibody.
  • a toxin e.g., Mokal, VM-24
  • Figure 8D shows a ribbon diagram of a receptor ligand (e.g., GLP-1, exendin-4) inserted into or replacing a portion of the knob domain of a heavy chain region of a bovine B
  • Figure 8F shows a cartoon depicting a heavy chain region and light chain region of bovine BLV1H12 antibody.
  • Figure 8G shows a cartoon of a growth factor (e.g., bovine G-CSF) inserted into or replacing a portion of the knob domain of a heavy chain region of a bovine BLV1H12 antibody.
  • Figure 8H shows a cartoon of a toxin (e.g., Mokal, VM-24) inserted into or replacing a portion of the knob domain of a heavy chain region of a bovine BLV1H12 antibody.
  • a growth factor e.g., bovine G-CSF
  • a toxin e.g., Mokal, VM-24
  • Figure 81 shows a cartoon of a receptor ligand (e.g., GLP-1, exendin-4) inserted into or replacing a portion of the knob domain of a heavy chain region of a bovine BLV1H12 antibody.
  • the left panel shows both ends of the receptor ligand inserted into or replacing a portion of the knob domain; the right panel shows the N-terminus of the receptor ligand released from the knob domain after treatment with a protease.
  • Figure 8J shows a cartoon of a hormone (e.g.,
  • erythropoietin inserted into or replacing a portion of the knob domain of a heavy chain region of a bovine BLV1H12 antibody.
  • Said attachment of the growth factor, toxin, receptor ligand, and hormone can be by means of a polypeptide linker of sequence GGGGS (Ab-peptide LI) or GGGSGGGGS and GGGGSGGGS (Ab-peptide L2).
  • Another construct in which attachment is not by means of a linker is not shown in this cartoon.
  • Figure 9A-9E present illustrative mouse NFS-60 cell proliferative activity for the
  • Figure 9A-9B depict proliferative activity of bovine G-CSF and human G-CSF respectively.
  • Figure 9C depicts the lack of proliferative activity for bovine
  • FIG. 9D depicts proliferative activity of bovine G- CSF inserted into or replacing a portion of the knob domain in the absence of a linker (Ab-bGCSF L0).
  • Figure 9E depicts proliferative activity of bovine G-CSF inserted into or replacing a portion of the knob domain by means of a polypeptide linker of sequence GGGGS (Ab-bGCSF LI).
  • Figure 10A-10E present human granulocyte progenitor cell proliferative activities of the Ab-GCSF fusion proteins.
  • Figure 10A-10B depict proliferative activity of bovine G-CSF and human G-CSF respectively.
  • Figure IOC depicts the lack of proliferative activity for bovine BLV1H12 antibody (Ab) in the absence of G-CSF.
  • Figure 10D depicts proliferative activity of bovine G-CSF inserted into or replacing a portion of the knob domain in the absence of a linker (Ab-bGCSF LO).
  • Figure 10E depicts proliferative activity of bovine G-CSF inserted into or replacing a portion of the knob domain, said attachment by means of a polypeptide linker of sequence GGGGS (Ab-bGCSF LI).
  • Figure 11A-11B depict pharmacokinetics of Ab-bGCSF fusion proteins in mice.
  • Figure 12A-12B provide Proliferative activities of Ab-bGCSF fusion proteins on mice neutrophils that are blood stained and counted at the 10th day post-injection.
  • Figure 13A-13C display expression and purification of Ab-bGCSF fusion proteins in Pichia pastoris.
  • Figure 13 A shows a map of Pichia expression vector for an immunoglobulin construct provided herein.
  • Figure 13B provides a western blot post-induction of expression of the immunoglobulin constructs Ab-bGCSF L0 and Ab-bGCSF LI .
  • Figure 13C provides SDS-PAGE gel of purified Ab-bGCSF L0 and Ab-bGCSF LI expressed in Pichia at a yield of -70 ⁇ g per 100 mL culture.
  • Figure 14A-14C show vectors for expression of the immunoglobulin constructs described herein in free style HEK 293 cells.
  • Figure 14A provides a vector of Ab-bGCSF L0 heavy chain for expression in free style HEK 293 cells.
  • Figure 14B provides a vector of Ab-bGCSF LI heavy chain for expression in free style HEK 293 cells.
  • Figure 14C provides a vector of Ab- bGCSF light chain for expression in free style HEK 293 cells.
  • Figure 15A shows SDS-PAGE gel of purified antibody fusions.
  • Figure 15A SDS- PAGE gel of purified Ab-bGCSF L0 and Ab-bGCSF LI proteins from HEK 293 cells.
  • Figure 15B provides a SDS PAGE of the immunoglobulin constructs Ab-Protoxin2 comprising a GGGGS linker attached to both ends of protoxin2.
  • Figure 16A-16B provide SDS PAGE and activities of the immunoglobulin constructs Ab-Mokal L0 (no linker) and Ab-Mokal LI (linker).
  • Figure 16A provides a SDS PAGE of the immunoglobulin fusion proteins Ab-Mokal L0 and Ab-Mokal LI .
  • Figure 16B provides BLVlH12-Mokal fusion proteins inhibitory activities on T cells activation
  • Figure 17 provides BLVlH12-Mokal fusion proteins inhibitory activities on human peripheral blood mononuclear cells (PBMCs)
  • PBMCs peripheral blood mononuclear cells
  • Figure 18A-18C provide SDS PAGE and activities of the immunoglobulin constructs Ab-VM24 LI (GGGGS linker) and Ab-VM24 L2 (GGGSGGGGS and GGGGSGGGS linkers).
  • Figure 18A provides a SDS PAGE of the immunoglobulin fusion proteins Ab-VM24 LI and Ab-VM24 L2.
  • Figure 18B provides BLV1H12-VM24 LI fusion protein inhibitory activities on T cells activation.
  • Figure 18C provides BLV1H12-VM24 L2 fusion protein inhibitory activities on T cells activation.
  • Figure 19 provides a SDS PAGE of the immunoglobulin constructs Ab-GLP-1 and
  • Figure 20 provides activity of Ab-GLP-1 and Ab-Ex4 on HEK293 cells expressing
  • Figure 21 provides proliferative activity of Ab-hEPO fusion proteins on TF1 cells.
  • FIG 22A-C depicts ultralong CDR3 sequences.
  • the 5 full length ultralong CDR H3s reported in the literature contain between four and eight cysteines and are not highly homologous to one another; however, some conservation of cysteine residues with D H 2 could be found when the first cysteine of these CDR H3s was "fixed" prior to alignment.
  • Four of the seven sequences (BLV1H12, BLV5D3, BLV8C 11, and BF4E9) contain four cysteines in the same positions as D R 2, but also have additional cysteines.
  • BLV5B8 has two cysteines in common with the germline D R 2.
  • B-Ll and B-L2 are from initial sequences from bovine spleen, and the remaining are selected ultralong CDR H3 sequences from deep sequencing data.
  • the first group contains the longest CDR H3s identified, and appear clonally related.
  • the * indicates a sequence represented 167 times, suggesting it was strongly selected for function.
  • Several of the eight-cysteine sequences appear selected for function as they were represented multiple times, indicated in parentheses. Other representative sequences of various lengths are indicated in the last group.
  • the framework cysteine and tryptophan residues that define the CDR H3 boundaries are double-underlined.
  • the sequences BLV1H12 through UL-77 (left-most column) presented in Tables 2A-C are depicted broken apart into four segments to identify the segments of amino acid residues that are derived from certain germline sequences. Moving from left to right, the first segment is derived from the V H germline and is represented throughout the disclosure as a X 1 X 2 X 3 X 4 X 5 motif. The second segment is a string of spacer amino acid residues designated throughout the disclosure as X N residues. The third segment is a string of amino acid residues derived from the germline D R 2 region and the fourth segment is a string of amino acid residues derived from the germline 1 ⁇ 21 region.
  • the antibodies and fragments thereof comprise at least a portion of an ultralong CDR3.
  • the portion of the ultralong CDR3 may be derived from or based on an ultralong CDR3 sequence.
  • the portion of the ultralong CDR3 may be derived from or based on a stalk domain of an ultralong CDR3 sequence.
  • the portion of the ultralong CDR3 may be derived from or based on a knob domain of an ultralong CDR3 sequence.
  • the antibodies and fragments thereof may further comprise one or more therapeutic polypeptides. The therapeutic polypeptides may be inserted into the portion of the ultralong CDR3.
  • the therapeutic polypeptides may replace one or more amino acid residues in the amino acid sequence of the portion of the ultralong CDR3.
  • the therapeutic polypeptides may replace one or more nucleotides in the nucleic acid sequence of the portion of the ultralong CDR3.
  • the therapeutic polypeptides may be conjugated or attached to the portion of the ultralong CDR3.
  • the antibodies and fragments disclosed herein may further comprise one or more linkers. Additionally, the antibodies and fragments disclosed herein further comprise a cleavage site. A portion of the antibodies and fragments disclosed herien may be based on or derived from an antibody sequence from a different animal or specie from with the ultralong CDR3 is derived.
  • the ultralong CDR3 may be derived from or based on a bovine antibody sequence and the additional and another portion of the antibody sequence may be derived from or based on a non-bovine antibody sequence. Further details of the antibodies and fragments thereof are described herein.
  • the present disclosure provides antibodies or immunoglobulin constructs comprising ultralong CDR3 sequences or portions thereof.
  • the present disclosure provides an antibody comprising an ultralong CDR3.
  • the ultralong CDR3 may be 35 amino acids in length or more (e.g., 40 or more, 45 or more, 50 or more, 55 or more, 60 or more).
  • the ultralong CDR3 may comprise at least a portion of a knob domain of a CDR3, at least a portion of a stalk domain of a CDR3, or a combination thereof.
  • the portion of the knob domain of the CDR3 may comprise one or more conserved motifs derived from the knob domain of the ultralong CDR3.
  • the portion of the stalk domain of the CDR3 may comprise one or more conserved motis derived from the stalk domain of the ultralong CDR3.
  • Such an antibody may comprise at least 3 cysteine residues or more (e.g., 4 or more, 6 or more, 8 or more) within the ultralong CDR3.
  • the antibody may comprise one or more cysteine motifs.
  • the antibody may comprise a non-antibody sequence within the ultralong CDR3.
  • the antibody comprises a non-bovine sequence.
  • the non-bovine sequence can be linked to the ultralong CDR3 sequence.
  • the antibody may further comprise a linker.
  • the linker comprises an amino acids sequence of (GSG)n, GGGSGGGGS or GGGGSGGGS.
  • the antibody may comprise a non-bovine sequence within the ultralong CDR3.
  • the antibody may further comprise an antibody sequence, wherein the antibody sequence does not comprise an ultralong CDR3 sequence.
  • the antibody may further comprise an antibody sequence, wherein the amino acid sequence identitity of the antibody peptide sequence to the ultralong CDR3 peptide sequence is about 40% or less (e.g., about 35% or less, about 30%> or less, about 25% or less, about 20% or less, about 15% or lress, 10% or less, about 5% or less, about 3% or less, about 1% or less).
  • the antibody may comprise a cytotoxic agent or therapeutic polypeptide.
  • the cytotoxic agent or therapeutic polypeptide may be conjugated to the ultralong CDR3.
  • the antibody may bind to a target.
  • the target may be a protein target.
  • the protein target may be a transmembrane protein target.
  • the antibody may comprise at least a portion of a BLV1H12 and/or BLVCV1 antibody.
  • the antibody comprises at least a portion of a BLV5D3, BLV8C11, BF1H1, BLV5B8 and/or F18 antibody.
  • the antibody may comprise at least a portion of a human antibody.
  • the antibody may be a chimeric, recombinant, engineered, synthetic, humanized, fully human, or human engineered antibody.
  • the antibody may comprise antibody sequences from two or more different antibodies.
  • the two or more different antibodies may be from the same species.
  • the specie may be a bovine specie, human specie, or murine specie.
  • the two or more different antibodies may be from the same type of animal.
  • the two or more different antibodies may be from a cow.
  • the two or more different antibodies may be from a human.
  • the two or more different antibodies are from different species.
  • the two or more different antibodies are from a human specie and bovine specie.
  • the two or more diffent antibodies are from a bovine specie and a non-bovine specie.
  • the two or more different antibodies are from a human specie and a non-human specie.
  • the present disclosure provides an antibody comprising an ultralong CDR3, wherein the CDR3 is 35 amino acids in length or more and is derived from or based on a non-human sequence.
  • the ultralong CDR3 sequence may be derived from any species that naturally produces ultralong CDR3 antibodies, including ruminants such as cattle (Bos taurus).
  • the antibody may comprise at least a portion of a BLV1H12 and/or BLVCV1 antibody.
  • the antibody comprises at least a portion of a BLV5D3, BLV8C11, BF1H1, BLV5B8 and/or F18 antibody.
  • the ultralong CDR3 sequence may be derived from a camelid or shark CDR3 sequence.
  • the present disclosure provides an antibody comprising an ultralong CDR3, wherein the CDR3 comprises a non-antibody sequence.
  • the non-antibody sequence may be derived from any protein family including, but not limited to, chemokines, growth factors, peptides, cytokines, cell surface proteins, serum proteins, toxins, extracellular matrix proteins, clotting factors, secreted proteins, etc.
  • the non-antibody sequence may be derived from a therapeutic polypeptide.
  • the non-antibody sequence may be of human or non-human origin.
  • the non-antibody sequence may comprise a synthetic sequence.
  • the non-antibody sequence may comprise a portion of a non-antibody protein such as a peptide or domain.
  • the non-antibody sequence of an ultralong CDR3 may contain mutations from its natural sequence, including amino acid changes (e.g., substitutions), insertions or deletions. Engineering additional amino acids at the junction between the non-antibody sequence may be done to facilitate or enhance proper folding of the non-antibody sequence within the antibody.
  • the CDR3 may be 35 amino acids in length or more.
  • the ultralong CDR3 may comprise at least a portion of a knob domain of a CDR3, at least a portion of a stalk domain of a CDR3, or a combination thereof.
  • the portion of the knob domain of the CDR3 may comprise one or more conserved motifs derived from the knob domain of the ultralong CDR3.
  • the portion of the stalk domain of the CDR3 may comprise one or more conserved motis derived from the stalk domain of the ultralong CDR3.
  • the antibody comprises at least 3 cysteine residues or more.
  • the antibody can comprise one or more cysteine motifs.
  • the antibody may comprise at least a portion of a BLV1H12 and/or BLVCV1 antibody.
  • the antibody comprises at least a portion of a BLV5D3, BLV8C1 1 , BF1H1 , BLV5B8 and/or F18 antibody.
  • the present disclosure provides an antibody comprising an ultralong CDR3 and a non-bovine sequence.
  • the ultralong CDR3 can be derived from a ruminant.
  • the ruminant can be a bovine.
  • the non-bovine sequence can be derived from or based on a non- bovine mammal sequence.
  • the non-bovine sequence can be derived from or based on a human, mouse, rat, sheep, dog, and/or goat sequence.
  • the ultralong CDR3 sequence can comprise the non-bovine sequence.
  • the non-bovine sequence is linked to the ultralong CDR3 sequence.
  • the non-bovine sequence can be derived from or based on at least a portion of an antibody sequence.
  • the antibody sequence can encode a variable region, constant region or a combination thereof.
  • the CDR3 may be 35 amino acids in length or more.
  • the ultralong CDR3 may comprise at least a portion of a knob domain of a CDR3, at least a portion of a stalk domain of a CDR3, or a combination thereof.
  • the portion of the knob domain of the CDR3 may comprise one or more conserved motifs derived from the knob domain of the ultralong CDR3.
  • the portion of the stalk domain of the CDR3 may comprise one or more conserved motis derived from the stalk domain of the ultralong CDR3.
  • the antibody comprises at least 3 cysteine residues or more.
  • the antibody can comprise one or more cysteine motifs.
  • the present disclosure provides an antibody comprising an ultralong CDR3, wherein the CDR3 is 35 amino acids in length or more and comprises at least 3 cysteine residues or more, including, for example, 4 or more, 6 or more, and 8 or more.
  • the present disclosure provides for an antibody comprising an ultralong CDR3 wherein the CDR3 is 35 amino acids in length or more and comprises at least 3 cysteine residues or more and wherein the ultralong CDR3 is a component of a multispecific antibody.
  • the multispecific antibody may be bispecific or comprise greater valencies.
  • the present disclosure provides an antibody comprising an ultralong CDR3, wherein the CDR3 is 35 amino acids in length or more and comprises at least 3 cysteine residues or more, wherein the ultralong CDR3 is a component of an immuno conjugate.
  • the present disclosure provides an antibody comprising an ultralong CDR3, wherein the CDR3 is 35 amino acids in length or more and comprises at least 3 cysteine residues or more, wherein the antibody comprising an ultralong CDR3 binds to a transmembrane protein target.
  • transmembrane targets may include, but are not limited to, GPCRs, ion channels, transporters, and cell surface receptors.
  • the present disclosure provides an antibody comprising an ultralong CDR3, wherein the antibody comprising an ultralong CDR3 binds to a transmembrane protein target.
  • transmembrane targets may include, but are not limited to, GPCRs, ion channels, transporters, and cell surface receptors.
  • the CDR3 may be 35 amino acids in length or more.
  • the ultralong CDR3 may comprise at least a portion of a knob domain of a CDR3, at least a portion of a stalk domain of a CDR3, or a combination thereof.
  • the portion of the knob domain of the CDR3 may comprise one or more conserved motifs derived from the knob domain of the ultralong CDR3.
  • the portion of the stalk domain of the CDR3 may comprise one or more conserved motis derived from the stalk domain of the ultralong CDR3.
  • the antibody comprises at least 3 cysteine residues or more.
  • the antibody can comprise one or more cysteine motifs.
  • an immunoglobulin construct comprising a mammalian immunoglobulin heavy chain comprising at least a portion of complementarity- determining region 3 (CDR3H); and a therapeutic polypeptide, wherein the therapeutic polypeptide is inserted into or replaces at least a portion of the CDR3H.
  • the immunoglobulin construct may comprise one or more linkers.
  • the one or more linkers can connect the therapeutic polypeptide to the heavy chain.
  • the linker comprises an amino acid acid sequence of (GSG)n (SEQ ID NO: 342), GGGSGGGGS (SEQ ID NO: 337) or GGGGSGGGS.
  • the therapeutic polypeptide is selected from a hormone, a lymphokine, an interleukin, a chemokines, a cytokine and combinations thereof.
  • the therapeutic polypeptide is a cytokine.
  • the therapeutic polypeptide is a colony stimulating factor polypeptide.
  • the colony stimulating factor is macrophage colony- stimulating factor (M-CSF), Granulocyte- macrophage colony- stimulating factor (GM-CSF), Granulocyte colony- stimulating factor (G-CSF) or fragment, or variant thereof.
  • M-CSF macrophage colony- stimulating factor
  • GM-CSF Granulocyte- macrophage colony- stimulating factor
  • G-CSF Granulocyte colony- stimulating factor
  • the colony stimulating factor is mammalian G- CSF or derivative or variant thereof.
  • the colony stimulating factor is bovine G-CSF or derivative or variant thereof.
  • the therapeutic polypeptide is Mokal, Vm24, human GLP-1, Exendin-4, human EPO, human FGF21, human GMCSF, or human interferon-beta.
  • immunoglobulin constructs comprising a mammalian immunoglobulin heavy chain comprising a knob domain in the complementarity- determining region 3 (CDR3H) or fragment thereof; and a therapeutic polypeptide attached to said knob domain of the CDR3H, wherein said mammalian immunoglobulin is a bovine immunoglobulin.
  • the bovine immunoglobulin is a BLV1H12 antibody.
  • at least a portion of the knob domain is replaced by the therapeutic polypeptide.
  • the knob domain of the CDR3H may comprise one or more conserved motifs derived from the knob domain of the ultralong CDR3H.
  • the immunoglobulin construct may further comprise at least a portion of a stalk domain in the CDR3H.
  • the portion of the stalk domain of the CDRH3 may comprise one or more conserved motis derived from the stalk domain of the ultralong CDR33H.
  • antibodies or fragments thereof comprising a stalk domain in the complementarity-determining region 3 (CDR3H) or fragment thereof; and a therapeutic polypeptide.
  • the complementarity-determining region 3 (CDR3H) is derived from a bovine ultralong CDR3H.
  • the therapeutic polypeptide can be any of the therapeutic polypeptides disclosed herein.
  • the therapeutic polypeptide is Mokal, Vm24, GLP-1, Exendin-4, human EPO, human FGF21, human GMCSF, or human interferon-beta.
  • the therapeutic polypeptide can be attached to the stalk domain.
  • the antibody or fragment thereof further comprises a linker. The linker can attach the therapeutic polypeptide to the stalk domain.
  • the antibody or fragment thereof further comprises at least a portion of a knob domain in the CDR3H.
  • the linker attaches the therapeutic polypeptide to the knob domain.
  • the knob domain is attached to the stalk domain.
  • the portion of the knob domain of the CDR3 may comprise one or more conserved motifs derived from the knob domain of the ultralong CDR3.
  • the stalk domain of the CDR3 may comprise one or more conserved motis derived from the stalk domain of the ultralong CDR3.
  • an antibody or fragment thereof is provided herein.
  • the antibody or fragment thereof can comprise at least one immunoglobulin domain or fragment thereof; and a therapeutic polypeptide or derivative or variant thereof.
  • the therapeutic polypeptide, or derivative or variant thereof can be attached to the immunoglobulin domain.
  • the therapeutic polypeptide is Mokal, Vm24, GLP-1, Exendin-4, human EPO, human FGF21, human GMCSF, human interferon-beta, or derivative or variant thereof.
  • the immunoglobulin domain is an immunoglobulin A, an immunoglobulin D, an immunoglobulin E, an immunoglobulin G, or an immunoglobulin M.
  • the immunoglobulin domain can be an immunoglobulin A, an immunoglobulin D, an immunoglobulin E, an immunoglobulin G, or an immunoglobulin M.
  • the immunoglobulin domain can be an immunoglobulin A, an immunoglobulin D, an immunoglobulin E, an immunoglobulin G, or an immunoglob
  • the immunoglobulin domain is from a mammalian antibody. Alternatively, the immunoglobulin domain is from a chimeric antibody. In some instances, the immunoglobulin domain is from an engineered antibody or recombinant antibody. In other instances, the immunoglobulin domain is from a humanized, human engineered or fully human antibody. In certain embodiments, the mammalian antibody is a bovine antibody. In other instances, the mammalin antibody is a human antibody. In other instances, the mammalian antibody is a murine antibody. In some instances, the immunoglobulin domain is a heavy chain region comprising a knob domain in the complementarity- determining region 3 (CDR3H) or fragment thereof.
  • CDR3H complementarity- determining region 3
  • the therapeutic polypeptide can be attached to the knob domain.
  • the immunoglobulin domain is a heavy chain region comprising a stalk domain in the complementarity-determining region 3 (CDR3H) or fragment thereof.
  • the therapeutic polypeptide is attached to the stalk domain.
  • the antibody or fragment thereof further comprises a linker.
  • the linker can attach the therapeutic polypeptide to the immunoglobulin domain or fragment thereof.
  • the knob domain of the CDR3 may comprise one or more conserved motifs derived from the knob domain of the ultralong CDR3.
  • the stalk domain of the CDR3 may comprise one or more conserved motis derived from the stalk domain of the ultralong CDR3.
  • an immunoglobulin construct comprising at least one
  • the immunoglobulin domain is an immunoglobulin A, an immunoglobulin D, an immunoglobulin E, an immunoglobulin G, or an immunoglobulin M. In some embodiments, the immunoglobulin domain is an immunoglobulin A, an immunoglobulin D, an immunoglobulin E, an immunoglobulin G, or an immunoglobulin M. In some embodiments, the immunoglobulin domain is an immunoglobulin A, an immunoglobulin D, an immunoglobulin E, an immunoglobulin G, or an immunoglobulin M. In some embodiments, the immunoglobulin domain is an immunoglobulin A, an immunoglobulin D, an immunoglobulin E, an immunoglobulin G, or an immunoglobulin M. In some embodiments, the immunoglobulin domain is an immunoglobulin M. In some embodiments, the immunoglobulin domain is an immunoglobulin A, an immunoglobulin D, an immunoglobulin E, an immunoglobulin G, or an immunoglobulin M.
  • the immunoglobulin domain is from a mammalian or chimeric antibody. In other instances, the immunoglobulin domain is from a humanized, human engineered or fully human antibody. In certain embodiments, the mammalian antibody is a bovine antibody. In some instances, the mammalian antibody is a human antibody. In other instances, the mammalian antibody is a murine antibody. In an embodiment, the immunoglobulin domain is a heavy chain region comprising a knob domain in the complementarity- determining region 3 (CDR3H) or fragment thereof. In an embodiment, the G- CSF polypeptide is attached to the knob domain.
  • CDR3H complementarity- determining region 3
  • the immunoglobulin domain may be a heavy chain region comprising a stalk domain in the complementarity- determining region 3 (CDR3H) or fragment thereof.
  • the G-CSF polypeptide may be attached to the stalk domain.
  • the knob domain of the CDR3 may comprise one or more conserved motifs derived from the knob domain of the ultralong CDR3.
  • the stalk domain of the CDR3 may comprise one or more conserved motis derived from the stalk domain of the ultralong CDR3.
  • an immunoglobulin construct comprising at least one immunoglobulin domain or fragment thereof; and a G-CSF polypeptide or derivative or variant thereof attached to said immunoglobulin domain, wherein said G-CSF polypeptide is a bovine G-CSF polypeptide or derivative or variant thereof.
  • a pharmaceutical composition comprising an immunoglobulin construct provided herein, and a pharmaceutically acceptable carrier.
  • a method of preventing or treating a disease in a mammal in need thereof comprising administering a pharmaceutical composition described herein to said mammal.
  • the immunoglobulin domain may be a heavy chain region comprising a knob domain in the complementarity- determining region 3 (CDR3H) or fragment thereof.
  • the G-CSF polypeptide may be attached to the knob domain.
  • immunoglobulin domain may be a heavy chain region comprising a stalk domain in the
  • CDR3H complementarity- determining region 3
  • the G-CSF polypeptide may be attached to the stalk domain.
  • the knob domain of the CDR3 may comprise one or more conserved motifs derived from the knob domain of the ultralong CDR3.
  • the stalk domain of the CDR3 may comprise one or more conserved motis derived from the stalk domain of the ultralong CDR3.
  • an antibody or fragment thereof comprising: (a) a first antibody sequence, wherein at least a portion of the first antibody sequence is derived from at least a portion of an ultralong CDR3; and (b) a non-antibody sequence.
  • the antibody or fragment thereof may further comprise a second antibody sequence, wherein at least a portion of the second antibody sequence is derived from at least a portion of an ultralong CDR3.
  • the ultralong CDR3 from which the first antibody sequence and/or second antibody sequence may be derived from a ruminant.
  • the ruminant can be a cow.
  • At least a portion of the first antibody sequence and/or at least a portion of the second antibody sequence can be derived from a mammal.
  • the mammal may be a bovine.
  • the mammal is a non-bovine mammal, such as a human.
  • the first and/or second antibody sequences may be 3 or more amino acids in length.
  • the amino acids may be consecutive amino acids.
  • the amino acids are non-consecutive amino acids.
  • the first and/or second antibody sequences may comprise a bovine antibody sequence comprising 3 or more amino acids in length.
  • the bovine antibody may be a BLVH12, BLV5B8, BLVCV1, BLV5D3,
  • the first and/or second antibody sequences may comprise a human antibody sequence comprising 3 or moreore amino acids in length.
  • the portion of the first antibody sequence derived from at least a portion of the ultralong CDR3 and/or the portion of the second antibody sequence derived from at least a portion of the ultralong CDR3 can be 20 or fewer amino acids in length.
  • the portion of the first antibody sequence derived from at least a portion of the ultralong CDR3 and/or the portion of the second antibody sequence derived from at least a portion of the ultralong CDR3 may be 3 or more amino acids in length.
  • the first and/or second antibody sequences can comprise 1 or more, 2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, 10 or more, 15 or more, 20 or more, 30 or more, or 40 or more amino acid residues derived from a knob domain of the ultralong CDR3.
  • the 1 or more amino acid residues derived from the knob domain of the ultralong CDR3 may be a serine and/or cysteine residue.
  • the first and/or second antibody sequences may comprise 1 or more, 2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, or 10 or more amino acid residues derived from a stalk domain of the ultralong CDR3.
  • the first and/or second antibody sequences may comprise 1 or more, 2 or more, 3 or more, 4 or more, or 5 or more conserved motifs derived from a stalk domain of the ultralong CDR3.
  • the one or more conserved motifs derived from the stalk domain of the ultralong CDR3 may comprise a sequence selected from any one of SEQ ID NOS: 157-307 and SEQ ID NOS: 333-336.
  • the portion of the first antibody sequence derived from at least a portion of the ultralong CDR3 and/or the portion of the second antibody sequence derived from at least a portion of the ultralong CDR3 may comprise a sequence selected from any one of SEQ ID NOS: 157-307 and SEQ ID NOS: 333-336.
  • the portion of the first antibody sequence derived from at least a portion of the ultralong CDR3 and/or the portion of the second antibody sequence derived from at least a portion of the ultralong CDR3 may comprise a sequence that is 50% or more homologous to a sequence selected from any one of SEQ ID NOS: 157-224 and 235- 295.
  • the portion of the first antibody sequence derived from at least a portion of the ultralong CDR3 may comprise a sequence selected from any one of SEQ ID NOS: 157-234.
  • the portion of the first antibody sequence derived from at least a portion of the ultralong CDR3 may comprise a sequence that is 50% or more homologous to a sequence selected from any one of SEQ ID NOS: 157-224.
  • the portion of the first antibody sequence derived from at least a portion of the ultralong CDR3 may comprise a sequence that is 50%> or more homologous to a sequence selected from any one of SEQ ID NOS: 225-227.
  • the portion of the second antibody sequence derived from at least a portion of the ultralong CDR3 may comprise a sequence selected from any one of SEQ ID NOS: 235-307 and SEQ ID NOS: 333-336.
  • the portion of the second antibody sequence derived from at least a portion of the ultralong CDR3 may comprise a sequence that may be 50% or more homologous to a sequence selected from any one of SEQ ID NOS: 235-295.
  • the portion of the first antibody sequence derived from at least a portion of the ultralong CDR3 and the portion of the second antibody sequence derived from at least a portion of the ultralong CDR3 may be derived from the same ultralong CDR3 sequence.
  • the portion of the first antibody sequence derived from at least a portion of the ultralong CDR3 and the portion of the second antibody sequence derived from at least a portion of the ultralong CDR3 may be derived from two or more different ultralong CDR3 sequences.
  • the portions of the ultralong CDR3 of the first and/or second antibody sequences may be based on or derived from a BLV1H12 ultralong CDR3 sequence.
  • the portions of the ultralong CDR3 of the first and/or second antibody sequences may be based on or derived from a BLV5B8, BLVCV1, BLV5D3, BLV8C11, BF1H1, or F18 ultralong CDR3 sequence.
  • the antibody may further comprise one or more linker sequences.
  • the present disclosure also provides antibodies that comprise a heavy chain polypeptide, wherein the heavy chain polypeptide comprises at least a portion of an ultralong CDR3 sequence.
  • the heavy chain polypeptide may comprise a polypeptide sequence based on or derived from a polypeptide sequence of any one of SEQ ID NOS: 24-44.
  • the heavy chain polypeptide may comprise a polypeptide sequence encoded by a DNA sequence based on or derived from the DNA sequence of any one of SEQ ID NOS: 2-22.
  • a heavy chain polypeptide sequence may be considered substantially similar to a polypeptide sequence provided by any one of SEQ ID NOS: 24-44 where the heavy chain polypeptide sequence shares 60%, 70%, 80%, 90%, 95%), 99%), or more nucleic acid identity to a nucleotide sequence provided by any one of SEQ ID NOS: 24-44.
  • the antibodies may further comprise a light chain polypeptide.
  • the light chain polypeptide may comprise a polypeptide sequence based on or derived from a polypeptide sequence of SEQ ID NO: 23.
  • the light chain polypeptide may comprise a polypeptide sequence encoded by a DNA sequence based on or derived from the DNA sequence of SEQ ID NO: 1.
  • antibodies further comprising a light chain polypeptide, wherein the light chain polypeptide comprises an ultralong CDR3 sequence and the light chain polypeptide sequences are substantially similar to those polypeptide sequences provided by SEQ ID NO: 23.
  • a light chain polypeptide sequence may be considered substantially similar to a polypeptide sequence provided by SEQ ID NO: 1 where the light chain polypeptide sequence shares 60%, 70%, 80%, 90%, 95%, 99%, or more nucleic acid identity to a nucleotide sequence provided by any one of SEQ ID NO: 1.
  • the antibody may have therapeutic activity in an animal.
  • the antibody can have therapeutic activity in infectious disease in a subject.
  • the antibody may comprise a monoclonal antibody, polyclonal antibody, chimeric antibody, recombinant antibody, engineered antibody, or synthetic antibody.
  • the antibody may comprise a mammalian antibody.
  • the antibody may comprise a bovine antibody.
  • the antibody may comprise a G-CSF polypeptide, or derivative or variant thereof.
  • the antibody may comprise a mammalian G-CSF polypeptide, or derivative or variant thereof.
  • the antibody may comprise a bovine G-CSF, or derivative or variant thereof.
  • a pharmaceutical composition of therapeutic formulation comprises an antibody described herein and a pharmaceutically acceptable carrier.
  • the antibody is used in a method of treating a subject in need thereof, with a therapeutically effective amount of the antibody or a pharmaceutical composition described herein.
  • a nucleic acid molecule or a complement therof encodes a therapeutic immunoglobulin described herein.
  • the present disclosure provides genetic sequences (e.g., genes, nucleic acids, polynucleotides) encoding antibodies comprising ultralong CDR3 sequences or portions thereof.
  • the present disclosure provides genetic sequences (e.g., genes, nucleic acids, polynucleotides) encoding antibodies comprising the knob domain and/or knob domain of ultralong CDR3 sequences.
  • the present disclosure provides genetic sequences encoding an antibody or immunoglobulin construct described herein.
  • the present disclosure also provides genetic sequences (e.g., genes, nucleic acids, polynucleotides) encoding an ultralong CDR3 or portion thereof.
  • the present disclosure also provides genetic sequences (e.g., genes, nucleic acids, polynucleotides) encoding the knob domain and/or knob domain of an ultralong CDR3.
  • the present disclosure provides genetic sequences encoding an antibody comprising an ultralong CDR3.
  • the ultralong CDR3 may be 35 amino acids in length or more (e.g., 40 or more, 45 or more, 50 or more, 55 or more, 60 or more).
  • the ultralong CDR3 may comprise at least a portion of a knob domain of a CDR3, at least a portion of a stalk domain of a CDR3, or a combination thereof.
  • Such an antibody may comprise at least 3 cysteine residues or more (e.g., 4 or more, 6 or more, 8 or more) within the ultralong CDR3.
  • the antibody may comprise one or more cysteine motifs.
  • the antibody may comprise a non-antibody sequence within the ultralong CDR3.
  • the antibody comprises a non-bovine sequence.
  • the antibody may further comprise an antibody sequence.
  • the antibody may comprise a cytotoxic agent or therapeutic polypeptide.
  • the cytotoxic agent or therapeutic polypeptide may be conjugated to the ultralong CDR3.
  • the antibody may bind to a target.
  • the target may be a protein target, such as a transmembrane protein target.
  • the present disclosure provides genetic sequences encoding an antibody comprising an ultralong CDR3, wherein the CDR3 is 35 amino acids in length or more and is derived from or based on a non-human sequence.
  • the genetic sequences encoding the ultralong CDR3 may be derived from any species that naturally produces ultralong CDR3 antibodies, including ruminants such as cattle (Bos taurus).
  • the ultralong CDR3 sequence may be derived from a camelid or shark CDR3 sequence.
  • the present disclosure provides genetic sequences encoding an antibody comprising an ultralong CDR3, wherein the CDR3 comprises a non-antibody protein sequence.
  • the genetic sequences encoding the non-antibody protein sequences may be derived from any protein family including, but not limited to, chemokines, growth factors, peptides, cytokines, cell surface proteins, serum proteins, toxins, extracellular matrix proteins, clotting factors, secreted proteins, etc.
  • the non-antibody sequence may be derived from a therapeutic polypeptide.
  • the non-antibody protein sequence may be of human or non-human origin.
  • the non- antibody sequence may comprise a synthetic sequence.
  • the non-antibody sequence may comprise a portion of a non-antibody protein such as a peptide or domain.
  • the non-antibody protein sequence of an ultralong CDR3 may contain mutations from its natural sequence, including amino acid changes ⁇ e.g., substitutions), insertions or deletions. Engineering additional amino acids at the junction between the non-antibody sequence may be done to facilitate or enhance proper folding of the non-antibody sequence within the antibody.
  • the CDR3 may be 35 amino acids in length or more.
  • the ultralong CDR3 may comprise at least a portion of a knob domain of a CDR3, at least a portion of a stalk domain of a CDR3, or a combination thereof.
  • the antibody comprises at least 3 cysteine residues or more.
  • the antibody can comprise one or more cysteine motifs.
  • the present disclosure provides genetic sequences encoding an antibody comprising an ultralong CDR3 and a non-bovine sequence.
  • the ultralong CDR3 can be derived from a ruminant.
  • the ruminant can be a bovine.
  • the non-bovine sequence can be derived from or based on a non-bovine mammal sequence.
  • the non-bovine sequence can be derived from or based on a human, mouse, rat, sheep, dog, and/or goat sequence.
  • the non-bovine sequence can be within the ultralong CDR3.
  • the non-bovine sequence is linked or attached to the ultralong CDR3 sequence.
  • the non-bovine sequence can be derived from or based on at least a portion of an antibody sequence.
  • the antibody sequence can encode a variable region, constant region or a combination thereof.
  • the CDR3 may be 35 amino acids in length or more.
  • the ultralong CDR3 may comprise at least a portion of a knob domain of a CDR3, at least a portion of a stalk domain of a CDR3, or a combination thereof.
  • the antibody comprises at least 3 cysteine residues or more.
  • the antibody can comprise one or more cysteine motifs.
  • the present disclosure provides genetic sequences encoding an antibody comprising an ultralong CDR3, wherein the CDR3 is 35 amino acids in length or more and comprises at least 3 cysteine residues or more, including, for example, 4 or more, 6 or more, and 8 or more.
  • the present disclosure provides genetic sequences encoding an antibody comprising an ultralong CDR3 wherein the CDR3 is 35 amino acids in length or more and comprises at least 3 cysteine residues or more and wherein the ultralong CDR3 is a component of a multispecific antibody.
  • the multispecific antibody may be bispecific or comprise greater valencies.
  • the present disclosure provides genetic sequences encoding an antibody comprising an ultralong CDR3, wherein the CDR3 is 35 amino acids in length or more and comprises at least 3 cysteine residues or more, wherein the ultralong CDR3 is a component of an immunoconjugate.
  • the present disclosure provides genetic sequences encoding an antibody comprising an ultralong CDR3 wherein the CDR3 is 35 amino acids in length or more and comprises at least 3 cysteine residues or more and wherein the antibody comprising an ultralong CDR3 binds to a transmembrane protein target.
  • transmembrane targets may include, but are not limited to, GPCRs, ion channels, transporters, and cell surface receptors.
  • the present disclosure provides genetic sequences encoding an antibody comprising an ultralong CDR3, wherein the antibody comprising an ultralong CDR3 binds to a transmembrane protein target.
  • transmembrane targets may include, but are not limited to, GPCRs, ion channels, transporters, and cell surface receptors.
  • the CDR3 may be 35 amino acids in length or more.
  • the ultralong CDR3 may comprise at least a portion of a knob domain of a CDR3, at least a portion of a stalk domain of a CDR3, or a combination thereof.
  • the antibody comprises at least 3 cysteine residues or more.
  • the antibody can comprise one or more cysteine motifs.
  • the present disclosure provides genetic sequences encoding an antibody or fragment thereof comprising: (a) a first antibody sequence, wherein at least a portion of the first antibody sequence is derived from at least a portion of an ultralong CDR3; and (b) a non-antibody sequence.
  • the antibody or fragment thereof may further comprise a second antibody sequence, wherein at least a portion of the second antibody sequence is derived from at least a portion of an ultralong CDR3.
  • the ultralong CDR3 from which the first antibody sequence and/or second antibody sequence may be derived from a ruminant.
  • the ruminant can be a cow.
  • At least a portion of the first antibody sequence and/or at least a portion of the second antibody sequence can be derived from a mammal.
  • the mammal may be a bovine.
  • the mammal is a non- bovine mammal, such as a human.
  • the first and/or second antibody sequences may be 3 or more amino acids in length.
  • the amino acids may be consecutive amino acids.
  • the amino acids are non-consecutive amino acids.
  • the first and/or second antibody sequences may comprise a bovine antibody sequence comprising 3 or more amino acids in length.
  • the bovine antibody may be a BLVH12, BLV5B8, BLVCV1, BLV5D3, BLV8C11, BF1H1, or F18 antibody.
  • the first and/or second antibody sequences may comprise a human antibody sequence comprising 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, 10 or more, 15 or more, 20 or more, 30 or more, 40 or more, 50 or more, 60 or more, or 70 or more amino acids in length.
  • the portion of the first antibody sequence derived from at least a portion of the ultralong CDR3 and/or the portion of the second antibody sequence derived from at least a portion of the ultralong CDR3 can be 20 or fewer amino acids in length.
  • the portion of the first antibody sequence derived from at least a portion of the ultralong CDR3 and/or the portion of the second antibody sequence derived from at least a portion of the ultralong CDR3 may be 3 or more amino, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, 10 or more, 15 or more, or 20 or more acids in length.
  • the first and/or second antibody sequences can comprise 1 or more, 2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, 10 or more, 15 or more, 20 or more, 30 or more, or 40 or more amino acid residues derived from a knob domain of the ultralong CDR3.
  • the 1 or more amino acid residues derived from the knob domain of the ultralong CDR3 may be a serine and/or cysteine residue.
  • the first and/or second antibody sequences may comprise 1 or more, 2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, or 10 or more amino acid residues derived from a stalk domain of the ultralong CDR3.
  • the first and/or second antibody sequences may comprise 1 or more, 2 or more, 3 or more, 4 or more, or 5 or more conserved motifs derived from a stalk domain of the ultralong CDR3.
  • the one or more conserved motifs derived from the stalk domain of the ultralong CDR3 may comprise a sequence selected from any one of SEQ ID NOS: 157-307 and SEQ ID NOS: 333-336.
  • the portion of the first antibody sequence derived from at least a portion of the ultralong CDR3 and/or the portion of the second antibody sequence derived from at least a portion of the ultralong CDR3 may comprise a sequence selected from any one of SEQ ID NOS: 157-307 and SEQ ID NOS: 333-336.
  • the portion of the first antibody sequence derived from at least a portion of the ultralong CDR3 and/or the portion of the second antibody sequence derived from at least a portion of the ultralong CDR3 may comprise a sequence that is 50% or more homologous to a sequence selected from any one of SEQ ID NOS: 157-224 and 235-295.
  • the portion of the first antibody sequence derived from at least a portion of the ultralong CDR3 may comprise a sequence selected from any one of SEQ ID NOS: 157-234.
  • the portion of the first antibody sequence derived from at least a portion of the ultralong CDR3 may comprise a sequence that is 50% or more homologous to a sequence selected from any one of SEQ ID NOS: 157-224.
  • the portion of the first antibody sequence derived from at least a portion of the ultralong CDR3 may comprise a sequence that is 50% or more homologous to a sequence selected from any one of SEQ ID NOS: 225-227.
  • the portion of the second antibody sequence derived from at least a portion of the ultralong CDR3 may comprise a sequence selected from any one of SEQ ID NOS: 235-307 and SEQ ID NOS: 333-336.
  • the portion of the second antibody sequence derived from at least a portion of the ultralong CDR3 may comprise a sequence that may be 50% or more homologous to a sequence selected from any one of SEQ ID NOS: 235- 295.
  • the portion of the first antibody sequence derived from at least a portion of the ultralong CDR3 and the portion of the second antibody sequence derived from at least a portion of the ultralong CDR3 may be derived from the same ultralong CDR3 sequence.
  • the portion of the first antibody sequence derived from at least a portion of the ultralong CDR3 and the portion of the second antibody sequence derived from at least a portion of the ultralong CDR3 may be derived from two or more different ultralong CDR3 sequences.
  • the portions of the ultralong CDR3 of the first and/or second antibody sequences may be based on or derived from a BLV1H12 ultralong CDR3 sequence.
  • the portions of the ultralong CDR3 of the first and/or second antibody sequences may be based on or derived from a BLV5B8, BLVCV1 , BLV5D3, BLV8C1 1 , BF1H1 , or F18 ultralong CDR3 sequence.
  • the antibody may further comprise one or more linker sequences.
  • the present disclosure also provides isolated genetic sequences (e.g., genes, nucleic acids, polynucleotides, oligonucleotides) such as genetic sequences encoding antibodies that comprise an ultralong CDR sequence including, for example, a CDR3 sequence as provided by any one of SEQ ID NOS: 2-22. Also provided are ultralong CDR3 nucleic acid sequences that are substantially similar to those CDR3 sequences provided by any one of SEQ ID NOS: 2-22.
  • a CDR3 sequence may be considered substantially similar to a CDR3 sequence provided by any one of SEQ ID NOS: 2-22 where the CDR3 sequence shares 80%, 85%, 90%, 95%, 99%, or more, nucleic acid sequence identity to a CDR3 sequence provided by any one of SEQ ID NOS: 2-22 or hybridizes to any one of SEQ ID NOS: 2-22 under stringent hybridization conditions.
  • the present disclosure also provides isolated genetic sequences (e.g., genes, nucleic acids, polynucleotides, oligonucleotides) such as genetic sequences encoding antibodies that comprise a heavy chain polypeptide, wherein the heavy chain polypeptide comprises at least a portion of an ultralong CDR3 sequence.
  • the heavy chain polypeptide may comprise a polypeptide sequence of any one of SEQ ID NOS: 24-44.
  • the heavy chain polypeptide may comprise a polypeptide sequence encoded by the DNA of any one of SEQ ID NOS: 2-22.
  • isolated genetic sequences e.g., genes, nucleic acids, polynucleotides, oligonucleotides
  • genetic sequences encoding antibodies comprising a heavy chain polypeptide wherein the heavy chain polypeptide comprises an ultralong CDR3 sequence and the heavy chain polypeptide sequences are substantially similar to those polypeptide sequences provided by any one of SEQ ID NOS: 24-44.
  • a heavy chain polypeptide sequence may be considered substantially similar to a polypeptide sequence provided by any one of SEQ ID NOS: 24-44where the heavy chain polypeptide sequence shares 60%, 70%, 80%>, 90%>, 95%, 99%, or more nucleic acid identity to a nucleotide sequence provided by any one of SEQ ID NOS: 24-44or hybridizes to any one of SEQ ID NOS: 24-44under stringent hybridization conditions.
  • the isolated genetic sequences e.g., genes, nucleic acids, polynucleotides, oligonucleotides
  • genetic sequences encoding antibodies may further comprise a light chain polypeptide.
  • the light chain polypeptide may comprise a polypeptide sequence of SEQ ID NO: 23.
  • the light chain polypeptide may comprise a polypeptide sequence encoded by the DNA of SEQ ID NO: 1.
  • isolated genetic sequences e.g., genes, nucleic acids, polynucleotides, oligonucleotides
  • genetic sequences encoding antibodies further comprising a light chain polypeptide wherein the light chain polypeptide comprises an ultralong CDR3 sequence and the light chain polypeptide sequences are substantially similar to those polypeptide sequences provided by SEQ ID NO: 23.
  • a light chain polypeptide sequence may be considered substantially similar to a polypeptide sequence provided by SEQ ID NO: 1 where the light chain polypeptide sequence shares 60%, 70%, 80%, 90%, 95%, 99%), or more nucleic acid identity to a nucleotide sequence provided by any one of SEQ ID NO: 1 or hybridizes to SEQ ID NOS: 1 under stringent hybridization conditions.
  • the present disclosure provides collections, libraries and arrays of antibodies comprising ultralong CDR3 sequences.
  • members of the collections, libraries, or arrays may exhibit sequence diversity.
  • the present disclosure provides a library or an array of antibodies comprising ultralong CDR3 sequences wherein at least two members of the library or array differ in the positions of at least one of the cysteines in the ultralong CDR3 sequence.
  • Structural diversity may be enhanced through different numbers of cysteines in the ultralong CDR3 sequence (e.g., at least 3 or more cysteine residues such as 4 or more, 6 or more and 8 or more) and/or through different disulfide bond formation, and hence different loop structures.
  • the present disclosure provides for a library or an array of antibodies comprising ultralong CDR3 sequences wherein at least two members of the library or the array differ in at least one amino acid located between cysteines in the ultralong CDR3.
  • members of the library or the array can contain cysteines in the same positions of CDR3, resulting in similar overall structural folds, but with fine differences brought about through different amino acid side chains.
  • Such libraries or arrays may be useful for affinity maturation.
  • the present disclosure provides libraries or arrays of antibodies comprising ultralong CDR3 sequences wherein at least two of the ultralong CDR3 sequences differ in length (e.g., 35 amino acids in length or more such as 40 or more, 45 or more, 50 or more, 55 or more and 60 or more).
  • the amino acid and cysteine content may or may not be altered between the members of the library or the array.
  • Different lengths of ultralong CDR3 sequences may provide for unique binding sites, including, for example, due to steric differences, as a result of altered length.
  • the present disclosure provides libraries or arrays of antibodies comprising ultralong CDR3 sequences wherein at least two members of the library differ in the human framework used to construct the antibody comprising an ultralong CDR3.
  • the present disclosure provides libraries or arrays of antibodies comprising ultralong CDR3 sequences wherein at least two members of the library or the array differ in having a non-antibody protein sequence that comprises a portion of the ultralong CDR3.
  • Such libraries or arrays may contain multiple non-antibody protein sequences, including for chemokines, growth factors, peptides, cytokines, cell surface proteins, serum proteins, toxins, extracellular matrix proteins, clotting factors, secreted proteins, viral or bacterial proteins, etc.
  • the non-antibody protein sequence may be of human or non-human origin and may be comprised of a portion of a non-antibody protein such as a peptide or domain.
  • the non-antibody protein sequence of the ultralong CDR3 may contain mutations from its natural sequence, including amino acid changes (e.g., substitutions), or insertions or deletions. Engineering additional amino acids at the junction between the non-antibody sequence within the ultralong CDR3 may be done to facilitate or enhance proper folding of the non-antibody sequence within the antibody.
  • the present disclosure provides libraries or arrays of antibodies comprising ultralong CDR3 sequences wherein at least two members of the library or the array differ in having a non-bovine sequence.
  • the non-bovine sequence can be derived from or based on a non-bovine mammal sequence.
  • the non-bovine sequence can be derived from or based on a human, mouse, rat, sheep, dog, and/or goat sequence.
  • the non-bovine sequence can be within the ultralong CDR3.
  • the non-bovine sequence is linked or attached to the ultralong CDR3 sequence.
  • the non-bovine sequence can be derived from or based on at least a portion of an antibody sequence.
  • the antibody sequence can encode a variable region, constant region or a combination thereof.
  • the present disclosure provides libraries or arrays of antibodies comprising ultralong CDR3 sequences wherein at least two members of the library or array differ in having a cytoxic agent or therapeutic polypeptide that is conjugated to the ultralong CDR3.
  • the cytoxic agent or therapeutic polypeptide may include, but is not limited to, a chemotherapeutic agent, a drug, a growth inhibitory agent, a toxin (e.g., an enzymatically active toxin of bacterial, fungal, plant, or animal origin, or fragments thereof), or a radioactive isotope (e.g., a radio conjugate).
  • the cytotoxic agent or therapeutic polypeptide can be encoded by a non- antibody sequence.
  • the present disclosure provides libraries or arrays of antibodies comprising ultralong CDR3 sequences wherein at least two members of the library or array differ in binding to targets.
  • the target can be a protein target.
  • the protein target can be a transmembrane protein target.
  • transmembrane targets may include, but are not limited to, GPCRs, ion channels, transporters, and cell surface receptors.
  • the libraries or the arrays of the present disclosure may be in several formats well known in the art.
  • the library or the array may be an addressable library or an addressable array.
  • the library or array may be in display format, for example, the antibody sequences may be expressed on phage, ribosomes, mRNA, yeast, or mammalian cells.
  • the present disclosure provides cells comprising genetic sequences encoding antibodies comprising ultralong CDR3 sequences or portions thereof.
  • the present disclosure provides cells comprising genetic sequences encoding antibodies comprising at least a portion of a knob domain or at least a portion of a knob domain of an ultralong CDR3 sequence.
  • the present disclosure provides cells comprising genetic sequences (e.g., genes, nucleic acids, polynucleotides) encoding an ultralong CDR3 or portion thereof.
  • the present disclosure also provides cells comprising genetic sequences (e.g., genes, nucleic acids, polynucleotides) encoding the knob domain and/or knob domain of an ultralong CDR3.
  • the present disclosure provides cells expressing an antibody comprising an ultralong CDR3.
  • the cells may be prokaryotic or eukaryotic, and an antibody comprising an ultralong CDR3 may be expressed on the cell surface or secreted into the media.
  • an antibody When displayed on the cell surface an antibody preferentially contains a motif for insertion into the plasmid membrane such as a membrane spanning domain at the C-terminus or a lipid attachment site.
  • an antibody comprising an ultralong CDR3 may be secreted into the periplasm.
  • the cells When the cells are eukaryotic, they may be transiently transfected with genetic sequences encoding an antibody comprising an ultralong CDR3.
  • a stable cell line or stable pools may be created by transfecting or transducing genetic sequences encoding an antibody comprising an ultralong CDR3 by methods well known to those of skill in the art. Cells can be selected by fluorescence activated cell sorting (FACS) or through selection for a gene encoding drug resistance.
  • FACS fluorescence activated cell sorting
  • Cells useful for producing antibodies comprising ultralong CDR3 sequences include prokaryotic cells like E. coli, eukaryotic cells like the yeasts Saccharomyces cerevisiae and Pichia pastoris, insect cells (e.g., Sf9, Hi5), Chinese hamster ovary (CHO) cells, monkey cells like COS-1, or human cells like HEK-293, HeLa, SP-1.
  • prokaryotic cells like E. coli
  • eukaryotic cells like the yeasts Saccharomyces cerevisiae and Pichia pastoris
  • insect cells e.g., Sf9, Hi5
  • Chinese hamster ovary (CHO) cells monkey cells like COS-1
  • human cells like HEK-293, HeLa, SP-1.
  • the present disclosure provides methods for making libraries comprising antibodies comprising ultralong CDR3 sequences. Methods for making libraries of spatially addressed libraries are described in WO 2010/054007. Methods of making libraries in yeast, phage, E. coli, or mammalian cells are well known in the art.
  • the present disclosure also provides methods of screening libraries of antibodies comprising ultralong CDR3 sequences.
  • An "ultralong CDR3" or an “ultralong CDR3 sequence”, used interchangeably herein, comprises a CDR3 or CDR3 sequence that is not derived from a human antibody sequence.
  • An ultralong CDR3 may be 35 amino acids in length or longer, for example, 40 amino acids in length or longer, 45 amino acids in length or longer, 50 amino acids in length or longer, 55 amino acids in length or longer, or 60 amino acids in length or longer.
  • the length of the ultralong CDR3 may include a non-antibody sequence.
  • An ultralong CDR3 may comprise at least a portion of a knob domain and/or knob domain.
  • An ultralong CDR3 may comprise a non-antibody sequence, including, for example, a cytokine, chemokine, growth factor or hormone sequence.
  • the ultralong CDR3 is a heavy chain CDR3 (CDR-H3 or CDRH3).
  • the ultralong CDR3 is a sequence derived from or based on a ruminant (e.g., bovine) sequence.
  • An ultralong CDR3 may comprise at least 3 or more cysteine residues, for example, 4 or more cysteine residues, 6 or more cysteine residues, or 8 or more cysteine residues.
  • An ultralong CDR3 may comprise one or more cysteine motifs.
  • An ultralong CDR3 may comprise an amino acid sequence that is derived from or based on SEQ ID NOS: 23-44 or is encoded by a DNA sequence that is derived from or based on SEQ ID NOS: 2-22.
  • a variable region that comprises an ultralong CDR3 may include an amino acid sequence that is derived from or based on SEQ ID NOS: 23-44 or is encoded by a DNA sequence that is derived from or based on SEQ ID NOS: 2-22. Such a sequence may be derived from or based on a bovine germline VH gene sequence.
  • An ultralong CDR3 may comprise a sequence derived from or based on a non-human DH gene sequence (see, e.g., Koti, et al. (2010) Mol.
  • An ultralong CDR3 may comprise a sequence derived from or based on a JH sequence, (see e.g., Hosseini, et al. (2004) Int. Immunol. 16: 843-852).
  • an ultralong CDR3 may comprise a sequence derived from or based on a non-human VH sequence and/or a sequence derived from or based on a non-human DH sequence and/or a sequence derived from or based on a JH sequence, and optionally an additional sequence comprising two to six amino acids or more such as, for example, between the VH derived sequence and the DH derived sequence.
  • an ultralong CDR3 may comprise a sequence that is about 50% or more homologous to a sequence derived from or based on SEQ ID NOS: 23-44.
  • the ultralong CDR3 may comprise a sequence that is about 60%, 70%>, 80%), 85%o, 90%), 95%o, 97% or more homologous to a sequence derived from or based on SEQ ID NOS: 23-44.
  • an ultralong CDR3 may comprise a sequence that aligns to 5 or more amino acids to a sequence derived from or based SEQ ID NOS: 23-44.
  • the ultralong CDR3 may comprise a sequence that aligns to 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60 or more amino acids to a sequence derived from or based SEQ ID NOS: 23-44.
  • an ultralong CDR3 may comprise a sequence that comprises 5 or more consecutive amino acids to a sequence derived from or based SEQ ID NOS: 23-44.
  • the ultralong CDR3 may comprise a sequence that comprises 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60 or more consecutive amino acids to a sequence derived from or based SEQ ID NOS: 23-44.
  • an ultralong CDR3 may comprise a sequence that is about 50% or more homologous to a DNA sequence that is derived from or based on a SEQ ID NOS: 2-22.
  • the ultralong CDR3 may comprise a sequence that is about 60%, 70%, 80%, 85%, 90%, 95%, 97% or more homologous to a DNA sequence that is derived from or based on SEQ ID NOS: 2-22.
  • an ultralong CDR3 may comprise a sequence that aligns to 5 or more nucleic acids to a DNA sequence that is derived from or based SEQ ID NOS: 2-22.
  • the ultralong CDR3 may comprise a sequence that aligns to 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 80, 100, 120, 140, 150, 175, 200, 225, 250, 275, 300, 350, 400, 450, 500, 550, 600 or more nucleic acids to a DNA sequence that is derived from or based SEQ ID NOS: 2-22.
  • an ultralong CDR3 may comprise a sequence that comprises 5 or more consecutive nucleic acids to a DNA sequence that is derived from or based SEQ ID NOS: 2-22.
  • the ultralong CDR3 may comprise a sequence that comprises 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 80, 100, 120, 140, 150, 175, 200, 225, 250, 275, 300, 350, 400, 450, 500, 550, 600 or more consecutive amino acids to a DNA sequence that is derived from or based SEQ ID NOS: 2-22.
  • an ultralong CDR3 may comprise a sequence that is about 50% or more homologous to a sequence derived from or based on a knob domain sequence.
  • the ultralong CDR3 may comprise a sequence that is about 60%, 70%, 80%, 85%, 90%, 95%, 97% or more
  • an ultralong CDR3 may comprise a sequence that aligns to 5 or more amino acids to a sequence derived from or based a knob domain sequence.
  • the ultralong CDR3 may comprise a sequence that aligns to 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60 or more amino acids to a sequence derived from or based a knob domain sequence
  • an ultralong CDR3 may comprise a sequence that comprises 5 or more consecutive amino acids to a sequence derived from or based a knob domain sequence
  • the ultralong CDR3 may comprise a sequence that comprises 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60 or more consecutive amino acids to a sequence derived from or based a knob domain sequence.
  • an ultralong CDR3 may comprise a sequence that is about 50%> or more homologous to a sequence derived from or based on a knob domain sequence.
  • the ultralong CDR3 may comprise a sequence that is about 60%, 70%, 80%>, 85%, 90%, 95%, 97% or more homologous to a sequence derived from or based on a knob domain sequence.
  • an ultralong CDR3 may comprise a sequence that aligns to 5 or more amino acids to a sequence derived from or based a knob domain sequence
  • the ultralong CDR3 may comprise a sequence that aligns to 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60 or more amino acids to a sequence derived from or based a knob domain sequence
  • an ultralong CDR3 may comprise a sequence that comprises 5 or more consecutive amino acids to a sequence derived from or based a stalk domain sequence
  • the ultralong CDR3 may comprise a sequence that comprises 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60 or more consecutive amino acids to a sequence derived from or based a stalk domain sequence.
  • the antibodies disclosed herein may comprise at least a portion of an ultralong CDR3 derived from or based on a sequence of any of the ultralong CDR3s disclosed herein.
  • the sequence of the ultralong CDR3 or a portion thereof may be modified or altered to contain one or more non-bovine antibody-based nucleotides and/or amino acids.
  • the modifications and/or alterations in the sequence of the ultralong CDR3 or portion therof may improve one or more features of the expressed antibody. For example, the modifications and/or alterations may improve expression, folding, half-life, activity and/or solubility of the antibody.
  • polynucleotides, and antibodies disclosed herein refers to a biological molecule that has been identified and separated and/or recovered from at least one component of its natural environment.
  • Antagonist refers to any molecule that partially or fully blocks, inhibits, or neutralizes an activity (e.g., biological activity) of a polypeptide. Also encompassed by
  • antagonists are molecules that fully or partially inhibit the transcription or translation of mRNA encoding the polypeptide.
  • Suitable antagonist molecules include, e.g., antagonist antibodies or antibody fragments; fragments or amino acid sequence variants of a native polypeptide; peptides; antisense oligonucleotides; small organic molecules; and nucleic acids that encode polypeptide antagonists or antagonist antibodies.
  • Reference to "an” antagonist encompasses a single antagonist or a combination of two or more different antagonists.
  • Antist refers to any molecule that partially or fully mimics a biological activity of a polypeptide.
  • agonist molecules that stimulate the transcription or translation of mRNA encoding the polypeptide.
  • Suitable agonist molecules include, e.g., agonist antibodies or antibody fragments; a native polypeptide; fragments or amino acid sequence variants of a native polypeptide; peptides; antisense oligonucleotides; small organic molecules; and nucleic acids that encode polypeptides agonists or antibodies.
  • Reference to "an” agonist encompasses a single agonist or a combination of two or more different agonists.
  • An "isolated" antibody refers to one which has been identified and separated and/or recovered from a component of its natural environment. Contaminant components of its natural environment are materials which would interfere with diagnostic or therapeutic uses for the antibody, and may include enzymes, hormones, and other proteinaceous or nonproteinaceous solutes.
  • the antibody will be purified (1) to greater than 95% by weight of antibody (e.g., as determined by the Lowry method), and preferably to more than 99% by weight, (2) to a degree sufficient to obtain at least 15 residues of N-terminal or internal amino acid sequence (e.g., by use of a spinning cup sequenator), or (3) to homogeneity by SDS-PAGE under reducing or nonreducing conditions (e.g., using CoomassieTM blue or, preferably, silver stain).
  • Isolated antibody includes the antibody in situ within recombinant cells since at least one component of the antibody's natural environment will not be present. Similarly, isolated antibody includes the antibody in medium around recombinant cells. An isolated antibody may be prepared by at least one purification step.
  • An "isolated" nucleic acid molecule refers to a nucleic acid molecule that is identified and separated from at least one contaminant nucleic acid molecule with which it is ordinarily associated in the natural source of the antibody nucleic acid.
  • An isolated nucleic acid molecule is other than in the form or setting in which it is found in nature. Isolated nucleic acid molecules therefore are distinguished from the nucleic acid molecule as it exists in natural cells.
  • an isolated nucleic acid molecule includes a nucleic acid molecule contained in cells that express an antibody where, for example, the nucleic acid molecule is in a chromosomal location different from that of natural cells.
  • Variable domain residue numbering as in Kabat or amino acid position numbering as in Kabat refers to the numbering system used for heavy chain variable domains or light chain variable domains of the compilation of antibodies in Kabat et al, Sequences of Proteins of Immunological Interest, 5th Ed. Public Health Service, National Institutes of Health, Bethesda, Md. (1991). Using this numbering system, the actual linear amino acid sequence may contain fewer or additional amino acids corresponding to a shortening of, or insertion into, a FR or CDR of the variable domain.
  • a heavy chain variable domain may include a single amino acid insert (e.g., residue 52a according to Kabat) after residue 52 of H2 and inserted residues (e.g., residues 82a, 82b, and 82c, etc according to Kabat) after heavy chain FR residue 82.
  • the Kabat numbering of residues may be determined for a given antibody by alignment at regions of homology of the sequence of the antibody with a "standard" Kabat numbered sequence.
  • substantially similar refers to a sufficiently high degree of similarity between two numeric values (generally one associated with an antibody disclosed herein and the other associated with a reference/comparator antibody) such that one of skill in the art would consider the difference between the two values to be of little or no biological and/or statistical significance within the context of the biological characteristic measured by said values (e.g., Kd values).
  • the difference between said two values is preferably less than about 50%, preferably less than about 40%>, preferably less than about 30%>, preferably less than about 20%>, preferably less than about 10% as a function of the value for the reference/comparator antibody.
  • Binding affinity generally refers to the strength of the sum total of noncovalent interactions between a single binding site of a molecule (e.g., an antibody) and its binding partner (e.g., an antigen). Unless indicated otherwise, "binding affinity” refers to intrinsic binding affinity which reflects a 1 : 1 interaction between members of a binding pair (e.g., antibody and antigen).
  • the affinity of a molecule X for its partner Y can generally be represented by the dissociation constant. Affinity can be measured by common methods known in the art, including those described herein. Low-affinity antibodies generally bind antigen slowly and tend to dissociate readily, whereas high-affinity antibodies generally bind antigen faster and tend to remain bound longer. A variety of methods of measuring binding affinity are known in the art, any of which can be used for purposes of the present disclosure.
  • An "on-rate” or “rate of association” or “association rate” or “k on” can be determined with a surface plasmon resonance technique such as Biacore (e.g., Biacore A100, BiacoreTM-2000, BiacoreTM-3000, Biacore, Inc., Piscataway, N.J.) carboxymethylated dextran biosensor chips (CM5, Biacore Inc.) and according to the supplier's instructions.
  • Biacore e.g., Biacore A100, BiacoreTM-2000, BiacoreTM-3000, Biacore, Inc., Piscataway, N.J.
  • CM5, Biacore Inc. carboxymethylated dextran biosensor chips
  • Vector refers to a nucleic acid molecule capable of transporting another nucleic acid to which it has been linked.
  • plasmid refers to a circular double stranded DNA loop into which additional DNA segments may be ligated.
  • phage vector Another type of vector is a viral vector, wherein additional DNA segments may be ligated into the viral genome.
  • Certain vectors are capable of autonomous replication in a host cell into which they are introduced (e.g., bacterial vectors having a bacterial origin of replication and episomal mammalian vectors).
  • vectors e.g., non-episomal mammalian vectors
  • vectors can be integrated into the genome of a host cell upon introduction into the host cell, and thereby are replicated along with the host genome.
  • certain vectors are capable of directing the expression of genes to which they are operatively linked.
  • Such vectors are referred to herein as "recombinant expression vectors” (or simply, “recombinant vectors”).
  • expression vectors of utility in recombinant DNA techniques are often in the form of plasmids. Accordingly, "plasmid” and “vector” may, at times, be used interchangeably as the plasmid is a commonly used form of vector.
  • Gene refers to a nucleic acid (e.g., DNA) sequence that comprises coding sequences necessary for the production of a polypeptide, precursor, or R A (e.g., mR A, rR A, tR A).
  • the polypeptide can be encoded by a full length coding sequence or by any portion of the coding sequence so long as the desired activity or functional properties (e.g., enzymatic activity, ligand binding, signal transduction, immunogenicity, etc.) of the full-length or fragment are retained.
  • the term also encompasses the coding region of a structural gene and the sequences located adjacent to the coding region on both the 5' and 3' ends for a distance of about 1 kb or more on either end such that the gene corresponds to the length of the full-length mRNA. Sequences located 5' of the coding region and present on the mRNA are referred to as 5' non-translated sequences. Sequences located 3' or downstream of the coding region and present on the mRNA are referred to as 3' non-translated sequences.
  • the term "gene” encompasses both cDNA and genomic forms of a gene.
  • a genomic form or clone of a gene contains the coding region interrupted with non-coding sequences termed "introns” or “intervening regions” or “intervening sequences.”
  • Introns are segments of a gene that are transcribed into nuclear RNA (hnRNA); introns can contain regulatory elements such as enhancers. Introns are removed or “spliced out” from the nuclear or primary transcript; introns therefore are absent in the messenger RNA (mRNA) transcript.
  • mRNA messenger RNA
  • the mRNA functions during translation to specify the sequence or order of amino acids in a nascent polypeptide.
  • genomic forms of a gene can also include sequences located on both the 5' and 3' end of the sequences that are present on the RNA transcript.
  • flanking sequences or regions are referred to as “flanking" sequences or regions (these flanking sequences are located 5 ' or 3' to the non-translated sequences present on the mRNA transcript).
  • the 5' flanking region can contain regulatory sequences such as promoters and enhancers that control or influence the transcription of the gene.
  • the 3' flanking region can contain sequences that direct the termination of transcription, post transcriptional cleavage and polyadenylation.
  • Polynucleotide refers to polymers of nucleotides of any length, and include DNA and RNA.
  • the nucleotides can be deoxyribonucleotides, ribonucleotides, modified nucleotides or bases, and/or their analogs, or any substrate that can be incorporated into a polymer by DNA or RNA polymerase, or by a synthetic reaction.
  • a polynucleotide may comprise modified nucleotides, such as methylated nucleotides and their analogs. If present, modification to the nucleotide structure may be imparted before or after assembly of the polymer.
  • the sequence of nucleotides may be interrupted by non-nucleotide components.
  • a polynucleotide may be further modified after synthesis, such as by conjugation with a label.
  • Other types of modifications include, for example, "caps", substitution of one or more of the naturally occurring nucleotides with an analog, internucleotide modifications such as, for example, those with uncharged linkages (e.g., methyl phosphonates, phosphotriesters, phosphoamidates, carbamates, etc.) and with charged linkages (e.g., phosphorothioates, phosphorodithioates, etc.), those containing pendant moieties, such as, for example, proteins (e.g., nucleases, toxins, antibodies, signal peptides, poly-L-lysine, etc.), those with intercalators (e.g., acridine, psoralen, etc.), those containing chelators (e.g., metals, radio
  • any of the hydroxyl groups ordinarily present in the sugars may be replaced, for example, by phosphonate groups, phosphate groups, protected by standard protecting groups, or activated to prepare additional linkages to additional nucleotides, or may be conjugated to solid or semi-solid supports.
  • the 5' and 3' terminal OH can be phosphorylated or substituted with amines or organic capping group moieties of from 1 to 20 carbon atoms.
  • Other hydroxyls may also be derivatized to standard protecting groups.
  • Polynucleotides can also contain analogous forms of ribose or deoxyribose sugars that are generally known in the art, including, for example, 2'-0-methyl-, 2'-0-allyl, 2'- fluoro-or 2'-azido-ribose, carbocyclic sugar analogs, alpha-anomeric sugars, epimeric sugars such as arabinose, xyloses or lyxoses, pyranose sugars, furanose sugars, sedoheptuloses, acyclic analogs and a basic nucleoside analogs such as methyl riboside.
  • One or more phosphodiester linkages may be replaced by alternative linking groups.
  • linking groups include, but are not limited to, embodiments wherein phosphate is replaced by P(0)S("thioate”), P(S)S ("dithioate”), "(0)NR 2 ("amidate”), P(0)R, P(0)OR * , CO or CH 2 ("formacetal"), in which each R or R is independently H or substituted or unsubstituted alkyl (1-20 C) optionally containing an ether (-0-) linkage, aryl, alkenyl, cycloalkyl, cycloalkenyl or araldyl. Not all linkages in a polynucleotide need be identical. The preceding description applies to all polynucleotides referred to herein, including RNA and DNA.
  • Oligonucleotide refers to short, generally single stranded, generally synthetic polynucleotides that are generally, but not necessarily, less than about 200 nucleotides in length.
  • oligonucleotide and polynucleotide are not mutually exclusive. The description above for polynucleotides is equally and fully applicable to oligonucleotides.
  • Stringent hybridization conditions refer to conditions under which a probe will hybridize to its target subsequence, typically in a complex mixture of nucleic acids, but to no other sequences. Stringent conditions are sequence-dependent and will be different in different circumstances. Longer sequences hybridize specifically at higher temperatures. An extensive guide to the hybridization of nucleic acids is found in Tijssen, Techniques in Biochemistry and Molecular Biology—Hybridization with Nucleic Probes, "Overview of principles of hybridization and the strategy of nucleic acid assays” (1993). Generally, stringent conditions are selected to be about 5- 10°C lower than the thermal melting point (Tm) for the specific sequence at a defined ionic strength pH.
  • Tm thermal melting point
  • the Tm is the temperature (under defined ionic strength, pH, and nucleic concentration) at which 50% of the probes complementary to the target hybridize to the target sequence at equilibrium (as the target sequences are present in excess, at Tm, 50% of the probes are occupied at equilibrium).
  • Stringent conditions may also be achieved with the addition of destabilizing agents such as formamide.
  • a positive signal is at least two times background, preferably 10 times background hybridization.
  • Exemplary stringent hybridization conditions can be as following: 50%> formamide, 5xSSC, and 1% SDS, incubating at 42° C, or, 5xSSC, 1% SDS, incubating at 65° C, with wash in 0.2xSSC, and 0.1% SDS at 65° C.
  • Recombinant when used with reference to a cell, nucleic acid, protein, antibody or vector indicates that the cell, nucleic acid, protein or vector has been modified by the introduction of a heterologous nucleic acid or protein, the alteration of a native nucleic acid or protein, or that the cell is derived from a cell so modified.
  • recombinant cells express genes that are not found within the native (non-recombinant) form of the cell or express native genes that are overexpressed or otherwise abnormally expressed such as, for example, expressed as non-naturally occurring fragments or splice variants.
  • nucleic acid By the term “recombinant nucleic acid” herein is meant nucleic acid, originally formed in vitro, in general, by the manipulation of nucleic acid, e.g., using polymerases and endonucleases, in a form not normally found in nature. In this manner, operably linkage of different sequences is achieved.
  • an isolated nucleic acid, in a linear form, or an expression vector formed in vitro by ligating DNA molecules that are not normally joined are both considered recombinant for the purposes of this disclosure.
  • a recombinant nucleic acid is made and introduced into a host cell or organism, it will replicate non- recombinantly, e.g., using the in vivo cellular machinery of the host cell rather than in vitro manipulations; however, such nucleic acids, once produced recombinantly, although subsequently replicated non-recombinantly, are still considered recombinant for the purposes disclosed herein.
  • a "recombinant protein” is a protein made using recombinant techniques, e.g., through the expression of a recombinant nucleic acid as depicted herein.
  • Percent (%) amino acid sequence identity refers to 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 MegAlign (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.
  • amino acid polymers in which one or more amino acid residue is an artificial chemical mimetic of a
  • amino acid refers to naturally occurring and synthetic amino acids, as well as amino acid analogs and amino acid mimetics that function similarly to the naturally occurring amino acids.
  • Naturally occurring amino acids are those encoded by the genetic code, as well as those amino acids that are later modified, e.g., hydroxyproline, gamma-carboxyglutamate, and O- phospho serine.
  • Amino acid analogs refers to compounds that have the same basic chemical structure as a naturally occurring amino acid, e.g., an alpha carbon that is bound to a hydrogen, a carboxyl group, an amino group, and an R group, e.g., homoserine, norleucine, methionine sulfoxide, methionine methyl sulfonium. Such analogs can have modified R groups ⁇ e.g., norleucine) or modified peptide backbones, but retain the same basic chemical structure as a naturally occurring amino acid.
  • Amino acid mimetics refers to chemical compounds that have a structure that is different from the general chemical structure of an amino acid, but that functions similarly to a naturally occurring amino acid.
  • amino acid variants refers to amino acid sequences. With respect to particular nucleic acid sequences, conservatively modified variants refers to those nucleic acids which encode identical or essentially identical amino acid sequences, or where the nucleic acid does not encode an amino acid sequence, to essentially identical or associated ⁇ e.g., naturally contiguous) sequences. Because of the degeneracy of the genetic code, a large number of functionally identical nucleic acids encode most proteins. For instance, the codons GCA, GCC, GCG and GCU all encode the amino acid alanine.
  • nucleic acid variations are "silent variations,” which are one species of conservatively modified variations. Every nucleic acid sequence herein which encodes a
  • polypeptide also describes silent variations of the nucleic acid.
  • each codon in a nucleic acid except AUG, which is ordinarily the only codon for methionine, and TGG, which is ordinarily the only codon for tryptophan
  • TGG which is ordinarily the only codon for tryptophan
  • amino acid sequences one of skill will recognize that individual substitutions, deletions or additions to a nucleic acid, peptide, polypeptide, or protein sequence which alters, adds or deletes a single amino acid or a small percentage of amino acids in the encoded sequence is a "conservatively modified variant" including where the alteration results in the substitution of an amino acid with a chemically similar amino acid. Conservative substitution tables providing functionally similar amino acids are well known in the art. Such conservatively modified variants are in addition to and do not exclude polymorphic variants, interspecies homo logs, and alleles disclosed herein.
  • conservative substitutions include: 1) Alanine (A), Glycine (G); 2) Aspartic acid (D), Glutamic acid (E); 3) Asparagine (N), Glutamine (Q); 4) Arginine (R), Lysine (K); 5) Isoleucine (I), Leucine (L), Methionine (M), Valine (V); 6)
  • Antibodies are glycoproteins having similar structural characteristics. While antibodies may exhibit binding specificity to a specific antigen, immunoglobulins may include both antibodies and other antibody-like molecules which generally lack antigen specificity. Polypeptides of the latter kind are, for example, produced at low levels by the lymph system and at increased levels by myelomas.
  • Antibody "immunoglobulin” and “immunoglobulin construct” are used interchangeably in the broadest sense and include monoclonal antibodies ⁇ e.g., full length or intact monoclonal antibodies), polyclonal antibodies, multivalent antibodies, multispecific antibodies ⁇ e.g., bispecific antibodies so long as they exhibit the desired biological activity) and may also include certain antibody fragments (as described in greater detail herein).
  • the term “antibody” can refer to a full length antibody or a portion thereof.
  • An antibody can refer to a peptide comprising at least one antibody sequence.
  • the antibody sequence can comprise 5 or more amino acids of an antibody sequence.
  • the antibody sequence can comprise 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more amino acids of an antibody sequence.
  • the 5 or more amino acids may be consecutive amino acids of an antibody sequence.
  • the 5 or more amino acids are non-consecutive amino acids of an antibody sequence.
  • the 5 or more amino acids may comprise a conserved motif within the antibody sequence.
  • the 5 or more amino acids may comprise a conserved motif within an ultralong CDR3 sequence.
  • An antibody can be human, humanized, fully human and/or affinity matured.
  • An antibody can be a chimeric antibody.
  • An antibody can be a recombinant, engineered, or synthetic antibody.
  • An antibody may be a bovine, bovine engineered, fully bovine and/or affinity matured.
  • the bovine engineered antibody may comprise one or more nucleotides or peptides derived from a bovine antibody sequence.
  • a fully bovine antibody may comprise replacing one or more nucleotides or peptides from a non- bovine antibody sequence with one or more nucleotides or peptides based on a bovine antibody sequence.
  • An antibody may refer to immunoglobulins and immunoglobulin portions, whether natural or partially or wholly synthetic, such as recombinantly produced, including any portion thereof containing at least a portion of the variable region of the immunoglobulin molecule that is sufficient to form an antigen binding site.
  • an antibody or portion thereof includes any protein having a binding domain that is homologous or substantially homologous to an
  • an antibody may refer to an antibody that contains two heavy chains (which can be denoted H and FT) and two light chains (which can be denoted L and L'), where each heavy chain can be a full-length immunoglobulin heavy chain or a portion thereof sufficient to form an antigen binding site (e.g. heavy chains include, but are not limited to, VH, chains VH-CH1 chains and VH-CH1-CH2-CH3 chains), and each light chain can be a full-length light chain or a thereof sufficient to form an antigen binding site (e.g. light chains include, but are not limited to, VL chains and VL-CL chains). Each heavy chain (H and FT) pairs with one light chain (L and L', respectively).
  • H and FT heavy chains
  • L and L' light chains
  • antibodies minimally include all or at least a portion of the variable heavy (VH) chain and/or the variable light (VL) chain.
  • the antibody also can include all or a portion of the constant region.
  • a full-length antibody is an antibody having two full-length heavy chains (e.g. VH-CH 1 -CH2-CH3 or VH-CH1-CH2-CH3- CH4) and two full-length light chains (VL-CL) and hinge regions, such as antibodies produced by antibody secreting B cells and antibodies with the same domains that are produced synthetically.
  • an "antibody” refers to a protein of the immunoglobulin family or a polypeptide comprising fragments of an immunoglobulin that is capable of noncovalently, reversibly, and in a specific manner binding a corresponding antigen.
  • An exemplary antibody structural unit comprises a tetramer. Each tetramer is composed of two identical pairs of polypeptide chains, each pair having one "light” (about 25 kD) and one "heavy" chain (about 50-70 kD), connected through a disulfide bond.
  • the recognized immunoglobulin genes include the ⁇ , ⁇ , ⁇ , ⁇ , ⁇ , ⁇ , and ⁇ constant region genes, as well as the myriad immunoglobulin variable region genes.
  • Light chains are classified as either ⁇ or ⁇ .
  • Heavy chains are classified as ⁇ , ⁇ , ⁇ , ⁇ , or ⁇ , which in turn define the
  • the antibodies provided herein comprise at least one immunoglobulin domain from an avian antibody, reptilian antibody, amphibian antibody, insect antibody, or chimeric combinations thereof.
  • the antibodies can comprise at least one immunoglobulin domain from a chimeric antibody.
  • the chimeric antibody can be derived from two or more different species (e.g., mouse and human, bovine and human).
  • the antibodies can comprise at least one immunoglobulin domain from an engineered, recombinant or synthetic antibody.
  • engineered, recombinant or synthetic antibodies are created using antibody genes made in a laboratory or taken from cells.
  • the antibody genes can be derived from one or more mammals.
  • the antibody genes are derived from a human.
  • the antibody genes may be derived from a bovine.
  • the antibodies disclosed herein comprise at least one immunoglobulin domain from a humanized, human engineered or fully human antibody.
  • the antibody may comprise antibody sequences from two or more different antibodies.
  • the two or more different antibodies may be from the same species.
  • the specie may be a bovine specie, human specie, or murine specie.
  • the two or more different antibodies may be from the same type of animal.
  • the two or more different antibodies may be from a cow.
  • the two or more different antibodies may be from a human.
  • the two or more different antibodies are from different species.
  • the two or more different antibodies are from a human specie and bovine specie.
  • the two or more diffent antibodies are from a bovine specie and a non-bovine specie.
  • the two or more different antibodies are from a human specie and a non-human specie.
  • the two or more different antibodies may be from different animals.
  • the two different animals are a human and a cow.
  • the different animals may be from the same specie.
  • the different animals may be a cow and a water buffalo.
  • variable refers to the fact that certain portions of the variable domains (also referred to as variable regions) differ extensively in sequence among antibodies and are used in the binding and specificity of each particular antibody for its particular antigen. However, the variability is not evenly distributed throughout the variable domains of antibodies. It is
  • CDRs complementarity-determining regions
  • hypervariable regions both in the light-chain and the heavy-chain variable domains.
  • CDRs include those specified as Kabat, Chothia, and IMGT as shown herein within the variable region sequences.
  • the more highly conserved portions of variable domains are called the framework (FR).
  • the variable domains of native heavy and light chains each comprise four FR regions, largely adopting a ⁇ -sheet configuration, connected by three CDRs, which form loops connecting, and in some cases forming part of, the ⁇ -sheet structure.
  • the CDRs in each chain are held together in close proximity by the FR regions and, with the CDRs from the other chain, contribute to the formation of the antigen-binding site of antibodies (see Kabat et al., Sequences of Proteins of Immunological Interest. Fifth Edition, National Institute of Health, Bethesda, Md. (1991)).
  • the constant domains are not involved directly in binding an antibody to an antigen, but exhibit various effector functions, such as participation of the antibody in antibody-dependent cellular toxicity.
  • Papain digestion of antibodies produces two identical antigen-binding fragments, called “Fab” fragments, each with a single antigen-binding site, and a residual "Fc” fragment, whose name reflects its ability to crystallize readily.
  • Pepsin treatment yields an F(ab') 2 fragment that has two antigen-combining sites and is still capable of cross-linking antigen.
  • Fv refers to an antibody fragment which contains an antigen-recognition and antigen-binding site.
  • this region consists of a dimer of one heavy and one light chain variable domain in non-covalent association.
  • scFv single chain Fv
  • one heavy chain and one light chain variable domain can be covalently linked by a flexible peptide linker such that the light and heavy chains can associate in a "dimeric" structure analogous to that in a two-chain Fv (scFv) species. It is in this configuration that the three CDRs of each variable domain interact to define an antigen-binding site on the surface of the VH-VL dimer.
  • the six CDRs confer antigen-binding specificity to the antibody.
  • a single variable domain or half of an Fv comprising only three CDRs specific for an antigen
  • the Fab fragment also contains the constant domain of the light chain and the first constant domain (CHI) of the heavy chain.
  • Fab' fragments differ from Fab fragments by the addition of a few residues at the carboxy terminus of the heavy chain CHI domain including one or more cysteines from the antibody hinge region.
  • Fab'-SH is the designation herein for Fab' in which the cysteine residue(s) of the constant domains bear a free thiol group.
  • F(ab') 2 antibody fragments originally were produced as pairs of Fab' fragments which have hinge cysteines between them. Other chemical couplings of antibody fragments are also known.
  • the "light chains" of antibodies (immunoglobulins) from any vertebrate species can be assigned to one of two clearly distinct types, called kappa ( ⁇ ) and lambda ( ⁇ ), based on the amino acid sequences of their constant domains.
  • immunoglobulins can be assigned to different classes. There are five major classes of
  • immunoglobulins IgA, IgD, IgE, IgG, and IgM, and several of these can be further divided into subclasses (isotypes), e.g., IgGi, IgG 2 , IgG 3 , IgG 4 , IgAi, and IgA 2 .
  • the heavy-chain constant domains that correspond to the different classes of immunoglobulins are called ⁇ , ⁇ , ⁇ , ⁇ , and ⁇ , respectively.
  • the subunit structures and three-dimensional configurations of different classes of immunoglobulins are well known.
  • Antibody fragments comprise only a portion of an intact antibody, wherein the portion preferably retains at least one, preferably most or all, of the functions normally associated with that portion when present in an intact antibody.
  • antibody fragments include Fab, Fab', F(ab')2, single-chain Fvs (scFv), Fv, dsFv, diabody (e.g., (ds Fv) 2 ), Fd and Fd' fragments Fab fragments, Fd fragments, scFv fragments, linear antibodies, single-chain antibody molecules, minibodies, flex minibodies, bispecific fragments, and multispecific antibodies formed from antibody fragments (see, for example, Methods in Molecular Biology, Vol 207: Recombinant Antibodies for Cancer Therapy Methods and Protocols (2003); Chapter 1; p 3-25, Kipriyanov).
  • Other known fragments include, but are not limited to, scFab fragments (Hust et al, BMC
  • an antibody fragment comprises an antigen binding site of the intact antibody and thus retains the ability to bind antigen.
  • an antibody fragment for example one that comprises the Fc region, retains at least one of the biological functions normally associated with the Fc region when present in an intact antibody, such as FcRn binding, antibody half life modulation, ADCC function and complement binding.
  • an antibody fragment is a monovalent antibody that has an in vivo half life substantially similar to an intact antibody.
  • such an antibody fragment may comprise on antigen binding arm linked to an Fc sequence capable of conferring in vivo stability to the fragment.
  • an antibody fragment or antibody portion refers to any portion of a full-length antibody that is less than full length but contains at least a portion of the variable region of the antibody sufficient to form an antigen binding site (e.g.
  • antibody fragments include antibody derivatives produced by enzymatic treatment of full-length antibodies, as well as synthetically, e.g. recombinantly produced derivatives.
  • a "dsFv” refers to an Fv with an engineered intermolecular disulfide bond, which stabilizes the VH-VL pair.
  • a “Fd fragment” refers to a fragment of an antibody containing a variable domain
  • VH VH and one constant region domain (CHI) of an antibody heavy chain.
  • a “Fab fragment” refers to an antibody fragment that contains the portion of the full-length antibody that would results from digestion of a full-length immunoglobulin with papain, or a fragment having the same structure that is produced synthetically, e.g. recombinantly.
  • a Fab fragment contains a light chain (containing a VL and CL portion) and another chain containing a variable domain of a heavy chain (VH) and one constant region domain portion of the heavy chain (CHI); it can be recombinantly produced.
  • a "F(ab')2 fragment” refers to an antibody fragment that results from digestion of an immunoglobulin with pepsin at pH 4.0-4.5, or a synthetically, e.g. recombinantly, produced antibody having the same structure.
  • the F(ab')2 fragment contains two Fab fragments but where each heavy chain portion contains an additional few amino acids, including cysteine residues that form disulfide linkages joining the two fragments; it can be recombinantly produced.
  • a "Fab' fragment” refers to a fragment containing one half (one heavy chain and one light chain) of the F(ab')2 fragment.
  • a "Fd' fragment refers to a fragment of an antibody containing one heavy chain portion of a F(ab')2 fragment.
  • a "Fv' fragment” refers to a fragment containing only the VH and VL domains of an antibody molecule.
  • a "scFv fragment” refers to an antibody fragment that contains a variable light chain
  • variable heavy chain VL and variable heavy chain (VH), covalently connected by a polypeptide linker in any order.
  • the linker is of a length such that the two variable domains are bridged without substantial interference.
  • exemplary linkers are (Gly-Ser)n residues with some Glu or Lys residues dispersed throughout to increase solubility.
  • Diabodies are dimeric scFv; diabodies typically have shorter peptide linkers than scFvs, and they preferentially dimerize.
  • HsFv refers to antibody fragments in which the constant domains normally present in a Fab fragment have been substituted with a heterodimeric coiled-coil domain (see, e.g., Arndt et al. (2001) J Mol Biol. 7:312:221-228).
  • Hypervariable region may refer to the regions of an antibody variable domain which are hypervariable in sequence and/or form structurally defined loops.
  • antibodies comprise six
  • hypervariable or CDR regions three in the VH (HI, H2, H3), and three in the VL (LI, L2, L3).
  • a number of hypervariable region or CDR delineations are in use and are encompassed herein.
  • the Kabat Complementarity Determining Regions are based on sequence variability and are the most commonly used (Kabat et al., Sequences of Proteins of Immunological Interest. 5th Ed. Public Health Service, National Institutes of Health, Bethesda, Md. (1991)). Chothia refers instead to the location of the structural loops (Chothia and Lesk, J. Mol. Biol. 196:901-917 (1987)).
  • the AbM hypervariable regions represent a compromise between the Kabat CDRs and Chothia structural loops, (Chothia "CDRs") and are used by Oxford Molecular's AbM antibody modeling software.
  • the "contact" hypervariable regions are based on an analysis of the available complex crystal structures. The residues from each of these hypervariable regions are noted below. (See also, for example, Figure 1 and bold, italicized text for Kabat CDRs and underlined text for Chothia CDRs for 12.3 ICI antibody).
  • IMGT referes to the international ImMunoGeneTics Information System, as described by Lefrace et ah, Nucl. Acids, Res. 37; D1006-D1012 (2009), including for example, IMGT designated CDRs for antibodies (see also, for example, Figure 1 and bracketed text for 12.3 1C1 antibody).
  • Hypervariable regions may comprise "extended hypervariable regions" as follows:
  • variable domain residues are numbered according to Kabat et ah, Supra for each of these definitions.
  • “Framework” or “FR” residues are those variable domain residues other than the hypervariable region residues as herein defined.
  • “Framework regions” are the domains within the antibody variable region domains comprising framework residues that are located within the beta sheets; the FR regions are comparatively more conserved, in terms of their amino acid sequences, than the hypervariable regions.
  • “Monoclonal antibody” refers to an antibody from a population of substantially homogeneous antibodies, that is, for example, the individual antibodies comprising the population are identical and/or bind the same epitope(s), except for possible variants that may arise during production of the monoclonal antibody, such variants generally being present in minor amounts.
  • Such monoclonal antibody typically includes an antibody comprising a polypeptide sequence that binds a target, wherein the target-binding polypeptide sequence was obtained by a process that includes the selection of a single target binding polypeptide sequence from a plurality of polypeptide sequences.
  • the selection process can be the selection of a unique clone from a plurality of clones, such as a pool of hybridoma clones, phage clones or recombinant DNA clones.
  • the selected target binding sequence can be further altered, for example, to improve affinity for the target, to humanize the target binding sequence, to improve its production in cell culture, to reduce its immunogenicity in vivo, to create a multispecific antibody, etc., and that an antibody comprising the altered target binding sequence is also a monoclonal antibody of this disclosure.
  • each monoclonal antibody of a monoclonal antibody preparation is directed against a single determinant on an antigen.
  • the monoclonal antibody preparations are advantageous in that they are typically uncontaminated by other immunoglobulins.
  • 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 to be used in accordance with the present disclosure may be made by a variety of techniques, including, for example, the hybridoma method ⁇ e.g., Kohler et al, Nature, 256:495 (1975); Harlow et al, Antibodies: A Laboratory Manual, (Cold Spring Harbor Laboratory Press, 2nd ed. 1988); Hammerling et al., in: Monoclonal Antibodies and T-Cell Hybridomas 563-681, (Elsevier, N.Y., 1981)), recombinant DNA methods (see, e.g., U.S. Patent No.
  • phage display technologies see, e.g., Clackson et al, Nature, 352:624-628 (1991); Marks et al, J. Mol. Biol, 222:581-597 (1991); Sidhu et al, J. Mol. Biol. 338(2):299-310 (2004); Lee et al, J. Mol. Biol. 340(5): 1073-1093 (2004); Fellouse, Proc. Nat. Acad. Sci. USA 101(34): 12467-12472 (2004); and Lee et al. J. Immunol.
  • Humanized or “Human engineered” forms of non- human ⁇ e.g., murine, bovine) antibodies are chimeric antibodies that contain amino acids represented in human immunoglobulin sequences, including, for example, wherein minimal sequence is derived from non-human immunoglobulin.
  • humanized antibodies may be human antibodies in which some hypervariable region residues and possibly some FR residues are substituted by residues from analogous sites in non-human ⁇ e.g., rodent) antibodies.
  • humanized or human engineered antibodies may be non-human ⁇ e.g., rodent) antibodies in which some residues are substituted by residues from analogious sites in human antibodies (see, e.g., U.S. Patent No.
  • Humanized antibodies include human immunoglobulins (recipient antibody) in which residues from a hypervariable region of the recipient are replaced by residues from a hypervariable region of a non-human species (donor antibody) such as mouse, rat, rabbit or nonhuman primate having the desired specificity, affinity, and capacity.
  • donor antibody such as mouse, rat, rabbit or nonhuman primate having the desired specificity, affinity, and capacity.
  • framework region (FR) residues of the human immunoglobulin are replaced by corresponding non-human residues.
  • humanized antibodies may comprise residues that are not found in the recipient antibody or in the donor antibody, including, for example non-antibody sequences such as a chemokine, growth factor, peptide, cytokine, cell surface protein, serum protein, toxin, extracellular matrix protein, clotting factor, or secreted protein sequence. These modifications may be made to further refine antibody performance.
  • Humanized antibodies include human engineered antibodies, for example, as described by U.S. Patent No. 5,766,886, including methods for preparing modified antibody variable domains.
  • a humanized antibody may comprise substantially all of at least one, and typically two, variable domains, in which all or substantially all of the hypervariable loops correspond to those of a non-human immunoglobulin and all or substantially all of the FRs are those of a human immunoglobulin sequence.
  • a humanized antibody optionally may also comprise at least a portion of an immunoglobulin constant region (Fc), typically that of a human
  • Hybrid antibodies refer to immunoglobulin molecules in which pairs of heavy and light chains from antibodies with different antigenic determinant regions are assembled together so that two different epitopes or two different antigens can be recognized and bound by the resulting tetramer.
  • “Chimeric" antibodies have a portion of the heavy and/or light chain identical with or homologous to corresponding sequences in antibodies derived from a particular species or belonging to a particular antibody class or subclass, while the remainder of the chain(s) is identical with or homologous to corresponding sequences in antibodies derived from another species or belonging to another antibody class or subclass, as well as fragments of such antibodies, so long as they exhibit the desired biological activity (see e.g., Morrison et ah, Proc. Natl. Acad. Sci. USA 81 :6851-6855 (1984)).
  • Humanized antibody refers to a subset of chimeric antibodies.
  • Single-chain Fv or “scFv” antibody fragments may comprise the VH and VL domains of antibody, wherein these domains are present in a single polypeptide chain.
  • the scFv polypeptide further comprises a polypeptide linker between the VH and VL domains which enables the scFv to form the desired structure for antigen binding.
  • an "antigen" refers to a predetermined antigen to which an antibody can selectively bind.
  • the target antigen may be polypeptide, carbohydrate, nucleic acid, lipid, hapten or other naturally occurring or synthetic compound.
  • the target antigen is a polypeptide.
  • epitopes refer to that portion of an antigen capable of being recognized and specifically bound by a particular antibody.
  • the antigen is a polypeptide
  • epitopes can be formed both from contiguous amino acids and noncontiguous amino acids juxtaposed by tertiary folding of a protein. Epitopes formed from contiguous amino acids are typically retained upon protein denaturing, whereas epitopes formed by tertiary folding are typically lost upon protein denaturing.
  • An epitope typically includes at least 3, and more usually, at least 5 or 8-10 amino acids in a unique spatial conformation.
  • Antibodies may bind to the same or a different epitope on an antigen.
  • Antibodies may be characterized in different epitope bins. Whether an antibody binds to the same or different epitope as another antibody ⁇ e.g., a reference antibody or benchmark antibody) may be determined by competition between antibodies in assays ⁇ e.g., competitive binding assays). [00318] Competition between antibodies may be determined by an assay in which the immunoglobulin under test inhibits specific binding of a reference antibody to a common antigen.
  • RIA solid phase direct or indirect radioimmunoassay
  • EIA or ELISA solid phase direct or indirect enzyme immunoassay or enzyme- linked immunosorbent assay
  • sandwich competition assay including an ELISA assay (see Stahli et al, Methods in Enzymology 9:242-253 (1983)); solid phase direct biotin-avidin EIA (see Kirkland et al., J. Immunol.
  • solid phase direct labeled assay solid phase direct labeled sandwich assay (see Harlow and Lane, "Antibodies, A Laboratory Manual,” Cold Spring Harbor Press (1988)); solid phase direct label RIA using 1-125 label (see Morel et al., Molec. Immunol. 25(1):7-15 (1988)); solid phase direct biotin-avidin EIA (Cheung et al., Virology 176:546-552 (1990)); and direct labeled RIA (Moldenhauer et al, Scand. J. Immunol, 32:77-82 (1990)).
  • Competition binding assays may be performed using Surface Plasmon Resonance (SPR), for example, with a Biacore ® instrument for kinetic analysis of binding interactions.
  • SPR Surface Plasmon Resonance
  • an antibody comprising an ultralong CDR3 of unknown epitope specificity may be evaluated for its ability to compete for binding against a comparator antibody (e.g., a BA1 or BA2 antibody as described herein).
  • An assay may involve the use of purified antigen bound to a solid surface or cells bearing either of these, an unlabeled test immunoglobulin and a labeled reference
  • immunoglobulin Competitive inhibition may be measured by determining the amount of label bound to the solid surface or cells in the presence of the test immunoglobulin. Usually the test immunoglobulin is present in excess.
  • An assay may include antibodies binding to the same epitope as the reference antibody and antibodies binding to an adjacent epitope sufficiently proximal to the epitope bound by the reference antibody for steric hindrance to occur. Usually, when a competing antibody is present in excess, it will inhibit specific binding of a reference antibody to a common antigen by at least 50%, or at least about 70%, or at least about 80%), or least about 90%>, or at least about 95%>, or at least about 99%> or about 100% for a competitor antibody.
  • That an antibody “selectively binds” or “specifically binds” means that the antibody reacts or associates more frequently, more rapidly, with greater duration, with greater affinity, or with some combination of the above to an antigen or an epitope than with alternative substances, including unrelated proteins.
  • “Selectively binds” or “specifically binds” may mean, for example, that an antibody binds to a protein with a K D of at least about 0.1 mM, or at least about 1 ⁇ or at least about 0.1 ⁇ or better, or at least about 0.01 ⁇ or better. Because of the sequence identity between homologous proteins in different species, specific binding can include an antibody that recognizes a given antigen in more than one species.
  • Non-specific binding and “background binding” when used in reference to the interaction of an antibody and a protein or peptide refer to an interaction that is not dependent on the presence of a particular structure (e.g., the antibody is binding to proteins in general rather that a particular structure such as an epitope).
  • Diabodies refer to small antibody fragments with two antigen-binding sites, which fragments comprise a heavy-chain variable domain (VH) connected to a light-chain variable domain (VL) in the same polypeptide chain (VH-VL).
  • VH heavy-chain variable domain
  • VL light-chain variable domain
  • VH-VL polypeptide chain
  • a "human antibody” refers to one which possesses an amino acid sequence which corresponds to that of an antibody produced by a human and/or has been made using any of the techniques for making human antibodies as disclosed herein. This definition of a human antibody specifically excludes a humanized antibody comprising non-human antigen-binding residues.
  • affinity matured antibody refers to one with one or more alterations in one or more CDRs thereof which result in an improvement in the affinity of the antibody for antigen, compared to a parent antibody which does not possess those alteration(s).
  • Preferred affinity matured antibodies will have nanomolar or even picomolar affinities for the target antigen.
  • Affinity matured antibodies are produced by procedures known in the art. Marks et al, Bio/Technology 10:779-783 (1992) describes affinity maturation by VH and VL domain shuffling. Random mutagenesis of CDR and/or framework residues is described by: Barbas et al, Proc Nat. Acad. Sci.
  • Antibody effector functions refer to those biological activities attributable to the
  • Fc region (a native sequence Fc region or amino acid sequence variant Fc region) of an antibody, and vary with the antibody isotype.
  • antibody effector functions include: Clq binding and complement dependent cytotoxicity; Fc receptor binding; antibody-dependent cell-mediated cytotoxicity (ADCC); phagocytosis; down regulation of cell surface receptors (e.g. B cell receptor); and B cell activation.
  • ADCC antibody-dependent cell-mediated cytotoxicity
  • FcRs Fc receptors
  • cytotoxic cells e.g., Natural Killer (NK) cells, neutrophils, and macrophages
  • NK Natural Killer
  • the antibodies “arm” the cytotoxic cells and are absolutely required for such killing.
  • ADCC activity of a molecule of interest is summarized in Table 3 on page 464 of Ravetch and Kinet, Annu. Rev. Immunol 9:457-92 (1991).
  • an in vitro ADCC assay may be performed.
  • Useful effector cells for such assays include peripheral blood mononuclear cells (PBMC) and Natural Killer (NK) cells.
  • PBMC peripheral blood mononuclear cells
  • NK Natural Killer
  • ADCC activity of the molecule of interest may be assessed in vivo, e.g., in a animal model such as that disclosed in Clynes et al Proc. Natl. Acad. Sci. USA 95:652- 656 (1998).
  • Effector cells are leukocytes which express one or more FcRs and perform effector functions. Preferably, the cells express at least FcyRIII and perform ADCC effector function.
  • human leukocytes which mediate ADCC include peripheral blood mononuclear cells (PBMC), natural killer (NK) cells, monocytes, cytotoxic T cells and neutrophils; with PBMCs and NK cells being preferred.
  • the effector cells may be isolated from a native source, e.g., from blood.
  • Fc receptor or “FcR” describes a receptor that binds to the Fc region of an antibody.
  • the preferred FcR is a native sequence human FcR.
  • a preferred 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 these 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 tyro sine-based activation motif (IT AM) in its cytoplasmic domain.
  • Inhibiting receptor FcyRIIB contains an immunoreceptor tyro sine-based inhibition motif (ITIM) in its cytoplasmic domain, (see review M. in Daeron, Annu. Rev. Immunol. 15:203-234 (1997)).
  • FcRs are reviewed in Ravetch and Kinet, Annu. Rev. Immunol 9:457-92 (1991); Capel et al, Immunomethods 4:25-34 (1994); and de Haas et al, J. Lab. Clin. Med.
  • FcR neonatal receptor
  • FcRn the neonatal receptor
  • Binding to human FcRn in vivo and serum half life of human FcRn high affinity binding polypeptides can be assayed, e.g., in transgenic mice or transfected human cell lines expressing human FcRn, or in primates administered with the Fc variant polypeptides.
  • CDC complement dependent cytotoxicity
  • Activation of the classical complement pathway is initiated by the binding of the first component of the complement system (Clq) to antibodies (of the appropriate subclass) which are bound to their cognate antigen.
  • Clq first component of the complement system
  • a CDC assay for example, as described in Gazzano-Santoro et al, J. Immunol. Methods 202: 163 (1996), may be performed.
  • Fc region-comprising polypeptide refers to a polypeptide, such as an antibody or immunoadhesin (see definitions below), which comprises an Fc region.
  • the C-terminal lysine (residue 447 according to the EU numbering system) of the Fc region may be removed, for example, during purification of the polypeptide or by recombinant engineering the nucleic acid encoding the polypeptide.
  • blocking antibody or an “antagonist” antibody refers to one which inhibits or reduces biological activity of the antigen it binds.
  • Preferred blocking antibodies or antagonist antibodies substantially or completely inhibit the biological activity of the antigen.
  • Antist antibody refers to an antibody which mimics ⁇ e.g., partially or fully) at least one of the functional activities of a polypeptide of interest.
  • acceptor human framework refers to a framework comprising the amino acid sequence of a VL or VH framework derived from a human immunoglobulin framework, or from a human consensus framework.
  • immunoglobulin framework or human consensus framework may comprise the same amino acid sequence thereof, or may contain pre-existing amino acid sequence changes. Where pre-existing amino acid changes are present, preferably no more than 5 and preferably 4 or less, or 3 or less, pre-existing amino acid changes are present.
  • a "human consensus framework” refers to a framework which represents the most commonly occurring amino acid residues in a selection of human immunoglobulin VL or VH framework sequences.
  • the selection of human immunoglobulin VL or VH sequences is from a subgroup of variable domain sequences.
  • the subgroup of sequences is a subgroup as in Kabat et al, Sequences of Proteins of Immunological Interest, Fifth Edition, NIH Publication 91-3242, Bethesda Md. (1991), vols. 1-3.
  • the subgroup is subgroup kappa I as in Kabat et al, supra.
  • the subgroup is subgroup III as in Kabat et al, supra.
  • Disorder or “disease” refers to any condition that would benefit from treatment with a substance/molecule ⁇ e.g., an antibody comprising an ultralong CDR3 as disclosed herein) or method disclosed herein. This includes chronic and acute disorders or diseases including those pathological conditions which predispose the mammal to the disorder in question.
  • Treatment refers to clinical intervention in an attempt to alter the natural course of the individual or cell being treated, and can be performed either for prophylaxis or during the course of clinical pathology. Desirable effects of treatment include preventing occurrence or recurrence of disease, alleviation of symptoms, diminishment of any direct or indirect pathological consequences of the disease, preventing metastasis, decreasing the rate of disease progression, amelioration or palliation of the disease state, and remission or improved prognosis.
  • antibodies disclosed herein are used to delay development of a disease or disorder.
  • “Individual” ⁇ e.g., a “subject” refers to a vertebrate, preferably a mammal, more preferably a human. Mammals include, but are not limited to, farm animals (such as cows), sport animals, pets (such as cats, dogs and horses), primates, mice and rats.
  • mammal for purposes of treatment refers to any animal classified as a mammal, including humans, rodents ⁇ e.g., mice and rats), and monkeys; domestic and farm animals; and zoo, sports, laboratory, or pet animals, such as dogs, cats, cattle, horses, sheep, pigs, goats, rabbits, etc.
  • the mammal is selected from a human, rodent, or monkey.
  • “Pharmaceutically acceptable” refers to approved or approvable by a regulatory agency of the Federal or a state government or listed in the U.S. Pharmacopeia or other generally recognized pharmacopeia for use in animals, including humans.
  • “Pharmaceutically acceptable salt” refers to a salt of a compound that is
  • “Pharmaceutically acceptable excipient, carrier or adjuvant” refers to an excipient, carrier or adjuvant that can be administered to a subject, together with at least one antibody of the present disclosure, and which does not destroy the pharmacological activity thereof and is nontoxic when administered in doses sufficient to deliver a therapeutic amount of the compound.
  • “Pharmaceutically acceptable vehicle” refers to a diluent, adjuvant, excipient, or carrier with which at least one antibody of the present disclosure is administered.
  • “Providing a prognosis”, “prognostic information”, or “predictive information” refer to providing information, including for example the presence of cancer cells in a subject's tumor, regarding the impact of the presence of cancer (e.g., as determined by the diagnostic methods of the present disclosure) on a subject's future health (e.g., expected morbidity or mortality, the likelihood of getting cancer, and the risk of metastasis).
  • Terms such as “treating” or “treatment” or “to treat” or “alleviating” or “to alleviate” refer to both 1) therapeutic measures that cure, slow down, lessen symptoms of, and/or halt progression of a diagnosed pathologic condition or disorder and 2) prophylactic or preventative measures that prevent and/or slow the development of a targeted pathologic condition or disorder.
  • those in need of treatment include those already with the disorder; those prone to have the disorder; and those in whom the disorder is to be prevented.
  • Providing a diagnosis” or “diagnostic information” refers to any information, including for example the presence of cancer cells, that is useful in determining whether a patient has a disease or condition and/or in classifying the disease or condition into a phenotypic category or any category having significance with regards to the prognosis of or likely response to treatment (either treatment in general or any particular treatment) of the disease or condition.
  • diagnosis refers to providing any type of diagnostic information, including, but not limited to, whether a subject is likely to have a condition (such as a tumor), whether a subject's tumor comprises cancer stem cells, information related to the nature or classification of a tumor as for example a high risk tumor or a low risk tumor, information related to prognosis and/or information useful in selecting an appropriate treatment.
  • Selection of treatment can include the choice of a particular chemotherapeutic agent or other treatment modality such as surgery or radiation or a choice about whether to withhold or deliver therapy.
  • a "human consensus framework” refers to a framework which represents the most commonly occurring amino acid residues in a selection of human immunoglobulin VL or VH framework sequences.
  • the selection of human immunoglobulin VL or VH sequences is from a subgroup of variable domain sequences.
  • the subgroup of sequences is a subgroup as in Kabat et al, Sequences of Proteins of Immunological Interest, Fifth Edition, NIH Publication 91-3242, Bethesda Md. (1991), vols. 1-3.
  • the subgroup is subgroup kappa I as in Kabat et al, supra.
  • the subgroup is subgroup III as in Kabat et al, supra.
  • an "acceptor human framework” for the purposes herein refers to a framework comprising the amino acid sequence of a light chain variable domain (VL) framework or a heavy chain variable domain (VH) framework derived from a human immunoglobulin framework or a human consensus framework, as defined below.
  • An acceptor human framework "derived from” a human immunoglobulin framework or a human consensus framework may comprise the same amino acid sequence thereof, or it may contain amino acid sequence changes.
  • the number of amino acid changes are 10 or less, 9 or less, 8 or less, 7 or less, 6 or less, 5 or less, 4 or less, 3 or less, or 2 or less.
  • the VL acceptor human framework is identical in sequence to the VL human immunoglobulin framework sequence or human consensus framework sequence.
  • Antigen-binding site refers to the interface formed by one or more complementary determining regions.
  • An antibody molecule has two antigen combining sites, each containing portions of a heavy chain variable region and portions of a light chain variable region.
  • the antigen combining sites can contain other portions of the variable region domains in addition to the CDRs.
  • an “antibody light chain” or an “antibody heavy chain” refers to a polypeptide comprising the VL or VH, respectively.
  • the VL is encoded by the minigenes V (variable) and J (junctional), and the VH by minigenes V, D (diversity), and J.
  • Each of VL or VH includes the CDRs as well as the framework regions.
  • antibody light chains and/or antibody heavy chains may, from time to time, be collectively referred to as "antibody chains.” These terms encompass antibody chains containing mutations that do not disrupt the basic structure of VL or VH, as one skilled in the art will readily recognize.
  • Native antibodies refer to naturally occurring immunoglobulin molecules with varying structures.
  • native IgG antibodies are heterotetrameric glycoproteins of about 150,000 daltons, composed of two identical light chains and two identical heavy chains that are disulfide bonded. From N-to C-terminus, each heavy chain has a variable region (V H), also called a variable heavy domain or a heavy chain variable domain, followed by three constant domains (CHI, CH2, and CH3).
  • V H variable region
  • V L variable region
  • CL constant light domain
  • the light chain of an antibody may be assigned to one of two types, called kappa (K) and lambda (K), based on the amino acid sequence of its constant domain.
  • Combinatorial library refers to collections of compounds formed by reacting different combinations of interchangeable chemical "building blocks” to produce a collection of compounds based on permutations of the building blocks.
  • the building blocks are the component V, D and J regions (or modified forms thereof) from which antibodies are formed.
  • library or “collection” are used
  • a “combinatorial antibody library” refers to a collection of antibodies (or portions thereof, such as Fabs), where the antibodies are encoded by nucleic acid molecules produced by the combination of V, D and J gene segments, particularly human V, D and J germline segments.
  • the combinatorial libraries herein typically contain at least 50 different antibody (or antibody portions or fragment) members, typically at or about 50, 100, 500, 103, 1 x 103, 2 x 103, 3 x 103, 4x 103, 5 x 103, 6 x 103, 7 x 103, 8 x 103, 9 x 103, 1 x 104, 2 x 104, 3 x 104, 4x 104, 5 x 104, 6 x 104, 7 x
  • the resulting libraries or collections of antibodies or portions thereof, can be screened for binding to a target protein or modulation of a functional activity.
  • a "human combinatorial antibody library” refers to a collection of antibodies or portions thereof, whereby each member contains a VL and VH chains or a sufficient portion thereof to form an antigen binding site encoded by nucleic acid containing human germline segments produced as described herein.
  • a "variable germline segment” refers to V, D and J groups, subgroups, genes or alleles thereof. Gene segment sequences are accessible from known database (e.g. , National Center for Biotechnology Information (NCBI), the international ImMunoGeneTics information system® (IMGT), the Kabat database and the Tomlinson's VBase database (Lefranc (2003) Nucleic Acids Res., 31 :307-310; Martin et al. , Bioinformatics Tools for Antibody Engineering in Handbook of Therapeutic Antibodies, Wiley- VCH (2007), pp. 104-107). Tables 3-5 list exemplary human variable germline segments.
  • germline segments are set forth in SEQ ID NOS: 10-451 and 868.
  • a germline segment includes modified sequences thereof, that are modified in accord with the rules of sequence compilation provided herein to permit practice of the method.
  • germline gene segments include those that contain one amino acid deletion or insertion at the 5 ' or 3 ' end compared to any of the sequences of nucleotides set forth in SEQ ID NOS: 10-451 , 868.
  • variable heavy chain germline segments are assembled such that the VH segment is 5 ' to the DH segment which is 5 ' to the JH segment, thereby resulting in a nucleic acid sequence encoding a VH chain.
  • Variable light chain germline segments are assembled such that the VL segment is 5 ' to the JL segment, thereby resulting in a nucleic acid sequence encoding a VL chain.
  • a constant gene segment or segments also can be assembled onto the 3 ' end of a nucleic acid encoding a VH or VL chain.
  • Linkage refers to the joining of germline segments. Linkage can be direct or indirect. Germline segments can be linked directly without additional nucleotides between segments, or additional nucleotides can be added to render the entire segment in- frame, or nucleotides can be deleted to render the resulting segment in- frame. It is understood that the choice of linker nucleotides is made such that the resulting nucleic acid molecule is in-frame and encodes a functional and productive antibody.
  • "In- frame” or "linked in- frame” with reference to linkage of human germline segments means that there are insertions and/or deletions in the nucleotide germline segments at the joined junctions to render the resulting nucleic acid molecule in- frame with the 5 ' start codon (ATG), thereby producing a "productive" or functional full-length polypeptide.
  • the choice of nucleotides inserted or deleted from germline segments, particularly at joints joining various VD, DJ and VJ segments, is in accord with the rules provided in the method herein for V(D)J joint generation. For example, germline segments are assembled such that the VH segment is 5 ' to the DH segment which is 5 ' to the JH segment.
  • nucleotides can be inserted or deleted from the individual VH, DH or JH segments, such that the resulting nucleic acid molecule containing the joined VDJ segments are in- frame with the 5 ' start codon (ATG).
  • a portion of an antibody includes sufficient amino acids to form an antigen binding site.
  • a "reading frame” refers to a contiguous and non-overlapping set of three- nucleotide codons in DNA or RNA. Because three codons encode one amino acid, there exist three possible reading frames for given nucleotide sequence, reading frames 1 , 2 or 3. For example, the sequence ACTGGTCA will be ACT GGT CA for reading frame 1 , A CTG GTC A for reading frame 2 and AC TGG TCA for reading frame 3. Generally for practice of the method described herein, nucleic acid sequences are combined so that the V sequence has reading frame 1.
  • a "stop codon” refers to a three-nucleotide sequence that signals a halt in protein synthesis during translation, or any sequence encoding that sequence (e.g. a DNA sequence encoding an RNA stop codon sequence), including the amber stop codon (UAG or TAG)), the ochre stop codon (UAA or TAA)) and the opal stop codon (UGA or TGA)). It is not necessary that the stop codon signal termination of translation in every cell or in every organism. For example, in suppressor strain host cells, such as amber suppressor strains and partial amber suppressor strains, translation proceeds through one or more stop codon (e.g. the amber stop codon for an amber suppressor strain), at least some of the time.
  • the stop codon e.g. the amber stop codon for an amber suppressor strain
  • VH variable heavy chain or a “variable light” (VL) chain
  • VH domain VL domain
  • VH domain VL domain
  • heavy chain germline segments are designated as VH, DH and JH, and compilation thereof results in a nucleic acid encoding a VH chain.
  • Light chain germline segments are designated as VL or JL, and include kappa and lambda light chains (VK and JK; ⁇ and ⁇ .) and compilation thereof results in a nucleic acid encoding a VL chain. It is understood that a light chain is either a kappa or lambda light chain, but does not include a kappa/lambda combination by virtue of compilation of a VK and ⁇ .
  • a "degenerate codon” refers to three-nucleotide codon that specifies the same amino acid as a codon in a parent nucleotide sequence.
  • One of skill in the art is familiar with degeneracy of the genetic code and can identify degenerate codons.
  • Diversity with respect to members in a collection refers to the number of unique members in a collection. Hence, diversity refers to the number of different amino acid sequences or nucleic acid sequences, respectively, among the analogous polypeptide members of that collection.
  • a collection of polynucleotides having a diversity of 104 contains 104 different nucleic acid sequences among the analogous polynucleotide members.
  • the provided collections of polynucleotides and/or polypeptides have diversities of at least at or about 102, 103, 104, 105, 106, 107, 108, 109, 1010 or more.
  • Sequence diversity refers to a representation of nucleic acid sequence similarity and is determined using sequence alignments, diversity scores, and/or sequence clustering. Any two sequences can be aligned by laying the sequences side-by-side and analyzing differences within nucleotides at every position along the length of the sequences. Sequence alignment can be assessed in silico using Basic Local Alignment Search Tool (BLAST), an NCBI tool for comparing nucleic acid and/or protein sequences. The use of BLAST for sequence alignment is well known to one of skill in the art. The Blast search algorithm compares two sequences and calculates the statistical significance of each match (a Blast score). Sequences that are most similar to each other will have a high Blast score, whereas sequences that are most varied will have a low Blast score.
  • BLAST Basic Local Alignment Search Tool
  • a "polypeptide domain” refers to a part of a polypeptide (a sequence of three or more, generally 5 or 7 or more amino acids) that is a structurally and/or functionally distinguishable or definable.
  • Exemplary of a polypeptide domain is a part of the polypeptide that can form an independently folded structure within a polypeptide made up of one or more structural motifs (e.g. combinations of alpha helices and/or beta strands connected by loop regions) and/or that is recognized by a particular functional activity, such as enzymatic activity or antigen binding.
  • a polypeptide can have one, typically more than one, distinct domains.
  • the polypeptide can have one or more structural domains and one or more functional domains.
  • a single polypeptide domain can be distinguished based on structure and function.
  • a domain can encompass a contiguous linear sequence of amino acids.
  • a domain can encompass a plurality of non-contiguous amino acid portions, which are non-contiguous along the linear sequence of amino acids of the polypeptide.
  • a polypeptide contains a plurality of domains. For example, each heavy chain and each light chain of an antibody molecule contains a plurality of
  • immunoglobulin (Ig) domains each about 110 amino acids in length.
  • Ig domain refers to a domain, recognized as such by those in the art, that is distinguished by a structure, called the Immunoglobulin (Ig) fold, which contains two beta-pleated sheets, each containing anti-parallel beta strands of amino acids connected by loops. The two beta sheets in the Ig fold are sandwiched together by hydrophobic interactions and a conserved intra- chain disulfide bond. Individual immunoglobulin domains within an antibody chain further can be distinguished based on function. For example, a light chain contains one variable region domain (VL) and one constant region domain (CL), while a heavy chain contains one variable region domain (VH) and three or four constant region domains (CH). Each VL, CL, VH, and CH domain is an example of an immunoglobulin domain.
  • VL variable region domain
  • CL constant region domain
  • CH domain three or four constant region domains
  • variable domain refers to a specific Ig domain of an antibody heavy or light chain that contains a sequence of amino acids that varies among different antibodies.
  • Each light chain and each heavy chain has one variable region domain (VL, and, VH).
  • VL, and, VH variable region domain
  • the variable domains provide antigen specificity, and thus are responsible for antigen recognition.
  • Each variable region contains CDRs that are part of the antigen binding site domain and framework regions (FRs).
  • a "constant region domain” refers to a domain in an antibody heavy or light chain that contains a sequence of amino acids that is comparatively more conserved among antibodies than the variable region domain.
  • Each light chain has a single light chain constant region (CL) domain and each heavy chain contains one or more heavy chain constant region (CH) domains, which include, CHI, CH2, CH3 and CH4.
  • CH heavy chain constant region
  • Full-length IgA, IgD and IgG isotypes contain CHI, CH2 CH3 and a hinge region, while IgE and IgM contain CHI, CH2 CH3 and CH4.
  • CHI and CL domains extend the Fab arm of the antibody molecule, thus contributing to the interaction with antigen and rotation of the antibody arms.
  • Antibody constant regions can serve effector functions, such as, but not limited to, clearance of antigens, pathogens and toxins to which the antibody specifically binds, e.g. through interactions with various cells, biomolecules and tissues.
  • An "antibody or portion thereof that is sufficient to form an antigen binding site” means that the antibody or portion thereof contains at least 1 or 2, typically 3, 4, 5 or all 6 CDRs of the VH and VL sufficient to retain at least a portion of the binding specificity of the corresponding full-length antibody containing all 6 CDRs.
  • a sufficient antigen binding site at least requires CDR3 of the heavy chain (CDRH3). It typically further requires the CDR3 of the light chain (CDRL3).
  • CDR-LI corresponds to residues L24-L34
  • CDR-L2 corresponds to residues L50-L56
  • CDR-L3 corresponds to residues L89-L97
  • CDR-H1 corresponds to residues H31 - H35, 35a or 35b depending on the length
  • CDR-H2 corresponds to residues H50-H65
  • CDR-H3 corresponds to residues H95-H102.
  • a "peptide mimetic” refers to a peptide that mimics the activity of a polypeptide.
  • an erythropoietin (EPO) peptide mimetic is a peptide that mimics the activity of Epo, such as for binding and activation of the EPO receptor.
  • An "address” refers to a unique identifier for each locus in a collection whereby an addressed member ⁇ e.g. an antibody) can be identified.
  • An addressed moiety is one that can be identified by virtue of its locus or location. Addressing can be effected by position on a surface, such as a well of a microplate. For example, an address for a protein in a microwell plate that is F9 means that the protein is located in row F, column 9 of the microwell plate. Addressing also can be effected by other identifiers, such as a tag encoded with a bar code or other symbology, a chemical tag, an electronic, such RF tag, a color-coded tag or other such identifier.
  • An "array” refers to a collection of elements, such as antibodies, containing three or more members.
  • spatial array refers to an array where members are separated or occupy a distinct space in an array.
  • spatial arrays are a type of addressable array.
  • Examples of spatial arrays include micro titer plates where each well of a plate is an address in the array.
  • Spacial arrays include any arrangement wherein a plurality of different molecules, e.g., polypeptides, are held, presented, positioned, situated, or supported.
  • Arrays can include microtiter plates, such as 48-well, 96-well, 144-well, 192-well, 240-well, 288-well, 336-well, 384-well, 432-well, 480-well, 576-well, 672-well, 768-well, 864-well, 960-well, 1056-well, 1152-well, 1248-well, 1344-well, 1440-well, or 1536-well plates, tubes, slides, chips, flasks, or any other suitable laboratory apparatus.
  • arrays can also include a plurality of sub-arrays.
  • a plurality of sub-arrays encompasses an array where more than one arrangement is used to position the polypeptides.
  • multiple 96-well plates could constitute a plurality of sub-arrays and a single array.
  • An "addressable library” or “spatially addressed library” refers to a collection of molecules such as nucleic acid molecules or protein agents, such as antibodies, in which each member of the collection is identifiable by virtue of its address.
  • An "addressable array” refers to one in which the members of the array are identifiable by their address, the position in a spatial array, such as a well of a microtiter plate, or on a solid phase support, or by virtue of an identifiable or detectable label, such as by color, fluorescence, electronic signal (i.e. RF, microwave or other frequency that does not substantially alter the interaction of the molecules of interest), bar code or other symbology, chemical or other such label.
  • a spatial array such as a well of a microtiter plate, or on a solid phase support
  • an identifiable or detectable label such as by color, fluorescence, electronic signal (i.e. RF, microwave or other frequency that does not substantially alter the interaction of the molecules of interest), bar code or other symbology, chemical or other such label.
  • the members of the array are located at identifiable loci on the surface of a solid phase or directly or indirectly linked to or otherwise associated with the identifiable label, such as affixed to a microsphere or other particulate support (herein referred to as beads) and suspended in solution or spread out on a surface.
  • a microsphere or other particulate support herein referred to as beads
  • An addressable combinatorial antibody library refers to a collection of antibodies in which member antibodies are identifiable and all antibodies with the same identifier, such as position in a spatial array or on a solid support, or a chemical or RF tag, bind to the same antigen, and generally are substantially the same in amino acid sequence.
  • identifier such as position in a spatial array or on a solid support, or a chemical or RF tag
  • reference to an "addressable arrayed combinatorial antibody library” means that the antibody members are addressed in an array.
  • In silico refers to research and experiments performed using a computer. In silico methods include, but are not limited to, molecular modeling studies, biomolecular docking experiments, and virtual representations of molecular structures and/or processes, such as molecular interactions.
  • the antibody members of a library can be designed using a computer program that selects component V, D and J germline segments from among those input into the computer and joins them in- frame to output a list of nucleic acid molecules for synthesis.
  • the recombination of the components of the antibodies in the collections or libraries provided herein can be performed in silico by combining the nucleotide sequences of each building block in accord with software that contains rules for doing so. The process could be performed manually without a computer, but the computer provides the convenience of speed.
  • a “database” refers to a collection of data items.
  • reference to a database is typically with reference to antibody databases, which provide a collection of sequence and structure information for antibody genes and sequences.
  • Exemplary antibody databases include, but are not limited to, IMGT®, the international ImMunoGeneTics information system (imgt.cines.fr; see e.g., Lefranc et al.
  • a database also can be created by a user to include any desired sequences.
  • the database can be created such that the sequences are inputted in a desired format (e.g., in a particular reading frame; lacking stop codons; lacking signal sequences).
  • the database also can be created to include sequences in addition to antibody sequences.
  • Screening refers to identification or selection of an antibody or portion thereof from a collection or library of antibodies and/or portions thereof, based on determination of the activity or property of an antibody or portion thereof. Screening can be performed in any of a variety of ways, including, for example, by assays assessing direct binding (e.g. binding affinity) of the antibody to a target protein or by functional assays assessing modulation of an activity of a target protein.
  • Activity towards a target protein refers to binding specificity and/or modulation of a functional activity of a target protein, or other measurements that reflects the activity of an antibody or portion thereof towards a target protein.
  • a "target protein” or “protein target” refers to candidate proteins or peptides that are specifically recognized by an antibody or portion thereof and/or whose activity is modulated by an antibody or portion thereof. Modulating the activity can comprise increasing, decreasing, stimulating, or preventing the activity or expression of the target protein.
  • a target protein includes any peptide or protein that contains an epitope for antibody recognition. Target proteins include proteins involved in the etiology of a disease or disorder by virtue of expression or activity.
  • the target protein is a transmembrane protein target.
  • Transmembrane protein targets include, but are not limited to, GPCRs, ion channels, transporters, and cell surface receptors. Ion channels may be potassium ion channels, sodium ion channels, calcium ion channels, and voltage gated channels.
  • the antibodies disclosed herein modulate a Kvl .3 ion channel, Navl .7 ion channel, or acid sensing ion channel (ASIC).
  • the antibodies disclosed herein may modulate cell surface receptors such as GLP1R, GCGR, EPO receptor, FGFR, FGF21R, CSFR, GMCSFR, and GCSFR.
  • target proteins include, but are not limited to, cytokines, kinases, interferons, hormones, and growth factors.
  • the target proteins can be from a mammal or non-mammal.
  • the target proteins can be from a human.
  • the target proteins are from a bovine.
  • "Hit" refers to an antibody or portion thereof identified, recognized or selected as having an activity in a screening assay.
  • "Iterative" with respect to screening means that the screening is repeated a plurality of times, such as 2, 3, 4, 5 or more times, until a "Hit" is identified whose activity is optimized or improved compared to prior iterations.
  • High-throughput refers to a large-scale method or process that permits
  • BLAST Basic Local Alignment Search Tool
  • blastn is a program that compares a nucleotide query sequence against a nucleotide sequence database ⁇ e.g. GenBank).
  • BlastP is a program that compares an amino acid query sequence against a protein sequence database.
  • a BLAST bit score is a value calculated from the number of gaps and substitutions associated with each aligned sequence. The higher the score, the more significant the alignment.
  • a "human protein” refers to a protein encoded by a nucleic acid molecule, such as
  • DNA present in the genome of a human, including all allelic variants and conservative variations thereof.
  • a variant or modification of a protein is a human protein if the modification is based on the wildtype or prominent sequence of a human protein.
  • Naturally occurring amino acids refer to the 20 L-amino acids that occur in polypeptides. The residues are those 20 a-amino acids found in nature which are incorporated into protein by the specific recognition of the charged tRNA molecule with its cognate mRNA codon in humans.
  • Non-naturally occurring amino acids refer to amino acids that are not genetically encoded.
  • a non-natural amino acid is an organic compound that has a structure similar to a natural amino acid but has been modified structurally to mimic the structure and reactivity of a natural amino acid.
  • Non-naturally occurring amino acids thus include, for example, amino acids or analogs of amino acids other than the 20 naturally-occurring amino acids and include, but are not limited to, the D-isostereomers of amino acids.
  • Exemplary non-natural amino acids are known to those of skill in the art.
  • Nucleic acids include DNA, RNA and analogs thereof, including peptide nucleic acids (PNA) and mixtures thereof. Nucleic acids can be single or double-stranded.
  • probes or primers which are optionally labeled, such as with a detectable label, such as a fluorescent or radio label, single-stranded molecules are contemplated. Such molecules are typically of a length such that their target is statistically unique or of low copy number (typically less than 5, generally less than 3) for probing or priming a library.
  • a probe or primer contains at least 14, 16 or 30 contiguous nucleotides of sequence complementary to or identical to a gene of interest. Probes and primers can be 10, 20, 30, 50, 100 or more nucleic acids long.
  • a "peptide” refers to a polypeptide that is from 2 to 40 amino acids in length.
  • amino acids which occur in the various sequences of amino acids provided herein are identified according to their known, three-letter or one-letter abbreviations (Table 1).
  • the nucleotides which occur in the various nucleic acid fragments are designated with the standard single-letter designations used routinely in the art.
  • amino acid is an organic compound containing an amino group and a carboxylic acid group.
  • a polypeptide contains two or more amino acids.
  • amino acids include the twenty naturally-occurring amino acids, non-natural amino acids and amino acid analogs (i.e., amino acids wherein the a-carbon has a side chain).
  • amino acid residue refers to an amino acid formed upon chemical digestion
  • amino acid residue sequences represented herein by formulae have a left to right orientation in the conventional direction of amino -terminus to carboxyl-terminus.
  • amino acid residue is broadly defined to include the amino acids listed in the Table of Correspondence (Table 1) and modified and unusual amino acids, such as those referred to in 37 C.F.R. ⁇ 1.821-1.822, and incorporated herein by reference.
  • a dash at the beginning or end of an amino acid residue sequence indicates a peptide bond to a further sequence of one or more amino acid residues, to an amino -terminal group such as NH2 or to a carboxyl-terminal group such as COOH.
  • L-amino acid is identified by the standard three letter code (or single letter code) or the standard three letter code (or single letter code) with the prefix "L-"; the prefix "D-" indicates that the stereoisomeric form of the amino acid is D.
  • an “immuno conjugate” refers to an antibody conjugated to one or more
  • heterologous molecule(s) including but not limited to a cytotoxic agent, non-antibody peptide or therapeutic polypeptide.
  • An immuno conjugate may include non-antibody sequences.
  • the non- antibody sequence can be conjugated to the antibody.
  • the non-antibody sequence can be within the antibody sequence.
  • non-antibody peptide refers to a peptide encoded by a non-antibody antibody sequence.
  • a non-antibody peptide may be a hormone, a lymphokine, an interleukin, a chemokines, a cytokine or a peptide toxin.
  • therapeutic polypeptide means one or more peptides having demonstrated or potential use in treating, preventing, or ameliorating one or more diseases, disorders, or conditions in a subject in need thereof, as well as related peptides.
  • Therapeutic peptides include peptides found to have use in treating, preventing, or ameliorating one or more diseases, disorders, or conditions after the time of filing of this application.
  • Related peptides include fragments of therapeutic peptides, therapeutic peptide variants, and therapeutic peptide derivatives that retain some or all of the therapeutic activities of the therapeutic peptide.
  • therapeutic polypeptide or “therapeutic peptides” encompass modifications to the therapeutic peptides defined and/or disclosed herein.
  • the therapeutic polypeptide is selected from a hormone, a lymphokine, an
  • Therapeutic polypeptides can be peptides encoded by non-antibody sequences.
  • a derivative or a variant of a polypeptide is said to share "homology" or be
  • the derivative or variant is at least 75% the same as that of either the peptide or a fragment of the peptide having the same number of amino acid residues as the derivative. In certain embodiments, the derivative or variant is at least 85% the same as that of either the peptide or a fragment of the peptide having the same number of amino acid residues as the derivative. In certain embodiments, the amino acid sequence of the derivative is at least 90% the same as the peptide or a fragment of the peptide having the same number of amino acid residues as the derivative.
  • the amino acid sequence of the derivative is at least 95% the same as the peptide or a fragment of the peptide having the same number of amino acid residues as the derivative. In certain embodiments, the derivative or variant is at least 99% the same as that of either the peptide or a fragment of the peptide having the same number of amino acid residues as the derivative.
  • Kb kilobases
  • bp base pairs
  • Kb kilobases
  • bp base pairs
  • kD kilo-Daltons
  • Proteins sizes are estimated from gel electrophoresis, from sequenced proteins, from derived amino acid sequences, or from published protein sequences.
  • Oligonucleotides that are not commercially available can be chemically synthesized according to the solid phase phosphoramidite triester method first described by Beaucage and Caruthers, Tetrahedron Letters, 22: 1859-1862 (1981), using an automated synthesizer, as described in Van Devanter et al, Nucleic Acids Res., 12:6159-6168 (1984). Purification of oligonucleotides is by either native polyacrylamide gel electrophoresis or by anion-exchange chromatography as described in Pearson & Reanier, J. Chrom., 255: 137-149 (1983).
  • sequence of the cloned genes and synthetic oligonucleotides can be verified after cloning using, e.g., the chain termination method for sequencing double-stranded templates of Wallace et al, Gene, 16:21-26 (1981).
  • the nucleic acids encoding recombinant polypeptides of the present disclosure may be cloned into an intermediate vector before transformation into prokaryotic or eukaryotic cells for replication and/or expression.
  • the intermediate vector may be a prokaryote vector such as a plasmid or shuttle vector.
  • cattle are the only species where ultralong CDR3 sequences have been identified.
  • other species for example other ruminants, may also possess antibodies with ultralong CDR3 sequences.
  • Exemplary antibody variable region sequences comprising an ultralong CDR3 sequence identified in cattle include those designated as: BLV1H12 ⁇ see, SEQ ID NO: 22), BLV5B8 (see, SEQ ID NO: 23), BLV5D3 (see, SEQ ID NO: 24) and BLV8C11 (see, SEQ ID NO: 25) (see, e.g., Saini, et al (1999) Eur. J. Immunol 29: 2420-2426; and Saini and Kaushik (2002) Scand. J. Immunol.
  • BF4E9 see, SEQ ID NO: 26
  • BF1H1 see, SEQ ID NO: 27
  • F18 see, SEQ ID NO: 28
  • bovine antibodies are identified and/or produced. Multiple techniques exist to identify and/or produce antibodies.
  • Antibodies of the present disclosure may be isolated by screening including, high- throughput screening, of combinatorial libraries for antibodies with the desired activity or activities. For example, a variety of methods are known in the art for generating phage display libraries and screening such libraries for antibodies possessing the desired binding characteristics. Such methods are reviewed, e.g., in Hoogenboom et al.
  • phage display methods repertoires of VH and VL genes are separately cloned by polymerase chain reaction (PCR) and recombined randomly in phage libraries, which can then be screened for antigen-binding phage as described in Winter et al, Ann. Rev. Immunol, 12: 433-455 (1994).
  • Phage typically display antibody fragments, either as single-chain Fv (scFv) fragments or as Fab fragments. Libraries from immunized sources provide high-affinity antibodies to the immunogen without the requirement of constructing hybridomas.
  • Phage display libraries of bovine antibodies may be a source of bovine antibody gene sequences, including ultralong CDR3 sequences.
  • a non-human antibody is humanized to reduce imrnunogenicity to humans, while retaining the specificity and affinity of the parental non-human antibody.
  • 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 (e.g., the antibody from which the CDR residues are derived), e.g., to restore or improve antibody specificity or affinity.
  • Human framework regions that may be used for humanization include but are not limited to: framework regions selected using the "best-fit” method (see, e.g., Sims et al J.
  • Antibodies with ultralong CDR3 sequences may also include non-antibody sequences, such as cytokines, therapeutic polypeptides or growth factors, into the CDR3 region.
  • the resultant antibody can be effective in treating or preventing a disease or condition.
  • an antibody comprising an ultralong CDR3 inhibits tumor metastasis.
  • the cytokine, therapeutic polypeptide or growth factor may be shown to have an antiproliferative effect on at least one cell population.
  • the resultant antibody modulates the expression or activity of a target (e.g., protein target, transmembrane protein target).
  • a target e.g., protein target, transmembrane protein target.
  • an antibody comprising an ultralong CDR3 inhibits or blocks an ion channel.
  • the non-antibody sequence may be a hormone, a lymphokine, an interleukin, a chemokines, a cytokine, a peptide toxin, and combinations thereof.
  • cytokines, therapeutic polypeptides, toxins, lymphokines, growth factors, or other hematopoietic factors include
  • G-CSF Granulocyte colony- stimulating factor
  • M-CSF macrophage colony-stimulating factor
  • GM-CSF Granulocyte-macrophage colony- stimulating factor
  • Meg-CSF TNF, IL-1, IL-2, IL-3, IL-4, IL-5, IL-6, IL-7, IL-8, IL-9, IL-10, IL-11, IL-12, IL-13, IL-14, IL-15, IL-16, IL-17, IL-18, IFN (e.g., a-interferon, ⁇ -interferon, a ⁇ -interferon), TNF-alpha, TNF1, TNF2, thrombopoietin, stem cell factor, and erythropoietin (EPO).
  • IFN e.g., a-interferon, ⁇ -interferon, a ⁇ -interferon
  • TNF-alpha TNF1, TNF2, thrombopoie
  • Additional growth factors for use in the antibodies and/or pharmaceutical compositions of the present disclosure include: angiogenin, bone morp biogenic protein- 1, bone morphogenic protein-2, bone morphogenic protein-3, bone morphogenic protein-4, bone morphogenic protein-5, bone morphogenic protein-6, bone morphogenic protein-7, bone morphogenic protein-8, bone morphogenic protein-9, bone morphogenic protein- 10, bone morphogenic protein- 11, bone morphogenic protein- 12, bone morphogenic protein- 13, bone morphogenic protein- 14, bone morphogenic protein- 15, bone morphogenic protein receptor IA, bone morphogenic protein receptor IB, brain derived
  • fibroblast growth factor 4 fibroblast growth factor 5
  • fibroblast growth factor 6 fibroblast growth factor 7
  • fibroblast growth factor 8b fibroblast growth factor 8c
  • fibroblast growth factor 9 fibroblast growth factor 10
  • FGF21 fibroblast growth factor 21
  • the therapeutic polypeptide is a mammalian G-CSF, a growth hormone, a leptin, a a- interferon, a ⁇ -interferon, a ⁇ -interferon, a GM-CSF, a IL-11, a IL-10, a mokal (e.g., Moka, mokatoxin-1), or a VM-24.
  • the therapeutic polypeptide is a glucagon-like peptide 1 (GLP-1), exendin-4 (Ex-4), erythropoietin (EPO), fibroblast growth factor (FGF21), IL8, ziconotide, somatostatin, chlorotoxin, SDF1 (alpha), IL21, or derivative or variant thereof.
  • GLP-1 glucagon-like peptide 1
  • Ex-4 exendin-4
  • EPO erythropoietin
  • FGF21 fibroblast growth factor
  • IL8 ziconotide
  • somatostatin somatostatin
  • chlorotoxin SDF1 (alpha)
  • IL21 or derivative or variant thereof.
  • the G- CSF may be a bovine G-CSF.
  • the G-CSF, GM-CSF, EPO, FGF21, ⁇ -interferon and GLP-1 may be from a human.
  • the non-antibody sequence may comprise an amino acid sequence based on or derived from any of SEQ ID NOS: 317-332.
  • the non-antibody sequence may comprise an amino acid sequence that is 50%, 60%, 70% 80%, 90%, 95%, 97%, 99% identical to any of SEQ ID NOS: 317-332.
  • the non-antibody sequence may comprise an amino acid sequence that comprises 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or more amino acid residues of SEQ ID NOS: 317-332.
  • the amino acid residues may be consecutive. Alternatively, the amino acid residues are non-consecutive.
  • the non-antibody sequence may comprise at least a portion of any of SEQ ID NOS: 317-332.
  • the antibodies disclosed herein may comprise one or more sequences based on or derived from a mammalian, avian, reptilian, amphibian, fish, insect, bug, or arachnid sequence.
  • Mammals include, but are not limited to, cows, bison, buffalo, humans, mice, dogs, cats, sheep, goats, or rabbits.
  • Avians include, but are not limited to, chicken, geese, doves, eagles, sparrows, and pidgeons.
  • Reptiles include, but are not limited to, lizards, gators, snakes, and turtles.
  • Amphibians include, but are not limited to, frogs, salamanders, toads, and newts.
  • Fish include, but are not limited to, tuna, salmon, whales, and sharks.
  • Insects, bugs, and arachnids include, but are not limited to, flies, mosquitos, spiders, and scorpions.
  • the non-antibody sequence may be based on or derived from a bovine or human sequence.
  • the non-antibody sequence is based on or derived from a lizard, snail, snake or scorpion sequence.
  • the lizard may be a gila monster.
  • the snail may be a cone snail.
  • the non-antibody sequence is linked to an end of an ultralong
  • the non-antibody sequence can be linked to the 5' end or 3' end of the ultralong CDR3 nucleotide sequence.
  • the non-antibody sequence can be linked to the N-terminus or C-terminus of the ultralong CDR3 peptide sequence.
  • the non-antibody sequence is inserted within an ultralong
  • the non-antibody sequence is inserted between the stalk domain of an ultralong CDR3 sequence.
  • the non-antibody sequence can be inserted within the stalk domain of an ultralong CDR3 sequence.
  • the non-antibody sequence is inserted between the stalk domain and the knob domain of an ultralong CDR3 sequence.
  • the non- antibody sequence is inserted within the knob domain of an ultralong CDR3 sequence.
  • the non-antibody sequence replaces at least a portion of an ultralong CDR3 sequence.
  • the non-antibody sequence can replace about 1 or more, 2 or more, 3 or more, 4 or more, 5 or more, 10 or more, 15 or more, 20 or more, 25 or more, 30 or more, 35 or more, 40 or more, 45 or more, 50 or more, 55 or more amino acids of the ultralong CDR3 peptide sequence.
  • the non-antibody sequence can replace about 10% or more, 20% or more, 30%> or more, 40%) or more, 50%> or more, 55% or more, 60%> or more, 65%> or more, 70%> or more, 75% or more, 80%) or more, 85% or more, 90%> or more, 95% or more of the ultralong CDR3 peptide sequence.
  • the non-antibody sequence can replace at least a portion of a knob domain of an ultralong CDR3.
  • the non-antibody sequence can replace about 5 or more, 10 or more, 15 or more, 20 or more, 25 or more, 30 or more, 35 or more, 40 or more, 45 or more amino acids of the knob domain of an ultralong CDR3 peptide sequence.
  • the non-antibody sequence can replace about 10% or more, 20%) or more, 30% or more, 40% or more, 50% or more, 55% or more, 60% or more, 65% or more, 70%) or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% or more of the knob domain of the ultralong CDR3 peptide sequence.
  • the non-antibody sequence can replace at least a portion of a stalk domain of an ultralong CDR3.
  • the non-antibody sequence can replace about 1 or more, 2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, 10 or more, 11 or more, 12 or more, 13 or more, 14 or more, 15 or more, 20 or more amino acids of the stalk domain of an ultralong CDR3 peptide sequence.
  • the non-antibody sequence can replace about 10%) or more, 20% or more, 30% or more, 40% or more, 50% or more, 55% or more, 60% or more, 65%) or more, 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% or more of the stalk domain of the ultralong CDR3 peptide sequence.
  • the amino acids may be consecutive amino acids.
  • the amino acids are non-consecutive amino acids.
  • the ultralong CDR3 may comprise one or more conserved motifs.
  • the conserved motifs may be stalk domain conserved motifs as disclosed herein.
  • the conserved motifs may be knob domain conserved motifs as disclosed herein.
  • the non-antibody sequence replaces at least a portion of an ultralong CDR3 sequence.
  • the non-antibody sequence can replace about 5 or more, 10 or more, 15 or more, 20 or more, 25 or more, 30 or more, 40 or more, 50 or more, 55 or more, 60 or more, 70 or more, 80 or more, 90 or more, 100 or more, 110 or more, 120 or more, 130 or more, 140 or more, 150 or more, 160 or more, 170 or more nucleotides of the ultralong CDR3 nucleotide sequence.
  • the non-antibody sequence can replace about 10% or more, 20% or more, 30% or more, 40% or more, 50% or more, 55% or more, 60% or more, 65% or more, 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% or more of the ultralong CDR3 nucleotide sequence.
  • the non-antibody sequence can replace at least a portion of a knob domain of an ultralong CDR3.
  • the non-antibody sequence can replace about 5 or more, 10 or more, 15 or more, 20 or more, 25 or more, 30 or more, 40 or more, 50 or more, 55 or more, 60 or more, 70 or more, 80 or more, 90 or more, 100 or more, 110 or more, 120 or more, 130 or more, 140 or more nucleotides of the knob domain of an ultralong CDR3 nucleotide sequence.
  • the non-antibody sequence can replace about 10% or more, 20% or more, 30%> or more, 40%> or more, 50%> or more, 55% or more, 60% or more, 65%) or more, 70%> or more, 75% or more, 80%> or more, 85% or more, 90%> or more, 95% or more of the knob domain of the ultralong CDR3 nucleotide sequence.
  • the non-antibody sequence can replace at least a portion of a stalk domain of an ultralong CDR3.
  • the non-antibody sequence can replace about 5 or more, 10 or more, 15 or more, 20 or more, 25 or more, 30 or more, 35 or more, 40 or more, 45 or more, 50 or more, 55 or more, 60 or more, 65 or more, 70 or more nucleotides of the stalk domain of an ultralong CDR3 nucleotide sequence.
  • the non-antibody sequence can replace about 10% or more, 20% or more, 30% or more, 40% or more, 50% or more, 55% or more, 60%) or more, 65% or more, 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% or more of the stalk domain of the ultralong CDR3 nucleotide sequence.
  • the nucleotides may be consecutive nucleotides.
  • the nucleotides are non-consecutive nucleotides.
  • the ultralong CDR3 may comprise one or more conserved motifs.
  • the conserved motifs may be stalk domain conserved motifs as disclosed herein.
  • the conserved motifs may be knob domain conserved motifs as disclosed herein.
  • An antibody comprising an ultralong CDR3 sequence and a non-antibody sequence may further comprise one or more cleavage sites between the ultralong CDR3 sequence and the non-antibody sequence.
  • the one or more cleavage sites may be in front of the N-terminus of the non-antibody peptide sequence.
  • a cleavage site is inserted at the N-terminus of the non-antibody peptide sequence and at the C-terminus of the ultralong CDR3 peptide sequence.
  • the one or more cleave sites are behind the C-terminus of the non-antibody peptide sequence.
  • the cleavage site is inserted at the C-terminus of the non-antibody peptide sequence and at the N-terminus of the ultralong CDR3 peptide sequence.
  • the one or more cleavage sites may flank both the N-terminus and the C-terminus of the non-antibody peptide sequence.
  • the one or more cleavage sites may be upstream of the non-antibody nucleotide sequence.
  • the one or more cleavage sites may be at the 5' end of the non-antibody nucleotide sequence and at the 3' end of the ultralong CDR3 nucleotide sequence.
  • the one or more cleavage sites may be downstream of the non-antibody nucleotide sequence.
  • the one or more cleavage sites may be at the 3' end of the non-antibody nucleotide sequence and at the 5' end of the ultralong CDR3 nucleotide sequence.
  • the one or more cleavage sites may flank both the 5' end and the 3' end of the non-antibody nucleotide sequence.
  • the one or more cleavage sites may directly flank the non-antibody sequence. For example, there are zero nucleotides or amino acids between the cleavage site sequence and the non-antibody sequence.
  • the one or more cleavage sites may indirectly flank the non-antibody sequence.
  • nucleotides between the cleavage site nucleotide sequence and the non-antibody nucleotide sequence there are one or more nucleotides between the cleavage site nucleotide sequence and the non-antibody nucleotide sequence. There may be 2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, 10 or more, 12 or more, 15 or more, 20 or more nucleotides between the cleavage site nucleotide sequence and the non-antibody nucleotide sequence. In another example, there are one or more amino acids between the cleavage site peptide sequence and the non-antibody peptide sequence.
  • the cleavage site may be adjacent to the sequence based on or derived from the ultralong CDR3 sequence, linker sequence, non- antibody sequence, non-bovine sequence, or a combination thereof.
  • the cleavage site may be between the sequence based on or derived from the ultralong CDR3 sequence and the linker sequence.
  • the cleavage site may be between the sequence based on or derived from the ultralong CDR3 sequence and the non-antibody sequence.
  • the cleavage site may be between the linker sequence and the non-antibody sequence.
  • the cleavage site may be for a protease.
  • the protease may be a serine protease, threonine protease, cysteine protease, aspartate protease, or
  • the protease may include, but is not limited to, Factor Xa protease, chymotrypsin- like protease, trypsin-like protease, elastase-like protease, subtilisin-like protease, actinidain, bromelain, calpains, caspases, cathepsins, Mir 1 -CP, papain, HIV-1 protease, chymosin, renin, cathepsin D, pepsin, plasmepsin, nepenthesin, metalloexopeptidases, and metalloendopeptidases.
  • the cleavage site may be a cleavage site for Factor Xa or thrombin.
  • the cleavage site may comprise the amino acid sequence of IEGR.
  • the cleavage site is for a nuclease.
  • the antibody comprising the ultralong CDR3 sequence and non-antibody sequence may be cleaved by one or more proteases. Cleavage of the antibody by the one or more protease can result in release of one or more ends of the non-antibody peptide from the ultralong CDR3 region of the antibody.
  • cleavage of the antibody results in release of the N-terminus of the non- antibody peptide from the ultralong CDR3 region.
  • cleavage of the antibody results in release of the C-terminus of the non-antibody peptide from the ultralong CDR3 region.
  • the non-antibody sequence may be linked to the ultralong CDR3 sequence via one or more linkers.
  • the non-antibody sequence may be inserted with an ultralong CDR3 sequence.
  • two or more linkers are used to link the non-antibody sequence to the ultralong CDR3 sequence.
  • the two or more linkers may comprise the same sequence.
  • the two or more linkers comprise different sequences.
  • the one or more linker sequences may be the same length.
  • the one or more linker sequences may be different lengths.
  • the one or more linker sequences may be 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more or 10 or more amino acids in length.
  • the one or more linker sequences may comprise 1 or more, 2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, or 10 or more glycine residues.
  • the one or more linker sequences may comprise 2 or more, 3 or more, 4 or more, or 5 or more consecutive glycine residues.
  • the one or more linker sequences may comprise 1 or more serine residues.
  • the one or more linker sequences may comprise 1 or more, 2 or more, 3 or more, 4 or more, or 5 or more polar amino acid residues.
  • the polar amino acid residues may be selected from serine, threonine, asparagine, or glutamine.
  • the polar amino acid residues may comprise uncharged side chains.
  • the linkers may be attached to the N-terminal, C-terminal, or both N-and C-termini of the non-antibody peptide sequence.
  • the linkers may be attached to the 5 '-end, 3 '-end, or both the 5 '-and 3 'ends of the non-antibody nucleotide sequence.
  • the linker may comprise amino acid residues.
  • Exemplary amino acid linker components include a dipeptide, a tripeptide, a tetrapeptide or a pentapeptide.
  • Exemplary dipeptides include: valine- citrulline (vc or val-cit), alanine-phenylalanine (af or ala-phe).
  • Exemplary tripeptides include: glycine-valine-citrulline (gly-val-cit) and glycine-glycine-glycine (gly-gly-gly).
  • the linker may comprise an amino acid sequence of GGGSGGGGS (SEQ ID NO: 337) or
  • Amino acid residues which comprise an amino acid linker component include those occurring naturally, as well as minor amino acids and non-naturally occurring amino acids including analogs, such as citrulline.
  • Amino acid linker components can be designed and optimized in their selectivity for enzymatic cleavage by a particular enzymes, for example, a tumor-associated protease, cathepsin B, C and D, or a plasmin protease.
  • the ultralong CDR3 may be based on or derived from a single ultralong CDR3 sequence. Alternatively, the ultralong CDR3 is based on or derived from two or more ultralong CDR3 sequences. The two or more ultralong CDR3 sequences may be from the same animal. Alternatively, the two or more ultralong CDR3 sequences are from two or more different animals.
  • the ultralong CDR3 may comprise at least a portion of a stalk domain of an ultralong CDR3.
  • the antibodies disclosed herein may comprise 1 or more, 2 or more, 3 or more, 4 or more, 5 or more, 6 or more 7 or more, 8 or more, 9 or more, or 10 or more amino acids derived from or based on the stalk domain of the ultralong CDR3.
  • the antibodies disclosed herien may comprise 20 or fewer, 19 or fewer, 18 or fewer, 17 or fewer, 16 or fewer, 15 or fewer, 14 or fewer, 13 or fewer, 12 or fewer, 11 or fewer, 10 or fewer, 9 or fewer, 8 or fewer, 7 or fewer, 6 or fewer, 5 or fewer, 4 or fewer, 3 or fewer, or 2 or fewer amino acids derived from or based the stalk domain of the ultralong CDR3.
  • the amino acids may be consecutive amino acids. Alternatively, the amino acids are non-consecutive amino acids.
  • the antibodies disclosed herein may comprise a sequence that is 50% or more, 60%> or more, 70%> or more, 80%> or more, 85% or more, 90%> or more, 95% or more, 97% or more, 99% or more, or 100% homologous the sequence of the stalk domain of the ultralong CDR3.
  • the ultralong CDR3 may comprise one or more conserved motifs derived from or based on a stalk domain of the ultralong CDR3.
  • the antibodies disclosed herein may comprise 1 or more, 2 or more, 3 or more, 4 or more, or 5 or more conserved motifs derived from or based on the stalk domain of the ultralong CDR3.
  • the one or more conserved motifs derived from or based on the stalk domain of the ultralong CDR3 may comprise a sequence selected from any one of SEQ ID NOS: 157-307 and SEQ ID NOS: 333-336.
  • the antibodies disclosed herein may comprise a sequence that is 50% or more, 60% or more, 70% or more, 80% or more, 85% or more, 90% or more, 95% or more, 97% or more, 99% or more, or 100%) homologous to a sequence selected from any one of SEQ ID NOS: 157-224 and 235-295.
  • the antibodies disclosed herein may comprise a sequence that is 50% or more, 60% or more, 70% or more, 80% or more, 85% or more, 90% or more, 95% or more, 97% or more, 99% or more, or 100%) homologous to a sequence selected from any one of SEQ ID NOS: 225-227.
  • the one or more conserved motifs derived from or based on the stalk domain of the ultralong CDR3 may comprise a CT(T/S)VHQ motif.
  • the one or more conserved motifs derived from or based on the stalk domain of the ultralong CDR3 comprise a
  • CT(T/S)VHQX n motif In some instances, n is between 1 to 8, between 1 to 7, between 1 to 6, between 1 to 5, between 1 to 4, or between 1 to 3.
  • the one or more conserved motifs derived from or based on the stalk domain of the ultralong CDR3 may comprise a CX 1 X 2 X 3 X 4 Q motif.
  • X 1 may be a T, S, A, or G residue.
  • X 2 may be a T, S, A, P, or I residue.
  • X 3 may be a V or K residue.
  • X 4 may be an H, K, or Y residue.
  • the one or more conserved motifs derived from or based on the stalk domain of the ultralong CDR3 may comprise an X 1 X 2 VHQ motif.
  • X 1 may be a T, S, A, or G residue.
  • X 2 may be a T, S, A, P or I residue.
  • the one or more conserved motifs derived from or based on the stalk domain of the ultralong CDR3 may comprise a CX 1 X 2 VHQ motif.
  • X 1 may be a T, S, A, or G residue.
  • X 2 may be a T, S, A, P or I residue.
  • the one or more conserved motifs derived from or based on the stalk domain of the ultralong CDR3 may comprise an X 1 X 2 VX 3 Q motif.
  • X 1 may be a T, S, A, or G residue.
  • X 2 may be a T, S, A, P or I residue.
  • X 3 may be an H, Y or K residue.
  • the one or more conserved motifs derived from or based on the stalk domain of the ultralong CDR3 may comprise a CX 1 X 2 VX 3 Q motif.
  • X 1 may be a T, S, A, or G residue.
  • X 2 may be a T, S, A, P or I residue.
  • X 3 may be an H, Y or K residue.
  • the one or more conserved motifs derived from or based on the stalk domain of the ultralong CDR3 may comprise an X 1 X 2 K Q motif.
  • X 1 may be a T, S, A, or G residue.
  • X 2 may be a T, S, A, P or I residue.
  • the one or more conserved motifs derived from or based on the stalk domain of the ultralong CDR3 may comprise a CX 1 X 2 K Q motif X 1 may be a T, S, A, or G residue. X 2 may be a T, S, A, P or I residue.
  • the one or more conserved motifs derived from or based on the stalk domain of the ultralong CDR3 may comprise an YX 1 YX 2 motif.
  • X 1 may be a T, S, N, or I residue.
  • X 2 may be an E or D residue.
  • the one or more conserved motifs derived from or based on the stalk domain of the ultralong CDR3 may comprise an YX 1 YX 2 Y motif.
  • X 1 may be an L, S, T, or R residue.
  • X 2 may be a T, S, N or I residue.
  • the one or more conserved motifs derived from or based on the stalk domain of the ultralong CDR3 may comprise an YX 1 YX 2 YX 3 motif.
  • X 1 may be an L, S, T, or R residue.
  • X 2 may be a T, S, N or I residue.
  • X 3 may be an E or D residue.
  • the one or more conserved motifs derived from or based on the stalk domain of the ultralong CDR3 may comprise an YX J YX 2 YX 3 X 4 motif.
  • X 1 may be an L, S, T, or R residue.
  • X 2 may be a T, S, N or I residue.
  • X 3 may be an E or D residue.
  • X 4 may be an H, W, N, F, I or Y residue.
  • the one or more conserved motifs derived from or based on the stalk domain of the ultralong CDR3 may comprise an Y(E/D)X motif.
  • X may be an H, W, N, F, I or Y residue.
  • the one or more conserved motifs derived from or based on the stalk domain of the ultralong CDR3 may comprise an XY(E/D) motif.
  • X may be a T, S, N or I residue.
  • the one or more conserved motifs derived from or based on the stalk domain of the ultralong CDR3 may comprise an Y(E/D)X 1 X n W motif.
  • X 1 may be an H, W, N, F, I or Y residue. In some instances, n is between 1 to 4, between 1 to 3, or between 1 to 2.
  • the one or more conserved motifs derived from or based on the stalk domain of the ultralong CDR3 may comprise an Y(E/D)X 1 X 2 X 3 X 4 X 5 W motif.
  • X 1 may be an H, W, N, F, I or Y residue.
  • X 2 may be an Y, H, G, or N residue.
  • X3 may be a V, I, or A residue.
  • X 4 may be a D, N, T, or E residue.
  • X 5 may be an A, V, S, or T residue.
  • the antibodies disclosed herein may comprise a first conserved motif derived from or based on the stalk domain of the ultralong CDR3 selected from any of SEQ ID NOS: 157-234 and a second conserved motif derived from or based on the stalk domain of the ultralong CDR3 selected from any of SEQ ID NOS: 235-307 and SEQ ID NOS: 333-336.
  • the antibodies disclosed herein may comprise a first conserved motif derived from or based on the stalk domain of the ultralong CDR3 selected from a group comprising CT(T/S)VHQX n , CX ! X 2 X 3 X 4 Q, X 1 X 2 VHQ, CX !
  • the ultralong CDR3 may comprise at least a portion of a knob domain of an ultralong CDR3.
  • the antibodies disclosed herein may comprise 1 or more, 2 or more, 3 or more, 4 or more, 5 or more, 6 or more 7 or more, 8 or more, 9 or more, or 10 or more amino acids derived from or based on the knob domain of the ultralong CDR3.
  • the antibodies disclosed herien may comprise 20 or fewer, 19 or fewer, 18 or fewer, 17 or fewer, 16 or fewer, 15 or fewer, 14 or fewer, 13 or fewer, 12 or fewer, 1 1 or fewer, 10 or fewer, 9 or fewer, 8 or fewer, 7 or fewer, 6 or fewer, 5 or fewer, 4 or fewer, 3 or fewer, or 2 or fewer amino acids derived from or based the knob domain of the ultralong CDR3.
  • the amino acids may be consecutive amino acids. Alternatively, the amino acids are non-consecutive amino acids.
  • the antibodies disclosed herein may comprise a sequence that is 50% or more, 60%> or more, 70%> or more, 80%> or more, 85% or more, 90%> or more, 95% or more, 97% or more, 99% or more, or 100% homologous the sequence of the knob domain of the ultralong CDR3.
  • the ultralong CDR3 may comprise one or more conserved motifs derived from or based on a knob domain of the ultralong CDR3.
  • the antibodies disclosed herein may comprise 1 or more, 2 or more, 3 or more, 4 or more, or 5 or more conserved motifs derived from or based on the knob domain of the ultralong CDR3.
  • the one or more conserved motifs derived from or based on the knob domain may comprise a cysteine motif as disclosed herein.
  • one or more conserved motifs derived from or based on the knob domain comprises a C(P/S)DG motif.
  • the antibodies disclosed herein may comprise a sequence based on or derived from a mammal.
  • the mammal may be a bovine.
  • the mammal is a non-bovine mammal, such as a human.
  • the antibody sequences may be 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, 10 or more, 1 1 or more, 12 or more, 15 or more, 20 or more, 25 or more, 30 or more, 35 or more, 40 or more 45 or more, 50 or more, 55 or more, 60 or more, 65 or more 70 or more, 80 or more, 90 or more, 100 or more, 1 10 or more, 120 or more, 130 or more, 140 or more, 150 or more, 160 or more, 170 or more, 180 or more 190 or more, 200 or more, 220 or more, 230 or more, 240 or more 250 or more 260 or more, 270 or more, 280 or more, 290 or more or 300 or more amino acids in length.
  • the amino acids may be consecutive amino acids.
  • amino acids are non-consecutive amino acids.
  • the antibody sequences may comprise a bovine antibody sequence comprising 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, 10 or more, 1 1 or more, 12 or more, 15 or more, 20 or more, 25 or more, 30 or more, 35 or more, 40 or more 45 or more, 50 or more, 55 or more, 60 or more, 65 or more 70 or more, 80 or more, 90 or more, 100 or more, 1 10 or more, 120 or more, 130 or more, 140 or more, 150 or more, 160 or more, 170 or more, 180 or more 190 or more, 200 or more, 220 or more, 230 or more, 240 or more 250 or more 260 or more, 270 or more, 280 or more, 290 or more or 300 or more amino acids in length.
  • the bovine antibody may be a BLVH12, BLV5B8, BLVCV1 , BLV5D3, BLV8C1 1 , BF1H1 , or F18 antibody.
  • the antibody sequences may comprise a human antibody sequence comprising 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, 10 or more, 11 or more, 12 or more, 15 or more, 20 or more, 25 or more, 30 or more, 35 or more, 40 or more 45 or more, 50 or more, 55 or more, 60 or more, 65 or more 70 or more, 80 or more, 90 or more, 100 or more, 110 or more, 120 or more, 130 or more, 140 or more, 150 or more, 160 or more, 170 or more, 180 or more 190 or more, 200 or more, 220 or more, 230 or more, 240 or more 250 or more 260 or more, 270 or more, 280 or more, 290 or more or 300 or more amino acids in length.
  • the amino acids may
  • the antibody sequence based on or derived from at least a portion of the ultralong
  • the CDR3 can be 20 or fewer, 19 or fewer, 18 or fewer, 17 or fewer, 16 or fewer, 15 or fewer, 14 or fewer, 13 or fewer, 12 or fewer, 11 or fewer, 10 or fewer, 9 or fewer, 8 or fewer, 7 or fewer, 6 or fewer, or 5 or fewer amino acids in length.
  • the antibody sequence based on or derived from at least a portion of the ultralong CDR3 may be 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, 10 or more, 11 or more, 12 or more, 13 or more, 14 or more, or 15 or more amino acids in length.
  • the amino acids may be consecutive amino acids. Alternatively, the amino acids are non-consecutive amino acids.
  • CDR3 can contain 1 or more, 2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, 10 or more, 15 or more, 20 or more, 25 or more, 30 or more, 35 or more, 40 or more, 50 or more, 60 or more, 70 or more, 80 or more, 90 or more, or 100 or more nucleic acid modifications or alterations in the nucleotide sequence of the ultralong CDR3 from which it is based on or derived from.
  • the modifications and/or alterations may comprise substitutions, deletions, and/or insertions. Substitutions may comprise replacing one nucleic acid with another nucleic acid.
  • the nucleic acid may be a natural nucleic acid or a non-natural nucleic acid.
  • the antibody sequence based on or derived from at least a portion of the ultralong
  • CDR3 can contain 1 or more, 2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, 10 or more, 15 or more, 20 or more, 25 or more, 30 or more, 35 or more, 40 or more, 50 or more, or 60 or more amino acid modifications or alterations in the peptide sequence of the ultralong CDR3 from which it is based on or derived from.
  • the modifications and/or alterations may comprise substitutions, deletions, and/or insertions. Substitutions may comprise replacing one amino acid with another amino acid.
  • the amino acids to be substituted may contain one or more similar features to the amino acid by which it is replaced.
  • the features may include, but are not limited to, size, polarity, hydrophobicity, acidity, side chain, and bond formations.
  • the amino acid may be a natural amino acid or a non-natural amino acid.
  • the half-life of an antibody described herein is greater than the half-life of the un-conjugated therapeutic peptide or un-conjugated non-antibody peptide that is incorporated in the antibody. In some embodiments, the half-life of an antibody provided herein is greater than 4 hours when administered to a subject.
  • the half-life of an antibody provided herein is greater than 4 hours, greater than 6 hours, greater than 12 hours, greater than 24 hours, greater than 36 hours, greater than 2 days, greater than 3 days, greater than 4 days, greater than 5 days, greater than 6 days, greater than 7 days, greater than 8 days, greater than 9 days, greater than 10 days, greater than 11 days, greater than 12 days, greater than 13 days, or greater than 14 days when administered to a subject.
  • the subject is a mammal.
  • the subject is a mouse or a bovine.
  • the subject is a human.
  • a pharmaceutical composition comprising the antibody is administered to the subject once a day, every two days, every three days, every 4 days, every 7 days, every 10 days, every 14 days, every 21 days, every 28 days, every 2 months, or every three months.
  • the antibodies may be modified or altered to reduce immunogenicity.
  • the sequence of a partially bovine or non-bovine antibody may be modified or altered to reduce immunogenicity to humans.
  • a non-human antibody may be humanized to reduce imrnunogenicity to humans, while retaining the specificity and affinity of the parental non-human antibody.
  • a humanized antibody comprises one or more variable domains in which HVRs, e.g., CDRs, (or portions thereof) are derived from a non-human antibody, and FRs (or portions thereof) are derived from human antibody sequences.
  • HVRs e.g., CDRs
  • FRs or portions thereof
  • 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 (e.g., the antibody from which the HVR residues are derived), e.g., to restore or improve antibody specificity or affinity.
  • the antibodies comprising an ultralong CDR3 as disclosed herein are preferably monoclonal. Also encompassed within the scope of the disclosure are Fab, Fab', Fab'-SH and F(ab') 2 fragments of the antibodies comprising an ultralong CDR3 as provided herein. These antibody fragments can be created by traditional means, such as enzymatic digestion, or may be generated by recombinant techniques. Such antibody fragments may be chimeric or humanized. These fragments are useful for the diagnostic and therapeutic purposes set forth below.
  • Monoclonal antibodies are obtained from a population of substantially homogeneous antibodies, e.g., the individual antibodies comprising the population are identical except for possible naturally occurring mutations that may be present in minor amounts. Thus, the modifier "monoclonal" indicates the character of the antibody as not being a mixture of discrete antibodies.
  • the antibodies comprising an ultralong CDR3 as disclosed herein can be made using a hybridoma cell-based method first described by Kohler et ah, Nature, 256:495 (1975), or may be made by recombinant DNA methods.
  • Hybridoma cells can be generated by fusing B cells producing a desired antibody with an immortalized cell line, usually a myeloma cell line, so that the resulting fusion cells will be an immortalized cell line that secrets a particular antibody.
  • myeloma cells can be first transfected with a nucleic acid encoding a germline antibody V region and can be screened for the expression of the germline V region. Those myeloma cells with highest level of proteolytic light chain expression can be subsequently fused with B cells that produce an antibody with desired target protein specificity.
  • the fusion cells will produce two types of antibodies: one is a heterologous antibody containing an endogenous antibody chain (either heavy or light) operably joined to the recombinant germline V region (either heavy or light), and the other is the same antibody that the parental B cells would secrete (e.g. both endogenous heavy and light chains).
  • the operably joined heterologous heavy and light chains can be isolated by conventional methods such as chromatography and identification can be confirmed by target protein binding assays, assays identifying a unique tag of the germline polypeptide, or endopeptidase activity assays described in other sections of this disclosure. In some cases, where the heterologous antibody is the predominant type in quantity among the two types of antibodies, such isolation may not be needed.
  • the hybridoma cells may be seeded and grown in a suitable culture medium that preferably contains one or more substances that inhibit the growth or survival of the unfused, parental myeloma cells.
  • a suitable culture medium that preferably contains one or more substances that inhibit the growth or survival of the unfused, parental myeloma cells.
  • the culture medium for the hybridomas typically will include hypoxanthine, aminopterin, and thymidine (HAT medium), which substances prevent the growth of HGPRT-deficient cells.
  • Preferred myeloma cells are those that fuse efficiently, support stable high-level production of antibody by the selected antibody-producing cells, and are sensitive to a medium such as HAT medium.
  • myeloma cell lines may be murine myeloma lines, such as those derived from MOPC-21 and MPC-11 mouse tumors available from the Salk Institute Cell Distribution Center, San Diego, Calif. USA, and SP-2 or X63-Ag8-653 cells available from the American Type Culture Collection, Rockville, Md. USA.
  • Human myeloma and mouse-human heteromyeloma cell lines also have been described for the production of human monoclonal antibodies (Kozbor, J. Immunol, 133:3001 (1984); Brodeur et al., Monoclonal Antibody
  • Culture medium in which hybridoma cells are growing is assayed for production of antibodies comprising an ultralong CDR3.
  • the binding specificity of monoclonal antibodies produced by hybridoma cells may be determined by immunoprecipitation or by an in vitro binding assay, such as an enzyme- linked immuno adsorbent assay (ELISA).
  • ELISA enzyme- linked immuno adsorbent assay
  • the binding affinity of the monoclonal antibody can, for example, be determined by the Scatchard analysis of Munson et al., Anal. Biochem., 107:220 (1980).
  • the clones may be subcloned by limiting dilution procedures and grown by standard methods (Goding, Monoclonal Antibodies: Principles and Practice, pp. 59- 103 (Academic Press, 1986)). Suitable culture media for this purpose include, for example, D- MEM or RPMI-1640 medium.
  • the hybridoma cells may be grown in vivo as ascites tumors in an animal.
  • the monoclonal antibodies secreted by the subclones are suitably separated from the culture medium, ascites fluid, or serum by conventional immunoglobulin purification procedures such as, for example, protein A-Sepharose, hydroxylapatite chromatography, gel electrophoresis, dialysis, or affinity chromatography.
  • the antibodies comprising an ultralong CDR3 as disclosed herein may be made by using combinatorial libraries to screen for synthetic antibody clones with the desired activity or activities.
  • synthetic antibody clones are selected by screening phage libraries containing phage that display various fragments of antibody variable regions ⁇ e.g., scFv or Fab) fused to phage coat protein.
  • phage libraries may be panned, for example, by affinity chromatography against the desired antigen.
  • Clones expressing antibody fragments capable of binding to the desired antigen may be adsorbed to the antigen and thus separated from the non- binding clones in the library.
  • the binding clones may then be eluted from the antigen, and can be further enriched by additional cycles of antigen adsorption/elution.
  • Any of the antibodies comprising an ultralong CDR3 as disclosed herein may be obtained by designing a suitable antigen screening procedure to select for the phage clone of interest followed by construction of a full length antibody comprising an ultralong CDR3 clone using the VH and VL ⁇ e.g., from scFv or Fab) sequences from the phage clone of interest and suitable constant region (Fc) sequences described in Kabat et al., Sequences of Proteins of Immunological Interest, Fifth Edition, NIH Publication 91- 3242, Bethesda Md. (1991), vols. 1-3.
  • the antigen-binding domain of an antibody is formed from two variable (V) regions, one each from the light (VL) and heavy (VH) chains, that both present three hypervariable loops or complementarity-determining regions (CDRs).
  • Variable domains may be displayed functionally on phage, either as single-chain Fv (scFv, also referred to as single-chain antibody (SCA)) fragments, in which VH and VL are covalently linked through a short, flexible peptide, or as Fab fragments, in which they are each fused to a constant domain and interact non-covalently, as described in Winter et al., Ann. Rev. Immunol, 12: 433-455 (1994).
  • scFv or SCA encoding phage clones and Fab encoding phage clones may be separately or collectively referred to as "Fv phage clones" or "Fv clones”.
  • Repertoires of VH and VL genes may be separately cloned by polymerase chain reaction (PCR) and recombined randomly in phage libraries, which can then be searched for antigen-binding clones as described in Winter et al., Ann. Rev. Immunol, 12: 433-455 (1994).
  • Libraries from immunized sources provide high-affinity antibodies to the immunogen without the requirement of constructing hybridomas.
  • the naive repertoire may be cloned to provide a single source of human antibodies to a wide range of non-self and also self antigens without any immunization as described by Griffiths et al., EMBO J. 12: 725-734 (1993).
  • naive libraries can also be made synthetically by cloning the unrearranged V-gene segments from stem cells, and using PCR primers containing random sequence to encode the highly variable CDR3 regions and to accomplish rearrangement in vitro as described by Hoogenboom and Winter, J. Mol. Biol, 227: 381-388 (1992).
  • Filamentous phage is used to display antibody fragments by fusion to the minor coat protein pill.
  • Protein pill may include truncated forms of pill.
  • the antibody fragments can be displayed as single chain Fv fragments, in which VH and VL domains are connected on the same polypeptide chain by a flexible polypeptide spacer, (e.g., as described by Marks et al., J. Mol.
  • Fab fragments in which one chain is fused to pill (e.g., a truncated pill) and the other is secreted into the bacterial host cell periplasm where assembly of a Fab-coat protein structure which becomes displayed on the phage surface by displacing some of the wild type coat proteins, (e.g., as described in Hoogenboom et al., Nucl. Acids Res., 19: 4133-4137 (1991)).
  • Nucleic acid encoding antibody variable gene segments are recovered from the cells of interest and and may be amplified or copies made by recombinant DNA techniques (e.g., Kunkel mutagenesis).
  • recombinant DNA techniques e.g., Kunkel mutagenesis
  • the desired DNA may be obtained by isolating genomic DNA or mRNA from lymphocytes followed by polymerase chain reaction (PCR) with primers matching the 5' and 3' ends of rearranged VH and VL genes as described in Orlandi et al., Proc. Natl. Acad. Sci. (USA), 86: 3833-3837 (1989), thereby making diverse V gene repertoires for expression.
  • the V genes may be amplified from cDNA and genomic DNA, with back primers at the 5' end of the exon encoding the mature V-domain and forward primers based within the J-segment as described in Orlandi et al. (1989) and in Ward et al, Nature, 341 : 544-546 (1989).
  • back primers can also be based in the leader exon as described in Jones et al, Biotechnol, 9: 88-89 (1991), and forward primers within the constant region as described in Sastry et al, Proc. Natl. Acad. Sci. (USA), 86: 5728-5732 (1989).
  • degeneracy may be incorporated in the primers as described in Orlandi et al. (1989) or Sastry et al. (1989).
  • Library diversity may be enhanced or maximized by using PCR primers targeted to each V-gene family in order to amplify available VH and VL arrangements present in the immune cell nucleic acid sample, for example, as described in the method of Marks et al, J. Mol. Biol, 222: 581-597 (1991) or as described in the method of Orum et al, Nucleic Acids Res., 21 : 4491-4498 (1993).
  • rare restriction may be introduced within the PCR primer as a tag at one end as described in Orlandi et al. (1989), or by further PCR amplification with a tagged primer as described in Clackson et al, Nature, 352: 624-628 (1991).
  • Repertoires of synthetically rearranged V genes may be derived in vitro from V gene segments. Most of the human VH-gene segments have been cloned and sequenced (e.g., reported in Tomlinson et al, J. Mol. Biol, 227: 776-798 (1992)), and mapped (e.g., reported in Matsuda et al, Nature Genet., 3: 88-94 (1993); these cloned segments (including all the major conformations of the HI and H2 loop) may be used to generate diverse VH gene repertoires with PCR primers encoding H3 loops of diverse sequence and length as described in Hoogenboom and Winter, J. Mol.
  • VH repertoires may also be made with all the sequence diversity focused in a long H3 loop of a single length as described in Barbas et al, Proc. Natl. Acad. Sci. USA, 89: 4457-4461 (1992).
  • Human VK and ⁇ . segments have been cloned and sequenced (reported in Williams and Winter, Eur. J. Immunol, 23: 1456-1461 (1993)) and can be used to make synthetic light chain repertoires.
  • Synthetic V gene repertoires based on a range of VH and VL folds, and L3 and H3 lengths, will encode antibodies of considerable structural diversity.
  • V-gene encoding DNAs Following amplification of V-gene encoding DNAs, germline V-gene segments can be rearranged in vitro according to the methods of Hoogenboom and Winter, J. Mol. Biol, 227: 381-388 (1992).
  • Repertoires of antibody fragments may be constructed by combining VH and VL gene repertoires together in several ways. Each repertoire may be created in different vectors, and the vectors recombined in vitro, for example, as described in Hogrefe et al, Gene, 128: 119-126 (1993), or in vivo by combinatorial infection, for example, the loxP system described in
  • Both vectors contain in vivo recombination signals so that the VH and VL genes are recombined onto a single replicon and are co-packaged into phage virions.
  • These large libraries may provide large numbers of diverse antibodies of good affinity (K 1 of about 10 ⁇ 8 M).
  • the repertoires may be cloned sequentially into the same vector, for example, as described in Barbas et al, Proc. Natl. Acad. Sci. USA, 88: 7978-7982 (1991), or assembled together by PCR and then cloned, for example, as described in Clackson et al, Nature, 352: 624-628 (1991).
  • PCR assembly may also be used to join VH and VL DNAs with DNA encoding a flexible peptide spacer to form single chain Fv (scFv) repertoires.
  • in cell PCR assembly may be used to combine VH and VL genes within lymphocytes by PCR and then clone repertoires of linked genes as described in Embleton et al, Nucl. Acids Res., 20: 3831-3837 (1992).
  • the antibodies produced by naive libraries can be of moderate affinity (K 1 of about 10 6 to 10 7 M _1 ), but affinity maturation may also be mimicked in vitro by constructing and reselecting from secondary libraries as described in Winter et al (1994), supra.
  • mutation can be introduced at random in vitro by using error-prone polymerase (reported in Leung et al, Technique, 1 : 11-15 (1989)) in the method of Hawkins et al, J. Mol. Biol, 226: 889-896 (1992) or in the method of Gram et al, Proc. Natl. Acad. Sci. USA, 89: 3576- 3580 (1992).
  • affinity maturation may be performed by randomly mutating one or more CDRs, for example, using PCR with primers carrying random sequence spanning the CDR of interest, in selected individual Fv clones and screening for higher affinity clones.
  • WO 9607754 described a method for inducing mutagenesis in a complementarity determining region of an immunoglobulin light chain to create a library of light chain genes.
  • Another effective approach is to recombine the VH or VL domains selected by phage display with repertoires of naturally occurring V domain variants obtained from unimmunized donors and screen for higher affinity in several rounds of chain reshuffling as described in Marks et al, BiotechnoL, 10: 779-783 (1992). This technique allows the production of antibodies and antibody fragments with affinities in the 10 "9 M range.
  • the phage library samples are contacted with an immobilized protein under conditions suitable for binding of at least a portion of the phage particles with the adsorbent.
  • the conditions including pH, ionic strength, temperature and the like are selected to mimic physiological conditions.
  • the phages bound to the solid phase are washed and then eluted by acid, e.g., as described in Barbas et al, Proc. Natl. Acad. Sci. USA, 88: 7978-7982 (1991), or by alkali, ⁇ e.g., as described in Marks et al, J. Mol. Biol, 222: 581-597 (1991)), or by antigen competition, ⁇ e.g., in a procedure similar to the antigen competition method of Clackson et al, Nature, 352: 624-628 (1991)).
  • Phages may be enriched 20-1,000-fold in a single round of selection.
  • the enriched phages may be grown in bacterial culture and subjected to further rounds of selection.
  • the efficiency of selection depends on many factors, including the kinetics of dissociation during washing, and whether multiple antibody fragments on a single phage can simultaneously engage with antigen.
  • Antibodies with fast dissociation kinetics (and weak binding affinities) may be retained by use of short washes, multivalent phage display and high coating density of antigen in solid phase. The high density not only stabilizes the phage through multivalent interactions, but favors rebinding of phage that has dissociated.
  • DNA encoding the hybridoma-derived monoclonal antibodies or phage display Fv clones disclosed herein is readily isolated and sequenced using conventional procedures ⁇ e.g., by using oligonucleotide primers designed to specifically amplify the heavy and light chain coding regions of interest from hybridoma or phage DNA template).
  • the DNA can be placed into expression vectors, which are then transfected into host cells such as E. coli cells, simian COS cells, Chinese hamster ovary (CHO) cells, or myeloma cells that do not otherwise produce immunoglobulin protein, to obtain the synthesis of the desired monoclonal antibodies in the recombinant host cells.
  • DNA encoding Fv clones as disclosed herein may be combined with known DNA sequences encoding heavy chain and/or light chain constant regions ⁇ e.g., the appropriate DNA sequences can be obtained from Kabat et al, supra) to form clones encoding full or partial length heavy and/or light chains.
  • constant regions of any isotype can be used for this purpose, including IgG, IgM, IgA, IgD, and IgE constant regions, and that such constant regions may be obtained from any human or animal species.
  • a Fv clone derived from the variable domain DNA of one animal (such as human) species and then fused to constant region DNA of another animal species to form coding sequence(s) for "hybrid", full length heavy chain and/or light chain is included in the definition of "chimeric” and "hybrid” antibody as used herein.
  • a Fv clone derived from human variable DNA is fused to human constant region DNA to form coding sequence(s) for all human, full or partial length heavy and/or light chains.
  • DNA encoding an antibody comprising an ultralong CDR3 derived from a hybridoma disclosed herein may also be modified, for example, by substituting the coding sequence for human heavy-and light-chain constant domains in place of homologous murine sequences derived from the hybridoma clone (e.g., as in the method of Morrison et al. , Proc. Natl. Acad. Sci. USA, 81 : 6851-6855 (1984)).
  • DNA encoding a hybridoma or Fv clone-derived antibody or fragment can be further modified by covalently joining to the immunoglobulin coding sequence all or part of the coding sequence for a non-immunoglobulin polypeptide. In this manner, "chimeric" or “hybrid” antibodies are prepared that have the binding specificity of the Fv clone or hybridoma clone-derived antibodies disclosed herein.
  • the present disclosure provides antibody genes and proteins including, for example, chimeric, recombinant, engineered, synthetic, hybrid, bovine, fully bovine, bovinized, human, fully human or humanized antibody genes or proteins that comprise an ultralong CDR3 sequence.
  • the antibodies disclosed herein may selectively or specifically bind to an epitope of a target protein.
  • the antibody may be an antagonist (e.g., blocking) antibody or an agonist antibody.
  • variable region of the heavy and light chains are encoded by multiple germline gene segments separated by non-coding regions, or introns, and often are present on different chromosomes.
  • the genes for the human immunoglobulin heavy chain region contains approximately 65 variable (VH;) genes, 27 Diversity (DH) genes, and 6 Joining (JH) genes.
  • the human kappa ( ⁇ ) and lambda ( ⁇ ) light chains are also each encoded by a similar number of VL and JL gene segments, but do not include any D gene segments.
  • Exemplary VH, DH, JH and VL (VK or ⁇ ) and JL (JK or J ) germline gene segments are set forth in WO 2010/054007.
  • JH gene segment of the heavy chain locus are recombined, which is followed by the joining of one VH gene segment forming a rearranged VDJ gene that encodes a VH chain.
  • the rearrangement occurs only on a single heavy chain allele by the process of allelic exclusion.
  • Allelic exclusion is regulated by in- frame or "productive" recombination of the VDJ segments, which occurs in only about one-third of VDJ recombinations of the variable heavy chain.
  • ⁇ heavy chain that gets expressed on the surface of a pre-B cell and transmits a signal to shut off further heavy chain recombination, thereby preventing expression of the allelic heavy chain locus.
  • the surface- expressed ⁇ heavy chain also acts to activate the kappa ( ⁇ ) locus for rearrangement.
  • the lambda ( ⁇ ) locus is only activated for rearrangement if the ⁇ recombination is unproductive on both loci.
  • the light chain rearrangement events are similar to the heavy chain, except that only the VL and JL segments are recombined. Before primary transcription of each, the corresponding constant chain gene is added. Subsequent transcription and RNA splicing leads to mRNA that is translated into an intact light chain or heavy chain.
  • variable regions of antibodies confer antigen binding and specificity due to recombination events of individual germline V, D and J segments, whereby the resulting recombined nucleic acid sequences encoding the variable region domains differ among antibodies and confer antigen-specificity to a particular antibody.
  • the variation is limited to three complementarity determining regions (CDR1, CDR2, and CDR3) found within the N-terminal domain of the heavy (H) and (L) chain variable regions.
  • the CDRs are interspersed with regions that are more conserved, termed "framework regions" (FR).
  • FR framework regions
  • Each VH and VL is typically composed of three CDRs and four FRs arranged from the amino terminus to carboxy terminus in the following order: FR1, CDR1, FR2, CDR2, FR3, CDR3 and FR4. Sequence variability among VL and VH domains is generally limited to the CDRs, which are the regions that form the antigen binding site.
  • VH genes encode the N- terminal three framework regions, the first two complete CDRs and the first part of the third CDR), the DH gene encodes the central portion of the third CDR, and the JH gene encodes the last part of the third CDR and the fourth framework region.
  • the VL genes encode the first CDR and second CDR.
  • the third CDR (CDRL3) is formed by the joining of the VL and JL gene segments.
  • CDRs 1 and 2 are exclusively encoded by germline V gene segment sequences.
  • the VH and VL chain CDR3s form the center of the Ag-binding site, with CDRs 1 and 2 form the outside boundaries; the FRs support the scaffold by orienting the H and L CDRs.
  • an antigen binding site typically requires at least four of the CDRs make contact with the antigen's epitope, with CDR3 of both the heavy and light chain being the most variable and contributing the most specificity to antigen binding (see, e.g., Janis Kuby, Immunology, Third Edition, New York, W.H. Freeman and Company, 1998, pp. 115-118).
  • CDRH3 which includes all of the D gene segment, is the most diverse component of the Ab-binding site, and typically plays a critical role in defining the specificity of the Ab. In addition to sequence variation, there is variation in the length of the CDRs between the heavy and light chains.
  • the constant regions are encoded by sequences that are more conserved among antibodies. These domains confer functional properties to antibodies, for example, the ability to interact with cells of the immune system and serum proteins in order to cause clearance of infectious agents. Different classes of antibodies, for example IgM, IgD, IgG, IgE and IgA, have different constant regions, allowing them to serve distinct effector functions.
  • the present disclosure encompasses antibody fragments.
  • antibody fragments In certain circumstances there are advantages of using antibody fragments, rather than whole antibodies.
  • the smaller size of the fragments allows for rapid clearance, and may lead to improved access to solid tumors.
  • Antibody fragments include, but are not limited to, Fab, Fab', Fab'-SH, F(ab')2, Fv, Fv', Fd, Fd', scFv, hsFv fragments, and diabodies, and other fragments described below.
  • Fab fragment antigen binding fragment
  • Fab' fragment antigen binding fragment antigen binding domain antigen binding domain antigen binding domain antigen binding domain antigen binding domain antigen binding domains and having increased in vivo half-life, see U.S. Pat. No.
  • Diabodies are antibody fragments with two antigen binding sites that may be bivalent or bispecific. See, for example, EP 404,097; WO 1993/01161; Hudson et al, Nat. Med. 9: 129-134 (2003); and Hollinger et al, Proc. Natl. Acad. Sci. USA 90: 6444-6448 (1993).
  • Triabodies and tetrabodies are also described in Hudson et al, Nat. Med. 9: 129134 (2003).
  • Single-domain antibodies are antibody fragments comprising all or a portion of the heavy chain variable domain or all or a portion of the light chain variable domain of an antibody.
  • a single-domain antibody is a human single-domain antibody (Domantis, Inc., Waltham, Mass.; see, e.g., U.S. Pat. No. 6,248,516).
  • Antibody fragments can be made by various techniques, including but not limited to proteolytic digestion of an intact antibody as well as production by recombinant host cells (e.g. E. coli or phage), as described herein.
  • F(ab') 2 fragments can be isolated directly from
  • Fab and F(ab') 2 fragment with increased in vivo half-life comprising a salvage receptor binding epitope residues (see, e.g., in U.S. Patent No. 5,869,046).
  • Other techniques for the production of antibody fragments will be apparent to the skilled practitioner.
  • the antibody of choice is a single chain Fv fragment (scFv or single chain antibody (SCA)). See WO 93/16185; U.S. Patent Nos. 5,571,894; and 5,587,458.
  • Fv and sFv are the only species with intact combining sites that are devoid of constant regions; thus, they are suitable for reduced nonspecific binding during in vivo use.
  • sFv fusion proteins may be constructed to yield fusion of an effector protein at either the amino or the carboxy terminus of an sFv. See Antibody Engineering, ed. Borrebaeck, Supra.
  • the antibody fragment may also be a "linear antibody", for example, as described in U.S. Patent No. 5,641,870. Such linear antibody fragments may be monospecific or bispecific.
  • the present disclosure provides humanized antibodies comprising an ultralong
  • Humanized antibodies may include human engineered antibodies (see, e.g., Studnicka et al. (1994) Protein Eng. 7(6) 805-814; and U.S. Patent No. 5,766,886).
  • Various methods for constructing human engineered antibodies see, e.g., Studnicka et al. (1994) Protein Eng. 7(6) 805-814; and U.S. Patent No. 5,766,886).
  • humanizing non-human antibodies are known in the art.
  • a humanized antibody can have one or more amino acid residues introduced into it from a source which is human or non- human.
  • Humanization may be performed following the method of Studnicka (see, e.g., Studnicka et al. (1994) Protein Eng. 7(6) 805-814; and U.S. Patent No. 5,766,886), including the preparation of modified antibody variable domains. Humanization may alternatively be performed following the method of Winter and co-workers (Jones et al. (1986) Nature 321 :522-525; Riechmann et al. (1988) Nature 332:323-327; Verhoeyen et al.
  • humanized or human engineered antibodies are chimeric antibodies, including wherein substantially less than an intact human variable domain has been substituted by or incorporated into the corresponding sequence from a non-human species.
  • humanized antibodies may be human antibodies in which some hypervariable region residues and possibly some FR residues are substituted by residues from analogous sites in rodent antibodies.
  • humanized or human engineered antibodies may be non-human (e.g, rodent) antibodies in which some residues are substituted by residues from analogious sites in human antibodies (see, e.g., Studnicka et al. (1994) Protein Eng. 7(6) 805-814; and U.S. Patent No. 5,766,886).
  • variable domains both light and heavy
  • sequence of the variable domain of a rodent antibody is screened against the entire library of known human variable-domain sequences.
  • the human sequence which is closest to that of the rodent is then accepted as the human framework for the humanized antibody (Sims et al. (1993) J. Immunol. 151 :2296; Chothia et al. (1987) J. Mol. Biol. 196:901).
  • Another method uses a particular framework derived from the consensus sequence of all human antibodies of a particular subgroup of light or heavy chains. The same framework may be used for several different humanized antibodies (Carter et al. (1992) Proc. Natl. Acad. Sci. USA, 89:4285; Presta et al.
  • humanized antibodies are prepared by a process of analysis of the parental sequences and various conceptual humanized products using three-dimensional models of the parental and humanized sequences.
  • Three-dimensional immunoglobulin models are commonly available and are familiar to those skilled in the art.
  • Computer programs are available which illustrate and display probable three-dimensional conformational structures of selected candidate immunoglobulin sequences. Inspection of these displays permits analysis of the likely role of the residues in the functioning of the candidate immunoglobulin sequence, e.g., the analysis of residues that influence the ability of the candidate immunoglobulin to bind its antigen.
  • the humanized antibodies comprising an ultralong CDR3 may be deimmunized. Methods of deimmunizing an antibody or protein are well known in the art. The immunogenicity of therapeutic proteins such as antibodies is thought to result from the presence of T-cell epitopes which can bind MHC class II molecules and generate a proliferative and cytokine response in CD4+ helper T-cells.
  • T-cell epitopes can be predicted by in silico algorithms that identify residues required for binding MHC. Alternatively, epitopes can be identified directly by utilizing peripheral blood mononuclear cells from panels of human donors and measuring their response against the therapeutic protein when incubated with antigen presenting cells. Such in silico and in vitro systems are well known in the art [Jones TD, Crompton LJ, Carr FJ, Baker MP. Methods Mol Biol.
  • bovine antibodies comprising an ultralong
  • the bovine antibodies may be recombinant antibodies, engineered antibodies, synthetic antibodies, bovinized antibodies, or fully bovine antibodies.
  • Bovinized antibodies may include bovine engineered antibodies.
  • Methods for producing a bovinized antibody may comprise introducing one or more amino acid residues into it from a source which is a bovine.
  • methods for producing a bovinized antibody may comprise introducing one or more amino acid residues into it from a source which is a non-bovine.
  • Bovinization may be performed by preparing a modified antibody variable domains. Alternatively, bovinization may be performed by substituting hypervariable region sequences for the corresponding sequences of a bovine antibody. Accordingly, such "bovinized" or "bovine engineered” antibodies are chimeric antibodies.
  • Chimeric antibodies may include antibodies wherein substantially less than an intact bovine variable domain has been substituted by or incorporated into the corresponding sequence from a non-bovine species.
  • Bovinized or bovine engineered antibodies may be bovine antibodies in which some hypervariable region residues and constant region residues are substituted by residues from analogous sites in non-bovine antibodies.
  • bovinized, bovine engineered or fully bovine antibodies may be non-bovine (e.g, human) antibodies in which some residues are substituted by residues from analogious sites in bovine antibodies.
  • a bovine immunoglobuline region can be used to replace a non-bovine (e.g., human, rodent)
  • immunoglobulin region to produce a fully bovine, bovinized or bovine engineered antibody.
  • Bispecific antibodies are monoclonal, preferably human or humanized, antibodies that have binding specificities for at least two different antigens. For example, one of the binding specificities may be for a first antigen and the other may be for any other antigen. Exemplary bispecific antibodies may bind to two different epitopes of the same protein. Bispecific antibodies may also be used to localize cytotoxic agents to cells which express a particular protein. These antibodies possess a binding arm specific for the particular protein and an arm which binds the cytotoxic agent (e.g., saporin, anti-interferon-a, vinca alkaloid, ricin A chain, methotrexate or radioactive isotope hapten). Bispecific antibodies may be prepared as full length antibodies or antibody fragments (e.g., F(ab') 2 bispecific antibodies).
  • cytotoxic agent e.g., saporin, anti-interferon-a, vinca alkaloid, ricin A chain, methotrexate or radioactive isotope hapten
  • antibody variable domains with the desired binding specificities are fused to immunoglobulin constant domain sequences.
  • the fusion preferably is with an immunoglobulin heavy chain constant domain, comprising at least part of the hinge, CH2, and CH3 regions. It is preferred to have the first heavy- chain constant region (CHI), containing the site necessary for light chain binding, present in at least one of the fusions.
  • DNAs encoding the immunoglobulin heavy chain fusions and, if desired, the immunoglobulin light chain are inserted into separate expression vectors, and are co-transfected into a suitable host organism.
  • the bispecific antibodies are composed of a hybrid immunoglobulin heavy chain with a first binding specificity in one arm, and a hybrid immunoglobulin heavy chain-light chain pair (providing a second binding specificity) in the other arm.
  • This asymmetric structure may facilitate the separation of the desired bispecific compound from unwanted immunoglobulin chain combinations, as the presence of an immunoglobulin light chain in only one half of the bispecific molecule provides for a facile way of separation.
  • This approach is disclosed in WO 94/04690.
  • For further details of generating bispecific antibodies see, for example, Suresh et ah, Methods in Enzymology, 121 :210 (1986).
  • the interface between a pair of antibody molecules may can be engineered to maximize the percentage of heterodimers which are recovered from recombinant cell culture.
  • the preferred interface comprises at least a part of the C H3 domain of an antibody constant domain.
  • one or more small amino acid side chains from the interface of the first antibody molecule are replaced with larger side chains ⁇ e.g., tyrosine or tryptophan).
  • Compensatory "cavities" of identical or similar size to the large side chain(s) are created on the interface of the second antibody molecule by replacing large amino acid side chains with smaller ones ⁇ e.g., alanine or threonine). This provides a mechanism for increasing the yield of the heterodimer over other unwanted end-products such as homodimers.
  • Bispecific antibodies include cross-linked or "heteroconjugate" antibodies.
  • one of the antibodies in the heteroconjugate may be coupled to avidin, the other to biotin.
  • Such antibodies have, for example, been proposed to target immune system cells to unwanted cells (U.S. Patent No. 4,676,980), and for treatment of HIV infection (WO 91/00360, WO 92/00373, and EP 03089).
  • Heteroconjugate antibodies may be made using any convenient cross-linking methods. Suitable cross-linking agents are well known in the art, and are disclosed in U.S. Patent No.
  • bispecific antibodies may be prepared using chemical linkage.
  • Brennan et al., Science, 229: 81 (1985) describe a procedure wherein intact antibodies are proteolytically cleaved to generate F(ab') 2 fragments. These fragments are reduced in the presence of the dithiol complexing agent sodium arsenite to stabilize vicinal dithiols and prevent intermolecular disulfide formation.
  • the Fab' fragments generated are then converted to
  • thionitrobenzoate (TNB) derivatives One of the Fab'-TNB derivatives is then reconverted to the Fab'-thiol by reduction with mercaptoethylamine and is mixed with an equimolar amount of the other Fab'-TNB derivative to form the bispecific antibody.
  • the bispecific antibodies produced may be used as agents for the selective immobilization of enzymes.
  • bispecific antibodies have been produced using leucine zippers. See, e.g., Kostelny et al, J. Immunol, 148(5): 1547-1553 (1992).
  • the leucine zipper peptides from the Fos and Jun proteins were linked to the Fab' portions of two different antibodies by gene fusion.
  • the antibody homodimers were reduced at the hinge region to form monomers and then re-oxidized to form the antibody heterodimers. This method can also be utilized for the production of antibody homodimers.
  • the fragments comprise a heavy-chain variable domain (VH) connected to a light-chain variable domain (VL) by a linker which is too short to allow pairing between the two domains on the same chain. Accordingly, the VH and VL domains of one fragment are forced to pair with the complementary VL and VH domains of another fragment, thereby forming two antigen-binding sites.
  • VH and VL domains of one fragment are forced to pair with the complementary VL and VH domains of another fragment, thereby forming two antigen-binding sites.
  • sFv single-chain Fv
  • Antibodies with more than two valencies are contemplated.
  • trispecific antibodies can be prepared. See, e.g., Tutt et al. J. Immunol. 147: 60 (1991).
  • a multivalent antibody may be internalized (and/or catabolized) faster than a bivalent antibody by a cell expressing an antigen to which the antibodies bind.
  • the antibodies of the present disclosure may be multivalent antibodies (which are other than of the IgM class) with three or more antigen binding sites (e.g., tetravalent antibodies), which may be produced by recombinant expression of nucleic acid encoding the polypeptide chains of the antibody.
  • the multivalent antibody may comprise a dimerization domain and three or more antigen binding sites.
  • a preferred dimerization domain may comprise (or consist of) an Fc region or a hinge region. In this scenario, the antibody will comprise an Fc region and three or more antigen binding sites amino -terminal to the Fe region.
  • a preferred multivalent antibody may comprise (or consist of) three to about eight, but preferably four, antigen binding sites.
  • the multivalent antibody comprises at least one polypeptide chain (and preferably two polypeptide chains), wherein the polypeptide chain(s) comprise two or more variable domains.
  • the polypeptide chain(s) may comprise VDl-(Xl)n-VD2-(X2)n-Fc, wherein VD 1 is a first variable domain, VD2 is a second variable domain, Fc is one polypeptide chain of an Fc region, XI and X2 represent an amino acid or polypeptide, and n is 0 or 1.
  • the polypeptide chain(s) may comprise: VH-CH1- flexible linker-VH-CHl-Fc region chain; or VH-CHl-VH-CHl-Fc region chain.
  • a multivalent antibody may preferably further comprises at least two (and preferably four) light chain variable domain polypeptides.
  • a multivalent antibody may, for instance, comprise from about two to about eight light chain variable domain polypeptides.
  • the light chain variable domain polypeptides may comprise a light chain variable domain and, optionally, further comprise a CL domain.
  • amino acid sequence modification(s) of the antibodies comprising an ultralong CDR3 as described herein are contemplated.
  • Amino acid sequence variants including, for example, conservatively modified variants, of the antibody are prepared by introducing appropriate nucleotide changes into the antibody nucleic acid, or by peptide synthesis.
  • Such modifications include, for example, deletions from, and/or insertions into and/or substitutions of, residues within the amino acid sequences of the antibody. Any combination of deletion, insertion, and substitution is made to arrive at the final construct, provided that the final construct possesses the desired characteristics.
  • the amino acid alterations may be introduced in the subject antibody amino acid sequence at the time that sequence is made.
  • a useful method for identification of certain residues or regions of the antibody that are preferred locations for mutagenesis is called "alanine scanning mutagenesis" as described by Cunningham and Wells (1989) Science, 244: 1081-1085.
  • a residue or group of target residues are identified (e.g., charged residues such as arg, asp, his, lys, and glu) and replaced by a neutral or negatively charged amino acid (most preferably alanine or polyalanine) to affect the interaction of the amino acids with antigen.
  • Those amino acid locations demonstrating functional sensitivity to the substitutions then are refined by introducing further or other variants at, or for, the sites of substitution.
  • the site for introducing an amino acid sequence variation is
  • the nature of the mutation per se need not be predetermined. For example, to analyze the performance of a mutation at a given site, ala scanning or random mutagenesis is conducted at the target codon or region and the expressed immunoglobulins are screened for the desired activity.
  • Amino acid sequence insertions include amino-and/or carboxyl-terminal fusions ranging in length from one residue to polypeptides containing a hundred or more residues, as well as intrasequence insertions of single or multiple amino acid residues.
  • terminal insertions include an antibody with an N-terminal methionyl residue or the antibody fused to a cytotoxic polypeptide.
  • Other insertional variants of the antibody molecule include the fusion to the N-or C-terminus of the antibody to an enzyme (e.g., for ADEPT) or a polypeptide which increases the serum half- life of the antibody.
  • Glycosylation of polypeptides is typically either N-linked or O-linked.
  • N-linked refers to the attachment of the carbohydrate moiety to the side chain of an asparagine residue.
  • the tripeptide sequences asparagine-X-serine and asparagine-X-threonine, where X is any amino acid except proline, are the recognition sequences for enzymatic attachment of the carbohydrate moiety to the asparagine side chain.
  • X is any amino acid except proline
  • O-linked glycosylation refers to the attachment of one of the sugars N-aceylgalactosamine, galactose, or xylose to a hydroxyamino acid, most commonly serine or threonine, although 5-hydroxyproline or 5-hydroxylysine may also be used.
  • Addition of glycosylation sites to the antibody is conveniently accomplished by altering the amino acid sequence such that it contains one or more of the above-described tripeptide sequences (for N-linked glycosylation sites).
  • the alteration may also be made by the addition of, or substitution by, one or more serine or threonine residues to the sequence of the original antibody (for O-linked glycosylation sites).
  • the carbohydrate attached thereto may be altered.
  • antibodies with a mature carbohydrate structure that lacks fucose attached to an Fc region of the antibody have been described (see, e.g., US 2003/0157108, US
  • Antibodies with a bisecting N-acetylglucosamine (GlcNAc) in the carbohydrate attached to an Fc region of the antibody have been described (see, e.g., WO 2003/011878, and U.S. Patent No. 6,602,684).
  • Antigen-binding molecules with modified glycosylation have been described (see, e.g., WO
  • the preferred glycosylation variant herein comprises an Fc region, wherein a carbohydrate structure attached to the Fc region lacks fucose.
  • Such variants have improved ADCC function.
  • the Fc region further comprises one or more amino acid substitutions therein which further improve ADCC, for example, substitutions at positions 298, 333, and/or 334 of the Fc region (Eu numbering of residues).
  • Examples of publications related to "defucosylated" or "fucose-deficient" antibodies include: US 2003/0157108; WO 2000/61739; WO 2001/29246; US 2003/0115614 (now U.S. Patent No.6,946,292) US 2002/0164328 (now U.S. Patent No.
  • knockout cell lines such as alpha- 1,6-fucosyltransferase gene, FUT8, knockout CHO cells (Yamane-Ohnuki et al. Biotech. Bioeng. 87: 614 (2004)).
  • variants are an amino acid substitution variant. These variants have at least one amino acid residue in the antibody molecule replaced by a different residue.
  • the sites of greatest interest for substitutional mutagenesis include the hypervariable regions, but FR alterations are also contemplated. Conservative substitutions are shown in Table 2 under the heading of "preferred substitutions". If such substitutions result in a change in biological activity, then more substantial changes, denominated "exemplary substitutions", or as further described below in reference to amino acid classes, may be introduced and the products screened.
  • substitutions that differ significantly in their effect on maintaining (a) the structure of the polypeptide backbone in the area of the substitution, for example, as a sheet or helical conformation, (b) the charge or hydrophobicity of the molecule at the target site, or (c) the bulk of the side chain.
  • Naturally occurring amino acids are divided into groups based on common side-chain properties: (1) hydrophobic: norleucine, met, ala, val, leu, ile; (2) neutral hydrophilic: Cys, Ser, Thr, Asn, Gin; (3) acidic: asp, glu; (4) basic: his, lys, arg; (5) residues that influence chain orientation: gly, pro; and (6) aromatic: trp, tyr, phe.
  • Non-conservative substitutions will entail exchanging a member of one of these classes for another class.
  • substitutional variant involves substituting one or more hypervariable region residues of a parent antibody (e.g., a humanized or human antibody).
  • a parent antibody e.g., a humanized or human antibody.
  • the resulting variant(s) selected for further development will have improved biological properties relative to the parent antibody from which they are generated.
  • a convenient way for generating such a parent antibody e.g., a humanized or human antibody.
  • substitutional variants involves affinity maturation using phage display. Briefly, several hypervariable region sites (e.g., 6-7 sites) are mutated to generate all possible amino acid substitutions at each site. The antibodies thus generated are displayed from filamentous phage particles as fusions to the gene III product of Ml 3 packaged within each particle. The phage- displayed variants are then screened for their biological activity (e.g., binding affinity) as herein disclosed. In order to identify candidate hypervariable region sites for modification, alanine scanning mutagenesis can be performed to identify hypervariable region residues contributing significantly to antigen binding. Alternatively, or additionally, it may be beneficial to analyze a crystal structure of the antigen-antibody complex to identify contact points between the antibody and antigen.
  • Such contact residues and neighboring residues are candidates for substitution according to the techniques elaborated herein. Once such variants are generated, the panel of variants is subjected to screening as described herein and antibodies with superior properties in one or more relevant assays may be selected for further development.
  • Nucleic acid molecules encoding amino acid sequence variants of the antibody are prepared by a variety of methods known in the art. These methods include, but are not limited to, isolation from a natural source (in the case of naturally occurring amino acid sequence variants) or preparation by oligonucleotide-mediated (or site-directed) mutagenesis, PCR mutagenesis, and cassette mutagenesis of an earlier prepared variant or a non-variant version of the antibody.
  • the Fc region variant may comprise a human Fc region sequence (e.g., a human IgGl, IgG2, IgG3 or IgG4 Fc region) comprising an amino acid modification (e.g., a substitution) at one or more amino acid positions including that of a hinge cysteine.
  • a human Fc region sequence e.g., a human IgGl, IgG2, IgG3 or IgG4 Fc region
  • an amino acid modification e.g., a substitution
  • an antibody used in methods disclosed herein may comprise one or more alterations as compared to the wild type counterpart antibody, e.g,. in the Fc region. These antibodies would nonetheless retain substantially the same characteristics required for therapeutic utility as compared to their wild type counterpart. For example, it is thought that certain alterations can be made in the Fc region that would result in altered (e.g., either improved or diminished) Clq binding and/or Complement Dependent Cytotoxicity (CDC), e.g., as described in W099/51642. See also Duncan & Winter Nature 322:738-40 (1988); U.S. Patent No. 5,648,260; U.S. Patent No.
  • Fc region variants 5,624,821; and W094/29351 concerning other examples of Fc region variants.
  • WO00/42072 and WO 2004/056312 describe antibody variants with improved or diminished binding to FcRs. See, also, Shields et al. J. Biol. Chem. 9(2): 6591-6604 (2001).
  • Antibodies with increased half lives and improved binding to the neonatal Fc receptor (FcRn) which is responsible for the transfer of maternal IgGs to the fetus (Guyer et al., J. Immunol. 117:587 (1976) and Kim et al., J. Immunol. 24:249 (1994)), are described in US2005/0014934 (Hinton et al.).
  • These antibodies comprise an Fc reg on with one or more substitutions therein which improve binding of the Fc region to FcRn.
  • Polypeptide variants with altered Fc region amino acid sequences and increased or decreased Clq binding capability are described in U.S. Patent No. 6, 194,551 , W099/51642. See, also, Idusogie et al. J. Immunol. 164:4178-4184 (2000).
  • the present disclosure contemplates an antibody variant that possesses some but not all effector functions, which make it a desirable candidate for applications in which the half life of the antibody in vivo is important yet certain effector functions (such as complement and ADCC) are unnecessary or deleterious.
  • In vitro and/or in vivo cytotoxicity assays can be conducted to confirm the reduction/ depletion of CDC and/ or ADCC activities.
  • Fc receptor (FcR) binding assays can be conducted to ensure that the antibody lacks FcyR binding (hence likely lacking ADCC activity), but retains FcRn binding ability.
  • NK cells express FcyRIII only, whereas monocytes express FcyRI, FcyRII and FcyRIII.
  • FcR expression on hematopoietic cells is summarized in Table 3 on page 464 of Ravetch and Kinet, Annu. Rev. Immunol. 9:457-492 (1991).
  • Non-limiting examples of in vitro assays to assess ADCC activity of a molecule of interest is described in U.S. Pat. No. 5,500,362 (see, e.g. Hellstrom, I. et al. Proc. Nat' ! Acad. Sci. USA 83 :7059-7063 (1986)) and Hellstrom, I et al , Proc.
  • non-radioactive assays methods may be employed (see, for example, ACTITM non-radioactive cytotoxicity assay for flow cytometry
  • PBMC peripheral blood mononuclear cells
  • NK Natural Killer
  • ADCC activity of the molecule of interest may be assessed in vivo, e.g., in a animal model such as that disclosed in Clynes et al Proc. Nat'l Acad. Sci. USA 95 :652-656 (1998).
  • Clqbinding assays may also be carried out to confirm that the antibody is unable to bind Clq and hence lacks CDC activity. See, e.g.
  • a CDC assay may be performed (see, for example, Gazzano-Santoro et al , Immunol. Methods 202: 163 (1996); Cragg, M. S. et al, Blood 101 : 1045-1052 (2003); and Cragg, M. S, and M. J. Glennie, Blood 103 :27382743 (2004)).
  • FcRn binding and in vivo clearance/half life determinations can also be performed using methods known in the art (see, e.g. , Petkova, S. B. et al , Int'l Immunol. 18(12): 1759-1769 (2006)).
  • Antibodies with reduced effector function include those with substitution of one or more of Fc region residues 238, 265, 269, 270, 297, 327 and 329 (U.S. Pat. No. 6,737, 056).
  • Fc mutants include Fc mutants with substitutions at two or more of amino acid positions 265, 269, 270, 297 and 327, including the so-called "DANA" Fc mutant with substitution of residues 265 and 297 to alanine (U.S. Pat. No. 7,332,581).
  • an antibody variant comprises an Fc region with one or more amino acid substitutions which improve ADCC, e.g., substitutions at positions 298, 333, and/or 334 of the Fc region (EU numbering of residues).
  • alterations are made in the Fc region that result in altered
  • Those antibodies comprise an Fc region with one or more substitutions therein which improve binding of the Fc region to FcRn.
  • Fc variants include those with substitutions at one or more of Fc region residues: 238, 256, 265, 272, 286,303,305, 307, 311,312, 317, 340,356, 360, 362, 376, 378, 380, 382, 413, 424 or 434, e.g., substitution of Fc region residue 434 (U.S. Pat. No. 7,371,826).
  • the antibodies comprising an ultralong CDR3 as disclosed herein may be further modified to contain additional nonproteinaceous moieties that are known in the art and readily available.
  • the moieties suitable for derivatization of the antibody are water soluble polymers.
  • water soluble polymers include, but are not limited to, polyethylene glycol (PEG), copolymers of ethylene glycol/propylene glycol,
  • polyethylene glycol propionaldehyde may have advantages in manufacturing due to its stability in water.
  • the polymer may be of any molecular weight, and may be branched or unbranched.
  • the number of polymers attached to the antibody may vary, and if more than one polymers are attached, they can be the same or different molecules. In general, the number and/or type of polymers used for derivatization can be determined based on considerations including, but not limited to, the particular properties or functions of the antibody to be improved, whether the antibody derivative will be used in a therapy under defined conditions, etc.
  • nucleic acid encoding it is isolated and inserted into a replicable vector for further cloning (amplification of the DNA) or for expression.
  • DNA encoding the antibody is readily isolated and sequenced using conventional procedures ⁇ e.g., by using oligonucleotide probes that are capable of binding specifically to genes encoding the heavy and light chains of the antibody).
  • nucleic acid encoding an antibody comprising an ultralong CDR3, a variable region comprising an ultralong CDR3, or an ultralong CDR3, is isolated and inserted into a replicable vector for further cloning (amplification of the DNA) or for expression. Many vectors are available.
  • vector depends in part on the host cell to be used. Generally, preferred host cells are of either prokaryotic or eukaryotic (generally mammalian) origin. It will be appreciated that constant regions of any isotype can be used for this purpose, including IgG, IgM, IgA, IgD, and IgE constant regions, and that such constant regions can be obtained from any human or animal species.
  • Expression vectors containing regulatory elements from eukaryotic viruses are typically used in eukaryotic expression vectors, e.g., SV40 vectors, papilloma virus vectors, and vectors derived from Epstein-Barr virus.
  • exemplary eukaryotic vectors include pMSG, pAV009/A+, pMTO10/A+, pMAMneo-5, baculo virus pDSVE, and any other vector allowing expression of proteins under the direction of the CMV promoter, SV40 early promoter, SV40 later promoter, metallothionein promoter, murine mammary tumor virus promoter, Rous sarcoma virus promoter, polyhedrin promoter, or other promoters shown effective for expression in eukaryotic cells.
  • Some expression systems have markers that provide gene amplification such as thymidine kinase and dihydrofolate reductase.
  • markers that provide gene amplification such as thymidine kinase and dihydrofolate reductase.
  • high yield expression systems not involving gene amplification are also suitable, such as using a baculovirus vector in insect cells, with a nucleic acid sequence encoding a partially human ultralong CDR3 antibody chain under the direction of the polyhedrin promoter or other strong baculovirus promoters.
  • Polynucleotide sequences encoding polypeptide components of the antibodies disclosed herein can be obtained using standard recombinant techniques. Desired polynucleotide sequences may be isolated and sequenced from antibody producing cells such as hybridoma cells. Alternatively, polynucleotides can be synthesized using nucleotide synthesizer or PCR techniques. Once obtained, sequences encoding the polypeptides are inserted into a recombinant vector capable of replicating and expressing heterologous polynucleotides in prokaryotic hosts. Many vectors that are available and known in the art can be used for the purpose of the present disclosure.
  • Selection of an appropriate vector will depend mainly on the size of the nucleic acids to be inserted into the vector and the particular host cell to be transformed with the vector.
  • Each vector contains various components, depending on its function (amplification or expression of heterologous polynucleotide, or both) and its compatibility with the particular host cell in which it resides.
  • V regions comprising an ultralong CDR3 may optionally be fused to a C-region to produce an antibody comprising constant regions.
  • plasmid vectors containing replicon and control sequences which are derived from species compatible with the host cell are used in connection with these hosts.
  • the vector ordinarily carries a replication site, as well as marking sequences which are capable of providing phenotypic selection in transformed cells.
  • E. coli is typically transformed using pBR322, a plasmid derived from an E. coli species.
  • pBR322 contains genes encoding ampicillin (Amp) and tetracycline (Tet) resistance and thus provides easy means for identifying transformed cells.
  • pBR322 its derivatives, or other microbial plasmids or bacteriophage may also contain, or be modified to contain, promoters which can be used by the microbial organism for expression of endogenous proteins.
  • promoters which can be used by the microbial organism for expression of endogenous proteins. Examples of pBR322 derivatives used for expression of particular antibodies have been described (see, e.g., U.S. Patent No. 5,648,237).
  • phage vectors containing replicon and control sequences that are compatible with the host microorganism can be used as transforming vectors in connection with these hosts.
  • bacteriophage such as ⁇ TM-11 may be utilized in making a recombinant vector which can be used to transform susceptible host cells such as E. coli LE392.
  • the expression vectors disclosed herein may comprise two or more promoter-cistron pairs, encoding each of the polypeptide components.
  • a promoter is an untranslated regulatory sequence located upstream (5') to a cistron that modulates its expression.
  • Prokaryotic promoters typically fall into two classes, inducible and constitutive. Inducible promoter is a promoter that initiates increased levels of transcription of the cistron under its control in response to changes in the culture condition, e.g., the presence or absence of a nutrient or a change in temperature.
  • promoters recognized by a variety of potential host cells are well known.
  • the selected promoter can be operably linked to cistron DNA encoding the light or heavy chain by removing the promoter from the source DNA via restriction enzyme digestion and inserting the isolated promoter sequence into the vector disclosed herein.
  • Both the native promoter sequence and many heterologous promoters may be used to direct amplification and/or expression of the target genes.
  • heterologous promoters are utilized, as they generally permit greater transcription and higher yields of expressed target gene as compared to the native target polypeptide promoter.
  • Promoters suitable for use with prokaryotic hosts include: an ara B promoter, a
  • PhoA promoter PhoA promoter, ⁇ -galactamase and lactose promoter systems, a tryptophan (trp) promoter system and hybrid promoters such as the tac or the trc promoter.
  • trp tryptophan
  • other promoters that are functional in bacteria such as other known bacterial or phage promoters
  • Their nucleotide sequences have been published, thereby enabling a skilled worker operably to ligate them to cistrons encoding the target light and heavy chains ⁇ e.g., Siebenlist et al (1980) Cell 20: 269) using linkers or adaptors to supply any required restriction sites.
  • Suitable bacterial promoters are well known in the art and fully described in scientific literature such as Sambrook and Russell, supra, and Ausubel et al, supra.
  • Bacterial expression systems for expressing antibody chains of the recombinant catalytic polypeptide are available in, e.g., E. coli, Bacillus sp., and Salmonella (Palva et al, Gene, 22:229-235 (1983); Mosbach et al, Nature, 302:543-545 (1983)).
  • each cistron within the recombinant vector comprises a secretion signal sequence component that directs translocation of the expressed polypeptides across a membrane.
  • the signal sequence may be a component of the vector, or it may be a part of the target polypeptide DNA that is inserted into the vector.
  • the signal sequence should be one that is recognized and processed ⁇ e.g., cleaved by a signal peptidase) by the host cell.
  • the signal sequence is substituted by a prokaryotic signal sequence selected, for example PelB, OmpA, alkaline phosphatase, penicillinase, Ipp, or heat-stable enterotoxin II (STII) leaders, LamB, PhoE, and MBP.
  • a prokaryotic signal sequence selected, for example PelB, OmpA, alkaline phosphatase, penicillinase, Ipp, or heat-stable enterotoxin II (STII) leaders, LamB, PhoE, and MBP.
  • the signal sequences used in both cistrons of the expression system are STII signal sequences or variants thereof.
  • the production of the immunoglobulins according to the disclosure can occur in the cytoplasm of the host cell, and therefore does not require the presence of secretion signal sequences within each cistron.
  • immunoglobulin light and heavy chains are expressed, folded and assembled to form functional immunoglobulins within the cytoplasm.
  • Certain host strains e.g., the E. coli trxB-strains
  • Suitable host cells for cloning or expression of antibody-encoding vectors include prokaryotic or eukaryotic cells described herein.
  • the host cell is eukaryotic, e.g. a Chinese Hamster Ovary (CHO) cell, Human Embryonic Kidney (HEK) cell or lymphoid cell ⁇ e.g., YO, NSO, Sp20 cell).
  • CHO Chinese Hamster Ovary
  • HEK Human Embryonic Kidney
  • lymphoid cell ⁇ e.g., YO, NSO, Sp20 cell.
  • antibodies may be produced in bacteria, in particular when glycosylation and Fc effector function are not needed.
  • For expression of antibody fragments and polypeptides in bacteria see, e.g., U.S. Pat. Nos. 5,648,237, 5,789,199, and 5,840,523.
  • the antibody may be isolated from the bacterial cell paste in a soluble fraction and can be further purified.
  • eukaryotic microbes such as filamentous fungi or yeast are suitable cloning or expression hosts for antibody-encoding vectors, including fungi and yeast strains whose glycosylation pathways have been "humanized,” resulting in the production of an antibody with a partially or fully human glycosylation pattern. See Gemgross, Nat. Biotech.
  • Suitable host cells for the expression of glycosylated antibody are also derived from multicellular organisms (invertebrates and vertebrates). Examples of invertebrate cells include plant and insect cells. Numerous baculo viral strains have been identified which may be used in conjunction with insect cells, particularly for transfection of Spodoptera frugiperda cells. These examples are illustrative rather than limiting. Methods for constructing derivatives of any of the above-mentioned bacteria having defined genotypes are known in the art and described in, for example, Bass et al, Proteins, 8:309- 314 (1990).
  • E. coli, Serratia, or Salmonella species can be suitably used as the host when well known plasmids such as pBR322, pBR325, pACYC177, or pKN410 are used to supply the replicon.
  • plasmids such as pBR322, pBR325, pACYC177, or pKN410 are used to supply the replicon.
  • the host cell should secrete minimal amounts of proteolytic enzymes, and additional protease inhibitors may desirably be incorporated in the cell culture.
  • Plant cell cultures can also be utilized as hosts. See, e.g. U.S. Pat. Nos. 5,959,177,
  • Vertebrate cells may also be used as hosts.
  • mammalian cell lines that are adapted to grow in suspension may be useful.
  • useful mammalian host cell lines are monkey kidney CV1 line transformed by SV40 (COS-7); human embryonic kidney line (293 or 293 cells as described, e.g., in Graham et al, Gen VII '01. 36:59 (1977)); baby hamster kidney cells (BHK); mouse Sertoli cells (TM4 cells as described, e.g., in Mather, Biol. Reprod.
  • monkey kidney cells (CV1); African green monkey kidney cells (V ERO-76); human cervical carcinoma cells (HELA); canine kidney cells (MDCK; buffalo rat liver cells (BRL 3 A); human lung cells (W138); human liver cells (Hep G2); mouse mammary tumor (MMT 060562); TR1 cells, as described, e.g., in Mather et al, Annals ⁇ . Acad. Sci. 383:44-68 (1982); MRC 5 cells; and FS4 cells.
  • Other useful mammalian host cell lines include Chinese hamster ovary (CHO) cells, including DHFR' CHO cells (Urlaub et al, Proc. Natl. Acad. Sci.
  • a host cell comprises ⁇ e.g., has been transformed with): (1) a vector comprising a nucleic acid that encodes an amino acid sequence comprising the VL of the antibody and an amino acid sequence comprising the VH of the antibody, or (2) a first vector comprising a nucleic acid that encodes an amino acid sequence comprising the VL of the antibody and a second vector comprising a nucleic acid that encodes an amino acid sequence comprising the VH of the antibody.
  • nucleic acid encoding an antibody comprising an ultralong CDR3 is inserted into one or more expression vectors for further cloning and/or expression in a host cell.
  • Such nucleic acid may be readily isolated and sequenced using conventional procedures ⁇ e.g., by using oligonucleotide probes that are capable of binding specifically to genes encoding the heavy and light chains of the antibody).
  • Host cells are transformed with such expression vectors and cultured in conventional nutrient media modified as appropriate for inducing promoters, selecting transformants, or amplifying the genes encoding the desired sequences.
  • Transformation means introducing DNA into the prokaryotic host so that the DNA is replicable, either as an extrachromosomal element or by chromosomal integrant. Depending on the host cell used, transformation is done using standard techniques appropriate to such cells.
  • the calcium treatment employing calcium chloride is generally used for bacterial cells that contain substantial cell-wall barriers.
  • Another method for transformation employs polyethylene
  • glycol/DMSO glycol/DMSO.
  • electroporation Yet another technique used is electroporation.
  • Prokaryotic cells used to produce the polypeptides disclosed herein are grown in media known in the art and suitable for culture of the selected host cells.
  • suitable media include luria broth (LB) plus necessary nutrient supplements.
  • the media also contains a selection agent, chosen based on the construction of the expression vector, to selectively permit growth of prokaryotic cells containing the expression vector. For example, ampicillin is added to media for growth of cells expressing ampicillin resistant gene.
  • any necessary supplements besides carbon, nitrogen, and inorganic phosphate sources may also be included at appropriate concentrations introduced alone or as a mixture with another supplement or medium such as a complex nitrogen source.
  • the culture medium may contain one or more reducing agents selected from the group consisting of glutathione, cysteine, cystamine, thioglycollate, dithioerythritol and dithiothreitol.
  • the prokaryotic host cells are cultured at suitable temperatures.
  • the preferred temperature ranges from about 20° C. to about 39° C, more preferably from about 25° C. to about 37° C, even more preferably at about 30° C.
  • the pH of the medium may be any pH ranging from about 5 to about 9, depending mainly on the host organism.
  • the pH is preferably from about 6.8 to about 7.4, and more preferably about 7.0.
  • an inducible promoter is used in the expression vector disclosed herein, protein expression is induced under conditions suitable for the activation of the promoter.
  • an ara B or phoA promoter may be used for controlling transcription of the polypeptides.
  • a variety of inducers may be used, according to the vector construct employed, as is known in the art.
  • the expressed polypeptides of the present disclosure are secreted into and recovered from the periplasm of the host cells or transported into the culture media. Protein recovery from the periplasm typically involves disrupting the microorganism, generally by such means as osmotic shock, sonication or lysis. Once cells are disrupted, cell debris or whole cells may be removed by centrifugation or filtration. The proteins may be further purified, for example, by affinity resin chromatography. Alternatively, proteins that are transported into the culture media may be isolated therein. Cells may be removed from the culture and the culture supernatant being filtered and concentrated for further purification of the proteins produced. The expressed polypeptides can be further isolated and identified using commonly known methods such as polyacrylamide gel electrophoresis (PAGE) and Western blot assay.
  • PAGE polyacrylamide gel electrophoresis
  • Antibody production may be conducted in large quantity by a fermentation process.
  • Large-scale fermentations have at least 1000 liters of capacity, preferably about 1,000 to 100,000 liters of capacity. These fermentors use agitator impellers to distribute oxygen and nutrients, especially glucose (a preferred carbon/energy source).
  • Small scale fermentation refers generally to fermentation in a fermentor that is no more than approximately 100 liters in volumetric capacity, and can range from about 1 liter to about 100 liters.
  • induction of protein expression is typically initiated after the cells have been grown under suitable conditions to a desired density, e.g., an OD550 of about 180-220, at which stage the cells are in the early stationary phase.
  • a desired density e.g., an OD550 of about 180-220
  • inducers may be used, according to the vector construct employed, as is known in the art and described above. Cells may be grown for shorter periods prior to induction. Cells are usually induced for about 12-50 hours, although longer or shorter induction time may be used.
  • host strains deficient for proteolytic enzymes can be used for the present disclosure.
  • host cell strains may be modified to effect genetic mutation(s) in the genes encoding known bacterial proteases such as Protease III, OmpT, DegP, Tsp, Protease I, Protease Mi, Protease V, Protease VI and combinations thereof.
  • E. coli protease-deficient strains are available (see, e.g., Joly et al. (1998), supra; U.S. Patent No. 5,264,365; U.S. Patent No. 5,508,192; Hara et al, Microbial Drug Resistance, 2:63-72 (1996)).
  • E. coli strains deficient for proteolytic enzymes and transformed with plasmids overexpressing one or more chaperone proteins may be used as host cells in the expression systems disclosed herein.
  • Protein A immobilized on a solid phase is used for immuno affinity purification of the full length antibody products disclosed herein.
  • Protein A is a 41 kD cell wall protein from Staphylococcus aureas which binds with a high affinity to the Fc region of antibodies (see, e.g., Lindmark et al (1983) J. Immunol. Meth. 62: 1-13).
  • the solid phase to which Protein A is immobilized is preferably a column comprising a glass or silica surface, more preferably a controlled pore glass column or a silicic acid column. In some applications, the column has been coated with a reagent, such as glycerol, in an attempt to prevent nonspecific adherence of contaminants.
  • the preparation derived from the cell culture as described above is applied onto the Protein A immobilized solid phase to allow specific binding of the antibody of interest to Protein A.
  • the solid phase is then washed to remove contaminants non- specifically bound to the solid phase.
  • the antibody of interest is recovered from the solid phase by elution.
  • the vector components generally include, but are not limited to, one or more of the following: a signal sequence, an origin of replication, one or more marker genes, an enhancer element, a promoter, and a transcription termination sequence.
  • a vector for use in a eukaryotic host cell may also contain a signal sequence or other polypeptide having a specific cleavage site at the N-terminus of the mature protein or polypeptide of interest.
  • the heterologous signal sequence selected preferably is one that is recognized and processed ⁇ e.g., cleaved by a signal peptidase) by the host cell.
  • mammalian signal sequences as well as viral secretory leaders for example, the herpes simplex gD signal, are available.
  • the DNA for such precursor region is ligated in reading frame to DNA encoding the antibody.
  • Origin of Replication (ii) Origin of Replication
  • an origin of replication component is not needed for mammalian expression vectors.
  • the SV40 origin may be used only because it contains the early promoter.
  • Expression and cloning vectors may contain a selection gene, also termed a selectable marker.
  • Typical selection genes encode proteins that (a) confer resistance to antibiotics or other toxins, e.g., ampicillin, neomycin, methotrexate, or tetracycline, (b) complement auxotrophic deficiencies, where relevant, or (c) supply critical nutrients not available from complex media.
  • One example of a selection scheme utilizes a drug to arrest growth of a host cell.
  • Those cells that are successfully transformed with a heterologous gene produce a protein conferring drug resistance and thus survive the selection regimen.
  • Examples of such dominant selection use the drugs neomycin, mycophenolic acid and hygromycin.
  • Suitable selectable markers for mammalian cells are those that enable the identification of cells competent to take up the antibody nucleic acid, such as DHFR, thymidine kinase, metallothionein-I and -II, preferably primate metallothionein genes, adenosine deaminase, ornithine decarboxylase, etc.
  • cells transformed with the DHFR selection gene are first identified by culturing all of the transformants in a culture medium that contains methotrexate (Mtx), a competitive antagonist of DHFR.
  • Mtx methotrexate
  • An appropriate host cell when wild-type DHFR is employed is the Chinese hamster ovary (CHO) cell line deficient in DHFR activity ⁇ e.g., ATCC CRL-9096).
  • DHFR transformed or co-transformed with DNA sequences encoding an antibody, wild-type DHFR protein, and another selectable marker such as aminoglycoside 3 '-phosphotransferase (APH)
  • APH aminoglycoside 3 '-phosphotransferase
  • Expression and cloning vectors usually contain a promoter that is recognized by the host organism and is operably linked to the antibody polypeptide nucleic acid. Promoter sequences are known for eukaryotes. Virtually alleukaryotic genes have an AT -rich region located
  • N may be any nucleotide.
  • AATAAA sequence that may be the signal for addition of the poly A tail to the 3' end of the coding sequence. All of these sequences are suitably inserted into eukaryotic expression vectors.
  • Antibody polypeptide transcription from vectors in mammalian host cells is controlled, for example, by promoters obtained from the genomes of viruses such as polyoma virus, fowlpox virus, adenovirus (such as Adenovirus 2), bovine papilloma virus, avian sarcoma virus, cytomegalovirus, a retrovirus, hepatitis-B virus and Simian Virus 40 (SV40), from heterologous mammalian promoters, e.g., the actin promoter or an immunoglobulin promoter, from heat-shock promoters, provided such promoters are compatible with the host cell systems.
  • viruses such as polyoma virus, fowlpox virus, adenovirus (such as Adenovirus 2), bovine papilloma virus, avian sarcoma virus, cytomegalovirus, a retrovirus, hepatitis-B virus and Simian Virus 40 (SV40), from hetero
  • the early and late promoters of the SV40 virus are conveniently obtained as an
  • SV40 restriction fragment that also contains the SV40 viral origin of replication.
  • the immediate early promoter of the human cytomegalovirus is conveniently obtained as a Hindlll E restriction fragment.
  • a system for expressing DNA in mammalian hosts using the bovine papilloma virus as a vector is disclosed in U.S. Patent No. 4,419,446. A modification of this system is described in U.S. Patent No. 4,601,978.
  • the Rous Sarcoma Virus long terminal repeat can be used as the promoter.
  • Enhancer sequences are now known from mammalian genes (globin, elastase, albumin, a- fetoprotein, and insulin).
  • An enhancer from a eukaryotic cell virus may also be used. Examples include the SV40 enhancer on the late side of the replication origin (bp 100-270), the
  • the enhancer may be spliced into the vector at a position 5' or 3' to the antibody polypeptide-encoding sequence, but is preferably located at a site 5' from the promoter.
  • Expression vectors used in eukaryotic host cells will typically also contain sequences necessary for the termination of transcription and for stabilizing the mRNA. Such sequences are commonly available from the 5' and, occasionally 3', untranslated regions of eukaryotic or viral DNAs or cDNAs. These regions contain nucleotide segments transcribed as polyadenylated fragments in the untranslated portion of the mRNA encoding an antibody.
  • One useful transcription termination component is the bovine growth hormone polyadenylation region. See W094/11026 and the expression vector disclosed therein.
  • Suitable host cells for cloning or expressing the DNA in the vectors herein include higher eukaryote cells described herein, including vertebrate host cells. Propagation of vertebrate cells in culture (tissue culture) has become a routine procedure. Examples of useful mammalian host cell lines are monkey kidney CVl line transformed by SV40 (COS-7, ATCC CRL 1651); human embryonic kidney line (293 or 293 cells subcloned for growth in suspension culture, Graham et al, J. Gen Virol. 36:59 (1977)); baby hamster kidney cells (BHK, ATCC CCL 10); Chinese hamster ovary cells/-DHFR (CHO, Urlaub et al, Proc. Natl. Acad. Sci.
  • COS-7 monkey kidney CVl line transformed by SV40
  • human embryonic kidney line (293 or 293 cells subcloned for growth in suspension culture, Graham et al, J. Gen Virol. 36:59 (1977)
  • baby hamster kidney cells BHK,
  • mice Sertoli cells TM4, Mather, Biol. Reprod. 23:243-251 (1980); monkey kidney cells (CVl ATCC CCL 70); African green monkey kidney cells (VERO-76, ATCC CRL-1587); human cervical carcinoma cells (HELA, ATCC CCL 2); canine kidney cells (MDCK, ATCC CCL 34); buffalo rat liver cells (BRL 3A, ATCC CRL 1442); human lung cells (W138, ATCC CCL 75); human liver cells (Hep G2, HB 8065); mouse mammary tumor (MMT 060562, ATCC CCL51); TRI cells (Mather et al, Annals N.Y. Acad. Sci. 383:44-68 (1982)); MRC 5 cells; FS4 cells; and a human hepatoma line (Hep G2).
  • Any of the well-known procedures for introducing foreign nucleotide sequences into host cells may be used. These include the use of calcium phosphate transfection, polybrene, protoplast fusion, electroporation, biolistics, liposomes, microinjection, plasma vectors, viral vectors and any of the other well known methods for introducing cloned genomic DNA, cDNA, synthetic DNA, or other foreign genetic material into a host cell (see, e.g., Sambrook and Russell, supra). It is only necessary that the particular genetic engineering procedure used be capable of successfully introducing at least both genes into the host cell capable of expressing germline antibody polypeptide.
  • Host cells are transformed with the above-described expression or cloning vectors for antibody production and cultured in conventional nutrient media modified as appropriate for inducing promoters, selecting transformants, or amplifying the genes encoding the desired sequences.
  • the host cells used to produce an antibody of this disclosure may be cultured in a variety of media.
  • Commercially available media such as Ham's F10 (Sigma), Minimal Essential Medium ((MEM), (Sigma), RPMI-1640 (Sigma), and Dulbecco's Modified Eagle's Medium ((DMEM), Sigma) are suitable for culturing the host cells.
  • any of these media may be supplemented as necessary with hormones and/or other growth factors (such as insulin, transferrin, or epidermal growth factor), salts (such as sodium chloride, calcium, magnesium, and phosphate), buffers (such as HEPES), nucleotides (such as adenosine and thymidine), antibiotics (such as GENTAMYCINTM drug), trace elements (defined as inorganic compounds usually present at final concentrations in the micromolar range), and glucose or an equivalent energy source. Any other necessary supplements may also be included at appropriate concentrations that would be known to those skilled in the art.
  • the culture conditions such as temperature, pH, and the like, are those previously used with the host cell selected for expression, and will be apparent to the ordinarily skilled artisan.
  • the antibody can be produced intracellularly, or directly secreted into the medium. If the antibody is produced intracellularly, as a first step, the particulate debris, either host cells or lysed fragments, are removed, for example, by centrifugation or ultrafiltration. Where the antibody is secreted into the medium, supernatants from such expression systems are generally first concentrated using a commercially available protein concentration filter, for example, an Amicon or Millipore Pellicon ® ultrafiltration unit. A protease inhibitor such as PMSF may be included in any of the foregoing steps to inhibit proteolysis and antibiotics may be included to prevent the growth of adventitious contaminants.
  • a protease inhibitor such as PMSF may be included in any of the foregoing steps to inhibit proteolysis and antibiotics may be included to prevent the growth of adventitious contaminants.
  • the antibody composition prepared from the cells can be purified using, for example, hydroxylapatite chromatography, gel electrophoresis, dialysis, and affinity
  • affinity chromatography with affinity chromatography being the preferred purification technique.
  • the suitability of protein A as an affinity ligand depends on the species and isotype of any
  • Protein A can be used to purify antibodies that are based on human ⁇ , ⁇ 2, or ⁇ 4 heavy chains (Lindmark et al., J. Immunol. Meth. 62: 1-13 (1983)). Protein G is recommended for all mouse isotypes and for human ⁇ 3 (Guss et al, EMBO J. 5: 15671575 (1986)).
  • the matrix to which the affinity ligand is attached is most often agarose, but other matrices are available. Mechanically stable matrices such as controlled pore glass or poly(styrenedivinyl)benzene allow for faster flow rates and shorter processing times than can be achieved with agarose.
  • the Bakerbond ABXTM resin (J. T. Baker, Phillipsburg, N.J.) is useful for purification.
  • Other techniques for protein purification such as fractionation on an ion-exchange column, ethanol precipitation, Reverse Phase HPLC, chromatography on silica, chromatography on heparin SEPHAROSETM chromatography on an anion or cation exchange resin (such as a polyaspartic acid column), chromatofocusing, SDS- PAGE, and ammonium sulfate precipitation are also available depending on the antibody to be recovered.
  • Soluble forms of antibody or fragment present either in the cytoplasm or released from the periplasmic space may be further purified using methods known in the art, for example Fab fragments are released from the bacterial periplasmic space by osmotic shock techniques.
  • inclusion bodies comprising an antibody or fragment have formed, they can often bind to the inner and/or outer cellular membranes and thus will be found primarily in the pellet material after centrifugation.
  • the pellet material can then be treated at pH extremes or with chaotropic agent such as a detergent, guanidine, guanidine derivatives, urea, or urea derivatives in the presence of a reducing agent such as dithiothreitol at alkaline pH or tris carboxyethyl phosphine at acid pH to release, break apart, and solubilize the inclusion bodies.
  • the soluble antibody or fragment can then be analyzed using gel electrophoresis, immunoprecipitation or the like. If it is desired to isolate a solublized antibody or antigen binding fragment isolation may be accomplished using standard methods such as those set forth below and in Marston et al. (Meth. Enz., 182:264- 275 (1990)).
  • the mixture comprising the antibody of interest and contaminants may be subjected to low pH hydrophobic interaction chromatography using an elution buffer at a pH between about 2.5-4.5, preferably performed at low salt
  • concentrations e.g., from about 0-0.25 M salt.
  • an antibody or fragment may not be biologically active upon isolation.
  • Various methods for "refolding" or converting a polypeptide to its tertiary structure and generating disulfide linkages can be used to restore biological activity. Such methods include exposing the solubilized polypeptide to a pH usually above 7 and in the presence of a particular concentration of a chaotrope. The selection of chaotrope is very similar to the choices used for inclusion body solubilization, but usually the chaotrope is used at a lower concentration and is not necessarily the same as chaotropes used for the solubilization.
  • the refolding/oxidation solution will also contain a reducing agent or the reducing agent plus its oxidized form in a specific ratio to generate a particular redox potential allowing for disulfide shuffling to occur in the formation of the protein's cysteine bridge(s).
  • Some of the commonly used redox couples include cysteine/cystamine, glutathione (GSH)/dithiobis GSH, cupric chloride, dithiothreitol(DTT)/dithiane DTT, and 2-mercaptoethanol(bME)/di-thio-b(ME).
  • a cosolvent may be used to increase the efficiency of the refolding, and common reagents used for this purpose include glycerol, polyethylene glycol of various molecular weights, arginine and the like.
  • the disclosure also provides immuno conjugates (interchangeably termed “antibody- drug conjugates” or "ADC”), comprising any of the antibodies comprising an ultralong CDR3 as described herein conjugated to a cytotoxic agent such as a chemotherapeutic agent, a drug, a growth inhibitory agent, a toxin (e.g., an enzymatically active toxin of bacterial, fungal, plant, or animal origin, or fragments thereof), or a radioactive isotope (e.g., a radio conjugate).
  • the immuno conjugate comprises any of the antibodies comprising an ultralong CDR3 as described herein conjugated to a peptide.
  • the peptide may be a non-antibody peptide, therapeutic
  • polypeptide cytokine, hormone or growth factor.
  • the peptide may be encoded by a non-antibody sequence.
  • the antibody-drug conjugates may be used for the local delivery of cytotoxic or cytostatic agents.
  • drugs to kill or inhibit tumor cells in the treatment of cancer Syrigos and Epenetos (1999) Anticancer Research 19:605-614; Niculescu-Duvaz and Springer (1997) Adv. Drg Del. Rev. 26: 151-172; U.S. Patent No. 4,975,278) allows targeted delivery of the drug moiety to tumors, and intracellular accumulation therein, where systemic administration of these unconjugated drug agents may result in unacceptable levels of toxicity to normal cells as well as the tumor cells sought to be eliminated (Baldwin et al., (1986) Lancet pp. (Mar.
  • Toxins used in antibody- toxin conjugates include bacterial toxins such as diphtheria toxin, plant toxins such as ricin, small molecule toxins such as geldanamycin (Mandler et al (2000) Jour, of the Nat. Cancer Inst.
  • cytotoxic drugs may effect their cytotoxic and cytostatic effects by mechanisms including tubulin binding, DNA binding, or topoisomerase inhibition. Some cytotoxic drugs tend to be inactive or less active when conjugated to large antibodies or protein receptor ligands.
  • ZEVALIN ® is an antibody-radioisotope conjugate composed of a murine IgGl kappa monoclonal antibody directed against the CD20 antigen found on the surface of normal and malignant B lymphocytes and m In or 90 Y radioisotope bound by a thiourea linker-chelator (Wiseman et al (2000) Eur. Jour. Nucl. Med. 27(7):766-77; Wiseman et al (2002) Blood 99(12):4336-42; Witzig et al (2002) J. Clin. Oncol.
  • ZEVALIN has activity against B-cell non-Hodgkin's Lymphoma (NHL), administration results in severe and prolonged cytopenias in most patients.
  • MYLOTARGTM (gemtuzumab ozogamicin, Wyeth Pharmaceuticals), an antibody drug conjugate composed of a hu CD33 antibody linked to calicheamicin, was approved in 2000 for the treatment of acute myeloid leukemia by injection (Drugs of the Future (2000) 25(7):686; U.S. Patent Nos. 4,970,198; 5,079,233; 5,585,089; 5,606,040; 5,693,762; 5,739,116; 5,767,285;
  • Cantuzumab mertansine an antibody drug conjugate composed of the huC242 antibody linked via the disulfide linker SPP to the maytansinoid drug moiety, DM1
  • MLN-2704 an antibody drug conjugate composed of the anti-prostate specific membrane antigen (PSMA) monoclonal antibody linked to the maytansinoid drug moiety, DM1
  • PSMA anti-prostate specific membrane antigen
  • MMAE monomethylauristatin
  • cBR96 specific to Lewis Y on carcinomas
  • cACIO specific to CD30 on hematological malignancies
  • Enzymatically active toxins and fragments thereof that can be used include diphtheria A chain, nonbinding active fragments of diphtheria toxin, exotoxin A chain (from Pseudomonas aeruginosa), ricin A chain, abrin A chain, modeccin A chain, alpha-sarcin, Aleurites fordii proteins, dianthin proteins, Phytolaca americana proteins (PAPI, PAPII, and PAP-S), momordica charantia inhibitor, curcin, crotin, sapaonaria officinalis inhibitor, gelonin, mitogellin, restrictocin, phenomycin, enomycin, and the tricothecenes.
  • radionuclides are available for the production of radio conjugated antibodies. Examples include 212 Bi, 131 I, 131 In, 90 Y, and 186 Re. Conjugates of the antibody and cytotoxic agent are made using a variety of biiunctional protein-coupling agents such as N-succinimidyl-3-(2- pyridyldithiol) propionate (SPDP), iminothiolane (IT), biiunctional derivatives of imidoesters (such as dimethyl adipimidate HC1), active esters (such as disuccinimidyl suberate), aldehydes (such as glutaraldehyde), bis-azido compounds (such as bis (p-azidobenzoyl) hexanediamine), bis- diazonium derivatives (such as bis-(p-diazoniumbenzoyl)-ethylenedi
  • biiunctional protein-coupling agents such as N-succinimidyl
  • a ricin immunotoxin may be prepared as described in Vitetta et al., Science, 238: 1098 (1987).
  • Carbon- 14-labeled l-isothiocyanatobenzyl-3-methyldiethylene triaminepentaacetic acid (MX-DTPA) is an exemplary chelating agent for conjugation of radionucleotide to the antibody. See W094/11026.
  • Conjugates of an antibody and one or more small molecule toxins such as a calicheamicin, maytansinoids, dolastatins, aurostatins, a trichothecene, and CC1065, and the derivatives of these toxins that have toxin activity, are also contemplated herein.

Landscapes

  • Chemical & Material Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Organic Chemistry (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • General Health & Medical Sciences (AREA)
  • Medicinal Chemistry (AREA)
  • Immunology (AREA)
  • Biochemistry (AREA)
  • Biophysics (AREA)
  • Genetics & Genomics (AREA)
  • Molecular Biology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Toxicology (AREA)
  • Zoology (AREA)
  • Gastroenterology & Hepatology (AREA)
  • Animal Behavior & Ethology (AREA)
  • General Chemical & Material Sciences (AREA)
  • Nuclear Medicine, Radiotherapy & Molecular Imaging (AREA)
  • Pharmacology & Pharmacy (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Public Health (AREA)
  • Veterinary Medicine (AREA)
  • Peptides Or Proteins (AREA)
  • Virology (AREA)
  • Preparation Of Compounds By Using Micro-Organisms (AREA)
  • Micro-Organisms Or Cultivation Processes Thereof (AREA)
  • Medicines Containing Antibodies Or Antigens For Use As Internal Diagnostic Agents (AREA)

Abstract

Disclosed herein are immunoglobulin constructs comprising at least one immunoglobulin domain or fragment thereof; and a therapeutic polypeptide or derivative or variant thereof attached to or inserted into said immunoglobulin domain. Also provided are immunoglobulin constructs comprising a mammalian immunoglobulin heavy chain comprising at least a portion of a knob domain in the complementarity- determining region 3 (CDR3H) or fragment thereof; and a therapeutic polypeptide attached to or inserted into said knob domain of the CDR3H. Also provided are immunoglobulin constructs comprising a mammalian immunoglobulin heavy chain comprising at least a portion of a stalk domain in the complementarity-determining region 3 (CDR3H) or fragment thereof; and a therapeutic polypeptide attached to or inserted into said stalk domain of the CDR3H. Also described herein are methods and compositions comprising the immunoglobulin constructs described herein for treatment and prevention of a disease or condition in a subject.

Description

ULTRALONG COMPLEMENTARITY DETERMINING REGIONS
AND USES THEREOF
CROSS-REFERENCE TO RELATED APPLICATIONS
[0001] This application claims the benefit of U.S. Provisional Application No. 61/584,680 filed January 9, 2012, and U.S. Provisional Application No. 61/671,629, filed July 13, 2012, both of which are incorporated by reference herein in their entirety.
FIELD
[0002] Described herein are immunoglobulin constructs comprising at least a portion of an ultralong CDR3, methods of making such constructs, pharmaceutical compositions and
medicaments comprising such constructs, and methods of using such constructs and compositions to prevent, inhibit, and/or treat a disease or condition in a subject.
BACKGROUND
[0003] Antibodies are natural proteins that the vertebrate immune system forms in response to foreign substances (antigens), primarily for defense against infection. For over a century, antibodies have been induced in animals under artificial conditions and harvested for use in therapy or diagnosis of disease conditions, or for biological research. Each individual antibody producing cell produces a single type of antibody with a chemically defined composition, however, antibodies obtained directly from animal serum in response to antigen inoculation actually comprise an ensemble of non- identical molecules (e.g., polyclonal antibodies) made from an ensemble of individual antibody producing cells.
[0004] Some bovine antibodies have unusually long VH CDR3 sequences compared to other vertebrates. For example, about 10% of IgM contains "ultralong" CDR3 sequences, which can be up to 61 amino acids long. These unusual CDR3s often have multiple cysteines. Functional VH genes form through a process called V(D)J recombination, wherein the D-region encodes a significant proportion of CDR3. A unique D-region encoding an ultralong sequence has been identified in cattle. Ultralong CDR3s are partially encoded in the cattle genome, and provide a unique characteristic of their antibody repertoire in comparison to humans. Kaushik et al. (U.S. Patent Nos. 6,740,747 and 7,196,185) disclose several bovine germline D-gene sequences unique to cattle stated to be useful as probes and a bovine VDJ cassette stated to be useful as a vaccine vector. SUMMARY
[0005] The present disclosure provides antibodies that comprise an utralong CDR3 including, libraries that comprise an ultralong CDR3, and uses thereof.
[0006] The present disclosure also provides a library of antibodies or binding fragments thereof, wherein the antibodies or binding fragments thereof comprise an ultralong CDR3.
[0007] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 is 35 amino acids in length or longer, 40 amino acids in length or longer, 45 amino acids in length or longer, 50 amino acids in length or longer, 55 amino acids in length or longer, or 60 amino acids in length or longer.
[0008] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 is 35 amino acids in length or longer.
[0009] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 comprises 3 or more cysteine residues, 4 or more cysteine residues, 5 or more cysteine residues, 6 or more cysteine residues, 7 or more cysteine residues, 8 or more cysteine residues, 9 or more cysteine residues, 10 or more cysteine residues, 11 or more cysteine residues, or 12 or more cysteine residues.
[0010] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 comprises 3 or more cysteine residues.
[0011] In some embodiments of each or any of the above or below mentioned embodiments, the antibodies or binding fragments thereof comprise a cysteine motif.
[0012] In some embodiments of each or any of the above or below mentioned embodiments, the cysteine motif is selected from the group consisting of SEQ ID NOS: 45-156. In some
embodiments of each or any of the above or below mentioned embodiments, the cysteine motif is selected from the group consisting of SEQ ID NOS: 45-99. In some embodiments of each or any of the above or below mentioned embodiments, the cysteine motif is selected from the group consisting of SEQ ID NOS: 45-135. In some embodiments of each or any of the above or below mentioned embodiments, the cysteine motif is selected from the group consisting of SEQ ID NOS: 100-135. In some embodiments of each or any of the above or below mentioned embodiments, the cysteine motif is selected from the group consisting of SEQ ID NOS: 136-156.
[0013] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 comprises a non-human DH or a derivative thereof.
[0014] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 comprises a JH sequence or a derivative thereof. [0015] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 comprises: a non-human VH sequence or a derivative thereof, a non-human DH sequence or a derivative thereof; and/or a JH sequence or derivative thereof.
[0016] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 comprises an additional amino acid sequence comprising two to six amino acid residues or more positioned between the VH sequence and the DH sequence.
[0017] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 comprises a non-bovine sequence.
[0018] In some embodiments of each or any of the above or below mentioned embodiments, the non-bovine sequence is a non-antibody or a human sequence.
[0019] In some embodiments of each or any of the above or below mentioned embodiments, the non-bovine sequence replaces at least a portion of the ultralong CDR3.
[0020] In some embodiments of each or any of the above or below mentioned embodiments, the non-bovine sequence is a hormone, lymphokine, interleukin, chemokine, cytokine, toxin, or combination thereof.
[0021] In some embodiments of each or any of the above or below mentioned embodiments, the non-bovine sequence is a cytokine.
[0022] In some embodiments of each or any of the above or below mentioned embodiments, the cytokine is granulocyte colony- stimulating factor (G-CSF).
[0023] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 comprises an additional sequence that is a linker.
[0024] In some embodiments of each or any of the above or below mentioned embodiments, the linker is linked to a C-terminus, a N-terminus, or both C-terminus and N-terminus of the non- antibody sequence.
[0025] In some embodiments of each or any of the above or below mentioned embodiments, the linker is (GGGGS)n (SEQ ID NO: 339), where n is an integer between 0 and 5. Alternatively, or additionally, the linker is (GSG)n (SEQ ID NO: 342), GGGSGGGGS (SEQ ID NO: 337) or GGGGSGGGS (SEQ ID NO: 338)
[0026] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 comprises a X1X2X3X4X5Xn motif, wherein Xi is threonine (T), glycine (G), alanine (A), serine (S), or valine (V), wherein X2 is serine (S), threonine (T), proline (P), isoleucine (I), alanine (A), valine (V), or asparagine (N), wherein X3 is valine (V), alanine (A), threonine (T), or aspartic acid (D), wherein X4 is histidine (H), threonine (T), arginine (R), tyrosine (Y), phenylalanine (F), or leucine (L), wherein X5 is glutamine (Q), and wherein n is 27 - 54. [0027] In some embodiments of each or any of the above or below mentioned embodiments, the X!X2X3X4X5 motif is TTVHQ (SEQ ID NO: 159) or TSVHQ (SEQ ID NO: 160).
[0028] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 further comprises a (XaXb)z motif, wherein Xa is any amino acid residue, Xb is an aromatic amino acid selected from the group consisting of: tyrosine (Y), phenylalanine (F), tryptophan (W), and histidine (H), and wherein z is 1 - 4.
[0029] In some embodiments of each or any of the above or below mentioned embodiments, the (XaXb)z motif is YXYXYX.
[0030] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 comprises a X1X2X3X4X5Xn(XaXb)z motif, wherein X1 is threonine (T), glycine (G), alanine (A), serine (S), or valine (V), wherein X2 is serine (S), threonine (T), proline (P), isoleucine (I), alanine (A), valine (V), or asparagine (N), wherein X3 is valine (V), alanine (A), threonine (T), or aspartic acid (D), wherein X4 is histidine (H), threonine (T), arginine (R), tyrosine (Y), phenylalanine (F), or leucine (L), and wherein X5 is glutamine (Q), wherein Xa is any amino acid residue, Xb is an aromatic amino acid selected from the group consisting of: tyrosine (Y), phenylalanine (F), tryptophan (W), and histidine (H), wherein n is 27 - 54, and wherein z is 1 - 4.
[0031] In some embodiments of each or any of the above or below mentioned embodiments, the X!X2X3X4X5 motif is TTVHQ (SEQ ID NO: 159) or TSVHQ (SEQ ID NO: 160), and wherein the (XaXb)z motif is YXYXYX.
[0032] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 comprises TSVHQETKKYQ (SEQ ID NO.157).
[0033] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 comprises VHQETKKYQ (SEQ ID NO: 158).
[0034] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 comprises CTTVHQXn (SEQ ID NO. 223).
[0035] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 comprises CTSVHQXn (SEQ ID NO. 223), wherein n is 1-8.
[0036] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 comprises TTVHQ (SEQ ID NO. 159).
[0037] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 comprises TSVHQ (SEQ ID NO. 160).
[0038] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 comprises VHQ. [0039] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 comprises K Q.
[0040] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 comprises VYQ.
[0041] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 comprises CX1 X2 X3 X4Q (SEQ ID NO: 228), wherein X1 is T, S, A, or G, wherein X2 is T, S, A, P, or I, wherein X3 is V or K, and wherein X4 is H, K, or Y.
[0042] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 comprises CX1 X2VHQ (SEQ ID NO: 230), wherein X1 is T, S, A, or G, and wherein X2 is T, S, A, P, or I.
[0043] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 comprises CX1 X2VX3Q (SEQ ID NO: 232), wherein X1 is T, S, A, or G, wherein X2 is T, S, A, P, or I, and wherein X3 is H, Y, or K.
[0044] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 comprises CX1X2K Q (SEQ ID NO: 234), wherein X1 is T, S, A, or G, and wherein X2 is T, S, A, P, or I.
[0045] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 comprises YTYNYEW (SEQ ID NO: 235).
[0046] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 comprises YX!YX2 (SEQ ID NO: 296), wherein X2 is E or D.
[0047] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 comprises YX!YX2 Y (SEQ ID NO: 297).
[0048] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 comprises YEX, wherein X is H, W, N, F, I or Y.
[0049] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 comprises YDX, wherein X is H, W, N, F, I or Y.
[0050] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 comprises XYE, wherein X is T, S, N or I.
[0051] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 comprises XYD, wherein X is T, S, N or I.
[0052] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 comprises Y(E/D)X1XnW (SEQ ID NOS: 304-305), wherein X1 is H,W, N, F, I or Y, and wherein n is 1-4. [0053] In some embodiments of each or any of the above or below mentioned embodiments, the antibodies or binding fragments thereof are chimeric, human engineered, or humanized.
[0054] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 is a ruminant CDR3.
[0055] In some embodiments of each or any of the above or below mentioned embodiments, the ruminant is a cow.
[0056] The present disclosure also provides a library of polynucleotides encoding for antibodies or binding fragments thereof, wherein the encoded antibodies or binding fragments thereof comprise an ultralong CDR3.
[0057] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 is 35 amino acids in length or longer, 40 amino acids in length or longer, 45 amino acids in length or longer, 50 amino acids in length or longer, 55 amino acids in length or longer, or 60 amino acids in length or longer.
[0058] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 is 35 amino acids in length or longer.
[0059] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 comprises 3 or more cysteine residues, 4 or more cysteine residues, 5 or more cysteine residues, 6 or more cysteine residues, 7 or more cysteine residues, 8 or more cysteine residues, 9 or more cysteine residues, 10 or more cysteine residues, 11 or more cysteine residues, or 12 or more cysteine residues.
[0060] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 comprises 3 or more cysteine residues.
[0061] In some embodiments of each or any of the above or below mentioned embodiments, the antibodies or binding fragments thereof comprise a cysteine motif.
[0062] In some embodiments of each or any of the above or below mentioned embodiments, the cysteine motif is selected from the group consisting of SEQ ID NOS: 45-156. In some
embodiments of each or any of the above or below mentioned embodiments, the cysteine motif is selected from the group consisting of SEQ ID NOS: 45-99. In some embodiments of each or any of the above or below mentioned embodiments, the cysteine motif is selected from the group consisting of SEQ ID NOS: 45-135. In some embodiments of each or any of the above or below mentioned embodiments, the cysteine motif is selected from the group consisting of SEQ ID NOS: 100-135. In some embodiments of each or any of the above or below mentioned embodiments, the cysteine motif is selected from the group consisting of SEQ ID NOS: 136-156. [0063] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 comprises a non-human DH or a derivative thereof.
[0064] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 comprises a JH sequence or a derivative thereof.
[0065] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 comprises: a non-human VH sequence or a derivative thereof, a non-human DH sequence or a derivative thereof; and/or a JH sequence or derivative thereof.
[0066] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 comprises an additional amino acid sequence comprising two to six amino acid residues or more positioned between the VH sequence and the DH sequence.
[0067] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 comprises a non-bovine sequence.
[0068] In some embodiments of each or any of the above or below mentioned embodiments, the non-bovine sequence is a non-antibody or a human sequence.
[0069] In some embodiments of each or any of the above or below mentioned embodiments, the non-bovine sequence replaces at least a portion of the ultralong CDR3.
[0070] In some embodiments of each or any of the above or below mentioned embodiments, the non-antibody sequence is a hormone, lymphokine, interleukin, chemokine, cytokine, toxin, or combination thereof.
[0071] In some embodiments of each or any of the above or below mentioned embodiments, the non-bovine sequence is a cytokine.
[0072] In some embodiments of each or any of the above or below mentioned embodiments, the cytokine is granulocyte colony- stimulating factor (G-CSF).
[0073] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 comprises an additional sequence that is a linker.
[0074] In some embodiments of each or any of the above or below mentioned embodiments, the linker is linked to a C-terminus, a N-terminus, or both C-terminus and N-terminus of the non- antibody sequence.
[0075] In some embodiments of each or any of the above or below mentioned embodiments, the linker is (GGGGS)n (SEQ ID NO: 339), where n is an integer between 0 and 5. Alternatively, the linker is (GSG)n (SEQ ID NO: 342), GGGSGGGGS (SEQ ID NO: 337) or GGGGSGGGS (SEQ ID NO: 338).
[0076] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 comprises a X1-X2-X3-X4-X5 motif, wherein X1 is threonine (T), glycine (G), alanine (A), serine (S), or valine (V), wherein X2 is serine (S), threonine (T), proline (P), isoleucine (I), alanine (A), valine (V), or asparagine (N), wherein X3 is valine (V), alanine (A), threonine (T), or aspartic acid (D), wherein X4 is histidine (H), threonine (T), arginine (R), tyrosine (Y), phenylalanine (F), or leucine (L), and wherein X5 is glutamine (Q).
[0077] In some embodiments of each or any of the above or below mentioned embodiments, the X!X2X3X4X5 motif is TTVHQ (SEQ ID NO: 159) or TSVHQ (SEQ ID NO: 160).
[0078] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 further comprises a (XaXb)z motif, wherein Xa is an aromatic amino acid selected from the group consisting of: tyrosine (Y), phenylalanine (F), tryptophan (W), and histidine (H), wherein Xb is any amino acid residue, and wherein z is 1 -4.
[0079] In some embodiments of each or any of the above or below mentioned embodiments, the (XaXb)z motif is YXYXYX.
[0080] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 comprises a X1X2X3X4X5Xn(X6X7)z motif, wherein X1 is threonine (T), glycine (G), alanine (A), serine (S), or valine (V), wherein X2 is serine (S), threonine (T), proline (P), isoleucine (I), alanine (A), valine (V), or asparagine (N), wherein X3 is valine (V), alanine (A), threonine (T), or aspartic acid (D), wherein X4 is histidine (H), threonine (T), arginine (R), tyrosine (Y), phenylalanine (F), or leucine (L), and wherein X5 is glutamine (Q), wherein Xa is any amino acid residue, Xb is an aromatic amino acid selected from the group consisting of: tyrosine (Y), phenylalanine (F), tryptophan (W), and histidine (H), wherein n is 27 - 54, and wherein z is 1 - 4.
[0081] In some embodiments of each or any of the above or below mentioned embodiments, the X!X2X3X4X5 motif is TTVHQ (SEQ ID NO: 159) or TSVHQ (SEQ ID NO: 160), and wherein the (Xa-Xb)z motif is YXYXYX.
[0082] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 comprises TSVHQETKKYQ (SEQ ID NO. 157).
[0083] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 comprises VHQETKKYQ (SEQ ID NO: 158).
[0084] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 comprises CTTVHQXn (SEQ ID NO. 223).
[0085] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 comprises CTSVHQXn (SEQ ID NO. 224), wherein n is 1-8.
[0086] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 comprises TTVHQ (SEQ ID NO. 159). [0087] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 comprises TSVHQ (SEQ ID NO. 160).
[0088] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 comprises VHQ.
[0089] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 comprises K Q.
[0090] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 comprises VYQ.
[0091] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 comprises CX1 X2 X3 X4Q, wherein X1 is T, S, A, or G, wherein X2 is T, S, A, P, or I, wherein X3 is V or K, and wherein X4 is H, K, or Y.
[0092] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 comprises CX1 X2VHQ, wherein X1 is T, S, A, or G, and wherein X2 is T, S, A, P, or I.
[0093] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 comprises CX1 X2VX3Q, wherein X1 is T, S, A, or G, wherein X2 is T, S, A, P, or I, and wherein X3 is H, Y, or K.
[0094] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 comprises CX1 X2K Q, wherein X1 is T, S, A, or G, and wherein X2 is T, S, A, P, or I.
[0095] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 comprises YTYNYEW (SEQ ID NO: 235).
[0096] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 comprises YX1 YX2, wherein X2 is E or D.
[0097] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 comprises YX!YX2 Y.
[0098] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 comprises YEX, wherein X is H, W, N, F, I or Y.
[0099] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 comprises YDX, wherein X is H, W, N, F, I or Y.
[00100] In some embodiments of each or any of the above or below mentioned
embodiments, the ultralong CDR3 comprises XYE, wherein X is T, S, N or I.
[00101] In some embodiments of each or any of the above or below mentioned
embodiments, the ultralong CDR3 comprises XYD, wherein X is T, S, N or I. [00102] In some embodiments of each or any of the above or below mentioned embodiments, the ultralong CDR3 comprises Y(E/D)X1XnW, wherein X1 is H,W, N, F, I or Y, and wherein n is 1-4.
[00103] In some embodiments of each or any of the above or below mentioned
embodiments, the antibodies or binding fragments thereof are chimeric, human engineered, or humanized.
[00104] In some embodiments of each or any of the above or below mentioned
embodiments, the ultralong CDR3 is a ruminant CDR3.
[00105] In some embodiments of each or any of the above or below mentioned
embodiments, the ruminant is a cow.
[00106] In some embodiments of each or any of the above or below mentioned
embodiments, the antibodies or binding fragments thereof are present in a spatially addressed format.
[00107] In some embodiments of each or any of the above or below mentioned
embodiments, the polynucleotides coding for the antibodies or binding fragments thereof are present in a spatially addressed format.
[00108] The present disclosure also provides a library of vectors comprising any of the library of polynucleotides disclosed herein.
[00109] The present disclosure also provides a library of host cells comprising the any library of vectors disclosed herein.
[00110] In some embodiments of each or any of the above or below mentioned
embodiments, the cell is a bacteria, virus, or bacteriophage.
[00111] In some embodiments of each or any of the above or below mentioned
embodiments, the antibodies or binding fragments thereof are displayed on the cell surface.
[00112] In some embodiments of each or any of the above or below mentioned
embodiments, the antibodies or binding fragments thereof are secreted from the cell.
[00113] In some embodiments of each or any of the above or below mentioned
embodiments, the antibodies or binding fragments thereof are present in a spatially addressed format.
[00114] The present disclosure also provides an antibody or binding fragment thereof comprising an ultralong CDR3, wherein the ultralong CDR3 comprises a non-bovine sequence.
[00115] In some embodiments of each or any of the above or below mentioned
embodiments, the ultralong CDR3 is 35 amino acids in length or longer, 40 amino acids in length or longer, 45 amino acids in length or longer, 50 amino acids in length or longer, 55 amino acids in length or longer, or 60 amino acids in length or longer.
[00116] In some embodiments of each or any of the above or below mentioned
embodiments, the ultralong CDR3 is 35 amino acids in length or longer.
[00117] In some embodiments of each or any of the above or below mentioned
embodiments, the ultralong CDR3 comprises 3 or more cysteine residues, 4 or more cysteine residues, 5 or more cysteine residues, 6 or more cysteine residues, 7 or more cysteine residues, 8 or more cysteine residues, 9 or more cysteine residues, 10 or more cysteine residues, 11 or more cysteine residues, or 12 or more cysteine residues.
[00118] In some embodiments of each or any of the above or below mentioned
embodiments, the ultralong CDR3 comprises 3 or more cysteine residues.
[00119] In some embodiments of each or any of the above or below mentioned
embodiments, the antibodies or binding fragments thereof comprise a cysteine motif.
[00120] In some embodiments of each or any of the above or below mentioned
embodiments, the cysteine motif is selected from the group consisting of SEQ ID NOS: 45-156. In some embodiments of each or any of the above or below mentioned embodiments, the cysteine motif is selected from the group consisting of SEQ ID NOS: 45-99. In some embodiments of each or any of the above or below mentioned embodiments, the cysteine motif is selected from the group consisting of SEQ ID NOS: 45-135. In some embodiments of each or any of the above or below mentioned embodiments, the cysteine motif is selected from the group consisting of SEQ ID NOS: 100-135. In some embodiments of each or any of the above or below mentioned embodiments, the cysteine motif is selected from the group consisting of SEQ ID NOS: 136-156.
[00121] In some embodiments of each or any of the above or below mentioned
embodiments, the non-bovine sequence is a non-antibody sequence or a human sequence.
[00122] In some embodiments of each or any of the above or below mentioned
embodiments, the ultralong CDR3 comprises a non-human DH or a derivative thereof.
[00123] In some embodiments of each or any of the above or below mentioned
embodiments, the ultralong CDR3 comprises a JH sequence or a derivative thereof.
[00124] In some embodiments of each or any of the above or below mentioned
embodiments, the ultralong CDR3 comprises: a non-human VH sequence or a derivative thereof, a non-human DH sequence or a derivative thereof; and/or a JH sequence or derivative thereof.
[00125] In some embodiments of each or any of the above or below mentioned
embodiments, the ultralong CDR3 comprises an additional amino acid sequence comprising two to six amino acid residues or more positioned between the VH sequence and the DH sequence. [00126] In some embodiments of each or any of the above or below mentioned embodiments, the non-bovine sequence replaces at least a portion of the ultralong CDR3.
[00127] In some embodiments of each or any of the above or below mentioned
embodiments, the non-bovine sequence is a hormone, lymphokine, interleukin, chemokine, cytokine, toxin, or combination thereof.
[00128] In some embodiments of each or any of the above or below mentioned
embodiments, the non-bovine sequence is a cytokine.
[00129] In some embodiments of each or any of the above or below mentioned
embodiments, the cytokine is granulocyte colony- stimulating factor (G-CSF).
[00130] In some embodiments of each or any of the above or below mentioned
embodiments, the antibodies or binding fragments thereof are chimeric, human engineered, or humanized.
[00131] In some embodiments of each or any of the above or below mentioned
embodiments, the ultralong CDR3 is a ruminant CDR3.
[00132] In some embodiments of each or any of the above or below mentioned
embodiments, the ruminant is a cow.
[00133] The present disclosure also provides a polynucleotide encoding for any antibody or binding fragment thereof disclosed herein.
[00134] The present disclosure also provides a vector comprising any polynucleotide encoding for the antibody or binding fragment thereof disclosed herein.
[00135] The present disclosure also provides a host cell comprising any vector disclosed herein.
[00136] In some embodiments of each or any of the above or below mentioned
embodiments, the cell is a bacteria, virus, or bacteriophage.
[00137] In some embodiments of each or any of the above or below mentioned
embodiments, the antibody or binding fragment thereof is displayed on the surface of the cell.
[00138] In some embodiments of each or any of the above or below mentioned
embodiments, the antibody or binding fragment thereof is secreted from the cell.
[00139] The present disclosure also provides a method of producing an antibody or binding fragment thereof comprising an ultralong CDR3 or fragment thereof comprising culturing a host cell comprising a polynucleotide encoding any of the antibodies disclosed herein under conditions wherein the polynucleotide sequence is expressed and the antibody or binding fragment thereof comprising an ultralong CDR3 or fragment thereof is produced. [00140] In some embodiments of each or any of the above or below mentioned embodiments, the methods further comprise recovering the antibody or binding fragment thereof comprising an ultralong CDR3 or fragment thereof from the host cell culture.
[00141] The present disclosure also provides a pharmaceutical composition comprising any antibody or binding fragment thereof disclosed herein.
[00142] The present disclosure also provides a method of treating a mammal in need thereof comprising administering to the mammal an amount of any antibody disclosed herein.
[00143] In some embodiments of each or any of the above or below mentioned
embodiments, the mammal is a human.
[00144] In some embodiments is a recombinant antibody or fragment thereof, wherein at least a portion of the recombinant antibody or fragment thereof is based on or derived from at least a portion of an ultralong CDR3.
[00145] In some embodiments is an antibody or fragment thereof comprising at least a portion of an ultralong CDR3 sequence and at least a portion of a non-bovine sequence.
[00146] In some embodiments is an antibody or fragment thereof comprising (a) a first antibody sequence, wherein at least a portion of the first antibody sequence is derived from at least a portion of an ultralong CDR3; (b) a non-antibody sequence; and (c) optionally, a second antibody sequence, wherein at least a portion of the second antibody sequence is derived from at least a portion of an ultralong CDR3.
[00147] The antibodies disclosed herein may be a chimeric, human engineered, or humanized antibody. The antibodies disclosed herein may be a bovine engineered, bovinized, or fully bovine antibody. The antibodies disclosed herein may comprise a Fab, a scFv, dsFv, diabody, (dsFv)2, minibody, flex minibody or bi-specific fragment. The antibodies disclosed herein may be an isolated antibody.
[00148] The antibodies disclosed herein may further comprise a non-antibody sequence. The non-antibody sequence may be derived from a mammal. The mammal may be a bovine, human, or non-bovine mammal. The antibodies disclosed herein may comprise a non-antibody sequence derived from a non-bovine animal. The non-bovine animal may be a scorpion. The non-bovine animal may be a lizard. The lizard may be a gila monster. The non-antibody sequence may be a derived from a growth factor. The growth factor may be a GCSF, GMCSF or FGF21. The GCSF may be a bovine GCSF. Alternatively, the GCSF may be a human GCSF. The GMCSF and/or the FGF21 may be from a human. The non-antibody sequence may be a derived from a cytokine. The cytokine may be a beta-interferon. The non-antibody sequence may be a derived from a hormone. The hormone may be an exendin-4, GLP-1, somatostatin, or erythropoietin. The GLP-1 and/or erythropoietin may be from a human. The non-antibody sequence may be a derived from a toxin. The toxin may be a Mokal, VM-24, ziconotide, chlorotoxin, or protoxin2 (ProTxII). The non- antibody sequence may be IL8, ziconotide, somatostatin, chlorotoxin, SDFl(alpha), or IL21. The non-antibody sequence may comprise an amino acid sequence based on or derived from any of SEQ ID NOS: 317-332. The non-antibody sequence may replace at least a portion of the ultralong CDR3. The non-antibody sequence may be inserted into the sequence of the ultralong CDR3. The non-antibody sequence may be conjugated to at least a portion of the antibody (e.g., ultralong CDR3, variable region, heavy chain, light chain). The non-antibody sequence may be attached to the ultralong CDR3, linker, cleavage site, non-bovine sequence, non-ultralong CDR3 antibody sequence, or combination thereof. The non-antibody sequence may be adjacent to the ultralong CDR3, linker, cleavage site, non-bovine sequence, non-ultralong CDR3 antibody sequence, or combination thereof.
[00149] The antibodies disclosed herein may comprise an ultralong CDR3 may be based on or derived from a cow ultralong CDR3. At least a portion of the antibodies disclosed herein may be from a mammal. At least a portion of the first antibody sequence and/or at least a portion of the second antibody sequence of the antibodies disclosed herein may be from a mammal. The mammal may be a bovine, human or non-bovine mammal.
[00150] The antibodies disclosed herein may comprise 3 or more amino acids in length. The antibodies disclosed herein may comprise a sequence that may be based on or derived from an ultralong CDR3 disclosed herein. The antibodies disclosed herein may comprise 1 or more amino acid residues based on or derived from a stalk domain of the ultralong CDR3. The antibodies disclosed herein may comprise 1 or more amino acid residues based on or derived from a knob domain of the ultralong CDR3.
[00151] At least a portion of the antibodies disclosed herein may be based on or derived from at least a portion of an ultralong CDR3 disclosed herein. The portion of the antibody based on or derived from at least a portion of the ultralong CDR3 may be 20 or fewer amino acids in length. The portion of the antibody based on or derived from at least a portion of the ultralong CDR3 may be 3 or more amino acids in length
[00152] The antibodies disclosed herein may comprise 1 or more conserved motifs derived from a stalk domain of the ultralong CDR3. The 1 or more conserved motifs derived from the stalk domain of the ultralong CDR3 may comprise any of the stalk domain conserved motifs disclosed herein. [00153] The portion of the ultralong CDR3s disclosed herein may comprise at least a portion of a stalk domain of the ultralong CDR3, at least a portion of the knob domain of the ultralong CDR3, or a combination thereof.
[00154] The antibodies disclosed herein may comprise a sequence selected from any one of
SEQ ID NOS: 157-307 and SEQ ID NOS: 333-336. The antibodies disclosed herein may comprise a sequence that may be 50% or more homologous to a sequence selected from any one of SEQ ID NOS: 157-224 and 235-295.
[00155] A portion of any of the antibodies disclosed herein may be based on or derived from at least a portion of a single ultralong CDR3 sequence. A portion of the antibodies disclosed herein may be based on or derived from at least a portion of two or more different ultralong CDR3 sequences.
[00156] In any of the embodiments disclosed herein, the portion of the ultralong CDR3 is based on or derived from a BLV1H12 ultralong CDR3 sequence. The portion of the ultralong CDR3 may be based on or derived from a sequence that may be 50% or more homologous to a BLV1H12 ultralong CDR3 sequence. The portion of the ultralong CDR3 may be based on or derived from a BLV5B8, BLVCV1, BLV5D3, BLV8C11, BF1H1, or F18 ultralong CDR3 sequence. The portion of the ultralong CDR3 may be based on or derived from a sequence that may be 50% or more homologous to a BLV5B8, BLVCV1, BLV5D3, BLV8C11, BF1H1, or F18 ultralong CDR3 sequence.
[00157] The antibodies disclosed herein may comprise a first and/or second antibody sequence that comprises 3 or more amino acids in length. A portion of the first antibody sequence derived from at least a portion of the ultralong CDR3 and/or the portion of the second antibody sequence derived from at least a portion of the ultralong CDR3 may be 20 or fewer amino acids in length. A portion of the first antibody sequence derived from at least a portion of the ultralong CDR3 and/or the portion of the second antibody sequence derived from at least a portion of the ultralong CDR3 may be 3 or more amino acids in length.
[00158] In any of the embodiments disclosed herein, the first and/or second antibody sequences comprise one or more amino acid residues based on or derived from a stalk domain of the ultralong CDR3. The first and/or second antibody sequences may comprise one or more amino acid residues based on or derived from a knob domain of the ultralong CDR3. The one or more amino acid residues derived from the knob domain of the ultralong CDR3 may be a serine and/or cysteine residue. The first and/or second antibody sequences may comprise one or more conserved motifs derived from a stalk domain of the ultralong CDR3. The one or more conserved motifs derived from the stalk domain of the ultralong CDR3 may comprise a sequence selected from any one of SEQ ID NOS: 157-307 and SEQ ID NOS: 333-336.
[00159] In any of the embodiments disclosed herein, the portion of the first antibody sequence derived from at least a portion of the ultralong CDR3 and/or the portion of the second antibody sequence derived from at least a portion of the ultralong CDR3 comprises a sequence selected from any one of SEQ ID NOS: 157-307 and SEQ ID NOS: 333-336. The portion of the first antibody sequence derived from at least a portion of the ultralong CDR3 and/or the portion of the second antibody sequence derived from at least a portion of the ultralong CDR3 may comprise a sequence that may be 50% or more homologous to a sequence selected from any one of SEQ ID NOS: 157-224 and 235-295. The portion of the first antibody sequence derived from at least a portion of the ultralong CDR3 may comprise a sequence selected from any one of SEQ ID NOS: 157-234. The portion of the first antibody sequence derived from at least a portion of the ultralong CDR3 may comprise a sequence that may be 50% or more homologous to a sequence selected from any one of SEQ ID NOS: 157-224.
[00160] In any of the embodiments disclosed herein, the portion of the second antibody sequence derived from at least a portion of the ultralong CDR3 comprises a sequence selected from any one of SEQ ID NOS: 235-307 and SEQ ID NOS: 333-336. The portion of the second antibody sequence derived from at least a portion of the ultralong CDR3 may comprise a sequence that may be 50%) or more homologous to a sequence selected from any one of SEQ ID NOS: 235-295. The portion of the first antibody sequence derived from at least a portion of the ultralong CDR3 and the portion of the second antibody sequence derived from at least a portion of the ultralong CDR3 may be derived from the same ultralong CDR3 sequence.
[00161] In any of the embodiments disclosed herein, the portion of the first antibody sequence derived from at least a portion of the ultralong CDR3 and the portion of the second antibody sequence derived from at least a portion of the ultralong CDR3 is derived from two or more different ultralong CDR3 sequences. The portions of the ultralong CDR3 of the first and/or second antibody sequences may be based on or derived from a BLV1H12 ultralong CDR3 sequence. The portions of the ultralong CDR3 of the first and/or second antibody sequences may be based on or derived from a sequence that may be 50% or more homologous to a BLV1H12 ultralong CDR3 sequence. The portions of the ultralong CDR3 of the first and/or second antibody sequences may be based on or derived from a BLV5B8, BLVCV1, BLV5D3, BLV8C11, BF1H1, or F18 ultralong CDR3 sequence. The portions of the ultralong CDR3 of the first and/or second antibody sequences may be based on or derived from a sequence that may be 50%> or more homologous to a BLV5B8, BLVCV1, BLV5D3, BLV8C11, BF1H1, or F18 ultralong CDR3 sequence.
[00162] In any of the embodiments disclosed herein, the ultralong CDR3 is based on or derived from an ultralong CDR3 that may be 35 or more amino acids in length. The ultralong CDR3 may be based on or derived from an ultralong CDR3 comprising 3 or more cysteine residues.
[00163] In any of the embodiments disclosed herein, the ultralong CDR3 is based on or derived from an ultralong CDR3 may comprise one or more cysteine motifs. The one or more cysteine motifs may be selected from the group consisting of SEQ ID NOS: 45-156. In some embodiments of each or any of the above or below mentioned embodiments, the cysteine motif is selected from the group consisting of SEQ ID NOS: 45-99. In some embodiments of each or any of the above or below mentioned embodiments, the cysteine motif is selected from the group consisting of SEQ ID NOS: 45-135. In some embodiments of each or any of the above or below mentioned embodiments, the cysteine motif is selected from the group consisting of SEQ ID NOS: 100-135. In some embodiments of each or any of the above or below mentioned embodiments, the cysteine motif is selected from the group consisting of SEQ ID NOS: 136-156.
[00164] The antibodies disclosed herein may be based on or derived from an ultralong CDR3 that may be 35 or more amino acids in length. The antibodies disclosed herein may be based on or derived from an ultralong CDR3 comprising 3 or more cysteine residues. The antibodies disclosed herein may be based on or derived from an ultralong CDR3 may comprise 1 or more cysteine motifs.
[00165] The antibodies disclosed herein may comprise an ultralong CDR3 that is 35 or more amino acids in length. The antibodies disclosed herein may comprise an ultralong CDR3 comprising 3 or more cysteine residues. The antibodies disclosed herein may comprise an ultralong CDR3 comprising one or more cysteine motifs.
[00166] In any of the embodiments disclosed herein, the ultralong CDR3 may be a heavy chain CDR3. The ultralong CDR3 may comprise an amino acid sequence derived from or based on a non-human DH sequence. The ultralong CDR3 may comprise an amino acid sequence derived from or based on a JH sequence. The ultralong CDR3 may comprise an amino acid sequence derived from or based on a non-human VH sequence; an amino acid sequence derived from or based on a non-human DH sequence; and/or an amino acid sequence derived from or based on a JH sequence. The ultralong CDR3 may comprise an additional amino acid sequence comprising at least about two amino acid residues positioned between the VH derived amino acid sequence and the DH derived amino acid sequence. [00167] Any of the antibodies disclosed herein may comprise a sequence based on or derived from a sequence selected from SEQ ID NOS: 24-44, the antibody or binding fragment thereof encoded by a DNA sequence based on or derived from the DNA of SEQ ID NOS: 2-22. Any of the antibodies disclosed herein may comprise a sequence based on or derived from a sequence selected from SEQ ID NO: 23, the antibody or binding fragment thereof encoded by a DNA sequence based on or derived from the DNA of SEQ ID NO: 1.
[00168] Any of the ultralong CDR3s disclosed herein may comprise a sequence based on or derived from a sequence selected from SEQ ID NOS: 24-44. Any of the antibodies disclosed herein may comprise a sequence based on or derived from a sequence selected from SEQ ID NO: 23. Any of the ultralong CDR3s disclosed herein may be encoded by a DNA sequence that may be derived from or based on SEQ ID NOS: 2-22. Any of the antibodies disclosed herein may comprise a portion encoded by a DNA sequence that may be derived from or based on SEQ ID NO: 1.
[00169] Any of the antibodies disclosed herein may comprise one or more linkers. Any of the antibodies disclosed herein may comprise a first linker sequence. Any of the antibodies disclosed herein may comprise a second linker sequence. The first and second linker sequences may comprise the same sequence. The first and second linker sequences may comprise different sequences. The first and/or second linker sequences may be the same length. The first and/or second linker sequences may be different lengths. The first and/or second linker sequences may be 3 or more amino acids in length.
[00170] The first and/or second linker sequence may attach the non-antibody sequence to the portion based on or derived from the portion of the ultralong CDR3. The first and/or second linker sequences may attach the non-antibody sequence to the first antibody sequence. The first and/or second linker sequences may attach the non-antibody sequence to the second antibody sequence. The first and/or second linker sequences may be adjacent to a non-antibody sequence, a portion of an ultralong CDR3 sequence, a cleavage site sequence, a non-bovine sequence, an antibody sequence, or a combination thereof.
[00171] The first and/or second linker sequences may comprise one or more glycine residues. The first and/or second linker sequences may comprise two or more consecutive glycine residues. The first and/or second linker sequences may comprise one or more serine residues. The first and/or second linker sequence may comprise one or more polar amino acid residues. The one or more polar amino acid residues may be selected from serine, threonine, asparagine, or glutamine. The the polar amino acid residues may comprise uncharged side chains. The first and/or second linker sequences may comprise the sequence (GGGGS)n, wherein n = 1 to 5; the sequence GGGSGGGGS; the sequence GGGGSGGGS; the sequence of (GSG)n, wherein n is greater than or equal to one; or a combination thereof.
[00172] Any of the antibodies disclosed herein may comprise one or more cleavage sites.
The one or more cleavage sites may comprise a recognition site for a protease. The protease may be a Factor Xa or thrombin. The one or more cleavage sites may comprise an amino acid sequence of IEGR.
[00173] The one or more cleavage site may be between a first antibody sequence and the non-antibody sequence. The one or more cleavage sites may be between a second antibody sequence and the non-antibody sequence. The one or more cleavage sites may be between the one or more linkers and the non-antibody sequence. The one or more cleavage sites may be between a first antibody sequence and the one or more linkers. The one or more cleavage sites may be between a second antibody sequence and the one or more linkers. The one or more cleavage sites may be adjacent to a non-antibody sequence, a portion of an ultralong CDR3 sequence, a linker sequence, an antibody sequence, or a combination thereof.
[00174] In some embodiments is library of antibodies or binding fragments thereof, wherein the antibodies or binding fragments thereof may comprise an ultralong CDR3.
[00175] In some embodiments is library of antibodies or binding fragments thereof, wherein the antibodies or binding fragments thereof may comprise any of the antibodies disclosed herein.
[00176] In some embodiments is nucleic acid library comprising a plurality of
polynucleotides comprising sequences coding for antibodies or binding fragments thereof, wherein the antibodies or binding fragments thereof may comprise an ultralong CDR3.
[00177] In some embodiments is nucleic acid library comprising a plurality of
polynucleotides comprising sequences coding for antibodies or binding fragments thereof, wherein the antibodies or binding fragments thereof may comprise any of the antibodies disclosed herein.
[00178] In some embodiments is polynucleotide comprising a nucleic acid sequence that encodes a variable region, wherein the variable region may comprise an ultralong CDR3.
[00179] In some embodiments is vector comprising a polynucleotide, wherein the polynucleotide comprises a nucleic acid sequence that encodes a variable region, wherein the variable region may comprise an ultralong CDR3.
[00180] In some embodiments is host cell comprising a polynucleotide, wherein the polynucleotide comprises a nucleic acid sequence that encodes a variable region, wherein the variable region may comprise an ultralong CDR3.
[00181] In some embodiments is polynucleotide comprising a nucleic acid sequence that encodes the antibody or binding fragment thereof of any of the antibodies disclosed herein. [00182] In some embodiments is vector comprising a polynucleotide, wherein the polynucleotide comprises a nucleic acid sequence that encodes the antibody or binding fragment thereof of any of the antibodies disclosed herein.
[00183] In some embodiments is host cell comprising a polynucleotide, wherein the polynucleotide comprises a nucleic acid sequence that encodes the antibody or binding fragment thereof of any of the antibodies disclosed herein.
[00184] In some embodiments is method of producing an antibody or binding fragment thereof comprising an ultralong CDR3 or fragment thereof comprising culturing a host cell comprising a polynucleotide, wherein the polynucleotide may comprise a nucleic acid sequence that encodes the antibody or binding fragment thereof of any of the antibodies disclosed herein under conditions wherein the polynucleotide sequence may be expressed and the antibody or binding fragment thereof comprising an ultralong CDR3 or fragment thereof may be produced. The method may comprise recovering the antibody or binding fragment thereof comprising the ultralong CDR3 or fragment thereof from the host cell culture.
[00185] In some embodiments is pharmaceutical composition comprising any of the antibodies disclosed herein. The pharmaceutical compostion may comprise two or more antibodies, wherein at least one of the two or more antibodies comprises at least a portion of an ultralong CDR3.
[00186] In some embodiments is pharmaceutical composition comprising (a) an antibody or fragment thereof comprising sequence based on or derived from at least a portion of an ultralong CDR3; and (b) a pharmaceutically acceptable excipient.
[00187] In some embodiments is method of treating a disease or condition in a subject in need thereof comprising administering to the mammal a therapeutically effective amount of any of the antibodies disclosed herein. In some instances, the antibodies disclosed herein comprise an ultralong CDR3 sequence and a non-antibody sequence. In some instances, the non-antibody sequence is selected from the group comprising Mokal, Vm24, human GLP-1, Exendin-4, beta- interferon, human EPO, human FGF21, human GMCSF, human interferon-beta, bovine GCSF, human GCSF, be IL8, ziconotide, somatostatin, chlorotoxin, SDFl(alpha), IL21 and a derivative or variant thereof. The non-antibody sequence may comprise an amino acid sequence based on or derived from any of SEQ ID NOS: 317-332.
[00188] The disease or condition may be selected from the group comprising autoimmune disease, heteroimmune disease or condition, inflammatory disease, pathogenic infection, thromboembolic disorder, respiratory disease or condition, metabolic disease, central nervous system (CNS) disorder, bone disease, cancer, blood disorder, obesity, diabetes, osteoporosis, anemia, or pain.
[00189] The disease or condition would benefit from the modulation of an ion channel. The ion channel may be selected from the group comprising a potassium ion channel, sodium ion channel, or acid sensing ion channel. The ion channel may be selected from the group comprising Kvl .3 ion channel, Navl .7 ion channel and acid sensing ion channel (ASIC).
[00190] The disease or condition would benefit from the modulation of a receptor. The receptor may be selected from the group comprising GLP1R, GCGR, EPO receptor, FGFR, FGF21R, CSFR, GMCSFR, IL8R, IL21R and GCSFR.
[00191] The disease or condition may be mastitis.
[00192] The subject may be a mammal. The mammal may be a bovine or human.
[00193] In some embodiments are crystals based on or derived from the antibodies disclosed herein. The crystals may have a space group P212121. In some instances, the crystal has the unit cell dimensions of "a" between about 40 to 80 angstroms, between 45 to about 75 angstroms, or between about 50 to about 75 angstroms; "b" between about 40 to 140 angstroms, between about 50 to about 130 angstroms, between about 55 to about 130 angstroms; and "c" between 100 to about 350 angstroms, between 120 to about 340 angstroms, or between about 125 to about 330 angstroms. The crystal may comprise a bovine antibody or portion thereof. The crystal may comprise a Fab fragment based on or derived from a bovine antibody. The crystal may be an isolated crystal.
[00194] In some embodiments, is an isolated crystal comprising a bovine antibody Fab fragment comprising SEQ ID NO: 24 and SEQ ID NO: 23, wherein the crystal has a space group P212121 and unit cell dimensions of a=71.4 angstroms, b=127.6 angstroms and c=127.9 angstroms.
[00195] In some embodiments, is an isolated crystal comprising a bovine antibody Fab fragment comprising SEQ ID NO: 340 and SEQ ID NO: 341 , wherein the crystal has a space group P212121 and unit cell dimensions of a=54.6 angstroms, b=53.7 angstroms and c=330.5 angstroms.
[00196] In any or all of the above or below disclosure (e.g., antibodies, uses, or methods) or embodiments utilizing an antibody comprising an ultralong CDR3, any antibody comprising an ultralong CDR3 may be used including, for example, any of the above mentioned antibodies comprising an ultralong CDR3.
BRIEF DESCRIPTION OF THE DRAWINGS
[00197] The foregoing summary, as well as the following detailed description of the disclosure, will be better understood when read in conjunction with the appended figures. For the purpose of illustrating the disclosure, shown in the figures are embodiments which are presently preferred. It should be understood, however, that the disclosure is not limited to the precise arrangements, examples and instrumentalities shown.
[00198] Figure 1A-C present the identification of a new structural domain in bovine antibodies. Figure 1 A shows a comparison of CDR H3 length amongst murine, human, and bovine repertoires. An ultralong subset of over 60 amino acids is uniquely found in bovine heavy chains. Figure IB shows sequences of representative CDR H3 from murine (mu), human (hu), or bovine sequences from the literature along with six bovine sequences (B-Sl to B-S4, and B-Ll and B-L2) from our deep sequencing results. The conserved cysteine of framework 3 and tryptophan of framework 4 that define CDR H3 boundaries in all antibody variable regions are shaded in grey for reference.. The lengths of the CDR H3s are indicated at the right. The murine antibodies include D44.1, an anti-HEL antibody, 93F3, an aldolase, and OKT3, a therapeutic antibody targeting human CD3. This antibody is unusual in having a free cysteine in CDR H3. The human antibodies include Yvo, a cryoglobulin, CR6261, an anti- influenza A hemaglutinin, and PG9, an anti-HIV antibody which has one of the longest human CDR H3s. The bovine antibodies represent the ultralong sequences in the literature, and short sequences for comparison. BLV5B8 and BLV1H12 (indicated in bold) were used in our structure determinations. Relatively conserved TTVHQ and CPDG motifs are in bold. Figure 1C shows crystal structures of BLV1H12 (left) and BLV5B8 (middle) Fabs compared to the 93F3 Fab with a "normal" CDR H3 (right). A superlong, two β- stranded stalk protrudes from each bovine VH immunoglobulin domain and terminates in an unusual three disulfide- linked knob domain.
[00199] Figure 2A-C present the structural diversity in ultralong bovine antibodies. Figure
2A shows a comparison of the structure of the two knobs showing differences in disulfide patterns. Close up views of the knobs of BLV1H12 (left) and BLV5H8 (right) are shown, in addition to a two-dimensional representation of the knob and its disulfide pattern. Disulfides are in numbered and circled. The sequences of the knob regions are shown below, with cysteines conserved with the DH2 germline gene segment underlined. The disulfide pattern is indicated above each sequence. Figure 2B shows an overlay of the variable regions of BLV1H12 and BLV5B8 shows structural homology in the variable regions except the upper part of the stalk and knob, which are
significantly divergent. Figure 2C shows surface and charge density representation of BLV1H12 (left) and BLV5B8 (right) showing different shapes and charge in the knob region.
[00200] Figure 3A-C present the genetic basis for ultralong antibody formation. Figure 3A shows the identification of VHBUL, a germline variable region used in ultralong antibodies. The leader sequence is in light grey, coding sequence is indicated with the amino acid translation above, the intron is in italics, and the unique TTVHQ extension, which forms a portion of the ascending strand of the stalk is in bold. The recombination signal sequence heptamer and nonamer are underlined. Figure 3B shows the VHBUL region is found on chromosome 21. Partial cattle metaphase spread (left) and enlarged chromosome 21 (top right) showing the location of VHBUL region in BTA21q24 by two-color FISH with BAC clones 318H2 and 14-74H6. International nomenclature for BTA21 is depicted at the bottom. Figure 3C shows a schematic of the bovine immunoglobulin loci depicting VHBUL, Dh2, and Υχΐχ, which are preferentially used in ultralong antibodies. The process of V(D)J recombination assembles the gene segments to form functional ultralong heavy and light chain genes, (bottom left) The V-D-J regions mapped onto the BLV1H12 Fab structure. VHBUL is unique in encoding CDR HI and CDR H2 residues that interact with the stalk, as well as a TTVHQ motif that initiates the ascending β-strand. Similarly, the Μχΐ light chain encodes CDR LI and CDR L2 residues that interact with the stalk. Arrows indicate areas of potential junctional diversity. Relatively long V-D insertions are indicated in purple. It is unclear whether this sequence results from N-additions, gene conversion, or another mechanism, (bottom right) A detailed depiction of the interactions of CDR HI , H2, LI , and L2 with the stalk of BLV1H12, as well as the location of the YxYxY motif of the descending strand.
[00201] Figure 4A-C depict deep sequence diversity of bovine ultralong VH CDR H3s. Figure 4A shows the distribution of the number of cysteines in bovine ultralong CDR H3s of IgM and IgG. Figure 4B shows the length distribution of ultralong CDR H3s. Note that clonal sequences selected during an immune response can bias the proportion at any given length. Figure 4C shows representative sequences of ultralong bovine VH CDR H3s. The terminal portion of the VHBUL region is shown, along with junctional diversity at the V-D joint, DH2 and ½ (top). The sequences of BLVH12 and BLV5B8 are shown for comparison, followed by 20 ultralong CDR H3 sequences (bottom). Cysteines conserved with DH2 are underlined. The conserved cysteine and tryptophan that define the CDR H3 boundaries in all antibody variable regions are highlighted in grey for reference. The CPDG motif is underlined in grey and the region of the descending strand encoding a YxYxY motif is underlined in grey.
[00202] Figure 5A-C show that cysteine mutations contribute to ultralong CDR H3 diversity. Figure 5A shows that the consensus of ultralong CDR H3 deep sequences aligns with DH2. A consensus sequence for three deep sequencing runs (from two cows) were determined, and aligned with one another and with DH2. The consensus aligns well except for some areas of insertions/deletions. Thus, either a single DH gene, or highly related genes, produce the diversity of sequences in ultralong CDR H3 antibodies. Figure 5B shows that the DH2 gene region analysis showing residues that can readily mutate to cysteine, including SH hotspots. The nucleotide sequence is above and translated amino-acid sequence below. RGYW hotspots, which are recognized by AID for SH and/or gene conversion, are boxed. Nucleotides at positions 3, 15, 19, 21, 25, 27, 31, 33, 39, 43, 45, 49, 51, 57, 60, 64, 73, 75, 79, 81, 84, 88, 90, 93, 97, 102, 106, 112, 117, 121, 123, 127, 129, 133, 139, and 145 in (B) can be altered in a single mutation to a cysteine- encoding codon. Figure 5C shows affinity maturation groups show mutation to and from cysteine. Several groups of clonally related sequences were identified and analyzed for somatic
hypermutation. Three groups are shown as examples (labeled 1 to 3 on the left). Sequence differences from cysteine are highlighted in grey. The number of times each sequence is represented in the cluster is shown at the right.
[00203] Figure 6A-D show bovine antibodies with ultralong CDR H3s bind antigen. Figure
6A shows immunization experimental scheme for identifying antigen-specific, ultralong CDR H3 antibodies. Heavy chain variable region mRNA was isolated, amplified by RT PCR, and paired with the invariant light chain to produce a small library of IgG produced in HEK293 cells. Figure 6B shows ELISA of 132 ultralong CDR H3 antibodies against BVDV (left), and binding activity of the "hits" B8, B9, and H12 in a titration assay (right). Figure 6C shows the sequences of B8, H9, and H12 in comparison to BLV1H12 and the germline DR2 region. Lengths (L) of the CDR H3 are indicated at the right. Cysteines conserved with DR2 are underlined. Figure 6D shows that H12 binds NS2-3 on cells. A flag-tagged BVDV NS2-3 protein construct was transfected into
HEK293A cells and stained with anti-Flag as a positive control (left), the H12 antibody (middle), and B8 (right). Binding assays with untransfected cells are shown on the bottom.
[00204] Figure 7A-B depict a model for ultralong CDR H3 diversification into novel minifolds. Figure 7A shows a schematic of the DR2 knob with 4 cysteines is shown on the left, with SH and/or gene conversion leading to a multitude of new cysteine patterns and new loops on the right. Figure 7B shows mechanisms for generating antibody diversity. In humans and mice (left), combinatorial diversity through V(D)J recombination and VH-VL pairing creates a multitude of different binding sites, which are further optimized following antigen exposure by somatic hypermutation. In cows (right), combinatorial diversity is severely limited; however, somatic mutation to and from cysteines can reshape the "knob" region, creating substantial structural diversity in ultralong CDR H3s. These antibodies may be further optimized through SH and may bind unique targets such as pores or channels.
[00205] Figure 8A-J depict schemes showing attachment of bovine G-CSF onto the knob domain of a heavy chain region of bovine BLV1H12 antibody to design an immunoglobulin construct described herein. Figure 8A shows a ribbon diagram of a heavy chain region and light chain region of bovine BLV1H12 antibody. The boxed region highlights the extended region of the ultralong CDR3 comprising the stalk and knob domain. Figure 8B shows a ribbon diagram of a growth factor (e.g., bovine G-CSF) inserted into or replacing a portion of the knob domain of a heavy chain region of a bovine BLV1H12 antibody. Figure 8C shows a ribbon diagram of a toxin (e.g., Mokal, VM-24) inserted into or replacing a portion of the knob domain of a heavy chain region of a bovine BLV1H12 antibody. Figure 8D shows a ribbon diagram of a receptor ligand (e.g., GLP-1, exendin-4) inserted into or replacing a portion of the knob domain of a heavy chain region of a bovine BLV1H12 antibody. Figure 8E shows a ribbon diagram of a hormone (e.g., erythropoietin) inserted into or replacing a portion of the knob domain of a heavy chain region of a bovine BLV1H12 antibody. Figure 8F shows a cartoon depicting a heavy chain region and light chain region of bovine BLV1H12 antibody. Figure 8G shows a cartoon of a growth factor (e.g., bovine G-CSF) inserted into or replacing a portion of the knob domain of a heavy chain region of a bovine BLV1H12 antibody. Figure 8H shows a cartoon of a toxin (e.g., Mokal, VM-24) inserted into or replacing a portion of the knob domain of a heavy chain region of a bovine BLV1H12 antibody. Figure 81 shows a cartoon of a receptor ligand (e.g., GLP-1, exendin-4) inserted into or replacing a portion of the knob domain of a heavy chain region of a bovine BLV1H12 antibody. The left panel shows both ends of the receptor ligand inserted into or replacing a portion of the knob domain; the right panel shows the N-terminus of the receptor ligand released from the knob domain after treatment with a protease. Figure 8J shows a cartoon of a hormone (e.g.,
erythropoietin) inserted into or replacing a portion of the knob domain of a heavy chain region of a bovine BLV1H12 antibody. Said attachment of the growth factor, toxin, receptor ligand, and hormone can be by means of a polypeptide linker of sequence GGGGS (Ab-peptide LI) or GGGSGGGGS and GGGGSGGGS (Ab-peptide L2). Another construct (Ab-peptide LO) in which attachment is not by means of a linker is not shown in this cartoon.
[00206] Figure 9A-9E present illustrative mouse NFS-60 cell proliferative activity for the
Ab-bGCSF fusion proteins. Figure 9A-9B depict proliferative activity of bovine G-CSF and human G-CSF respectively. Figure 9C depicts the lack of proliferative activity for bovine
BLV1H12 antibody in the absence of G-CSF. Figure 9D depicts proliferative activity of bovine G- CSF inserted into or replacing a portion of the knob domain in the absence of a linker (Ab-bGCSF L0). Figure 9E depicts proliferative activity of bovine G-CSF inserted into or replacing a portion of the knob domain by means of a polypeptide linker of sequence GGGGS (Ab-bGCSF LI).
[00207] Figure 10A-10E present human granulocyte progenitor cell proliferative activities of the Ab-GCSF fusion proteins. Figure 10A-10B depict proliferative activity of bovine G-CSF and human G-CSF respectively. Figure IOC depicts the lack of proliferative activity for bovine BLV1H12 antibody (Ab) in the absence of G-CSF. Figure 10D depicts proliferative activity of bovine G-CSF inserted into or replacing a portion of the knob domain in the absence of a linker (Ab-bGCSF LO). Figure 10E depicts proliferative activity of bovine G-CSF inserted into or replacing a portion of the knob domain, said attachment by means of a polypeptide linker of sequence GGGGS (Ab-bGCSF LI).
[00208] Figure 11A-11B depict pharmacokinetics of Ab-bGCSF fusion proteins in mice.
[00209] Figure 12A-12B provide Proliferative activities of Ab-bGCSF fusion proteins on mice neutrophils that are blood stained and counted at the 10th day post-injection.
[00210] Figure 13A-13C display expression and purification of Ab-bGCSF fusion proteins in Pichia pastoris. Figure 13 A shows a map of Pichia expression vector for an immunoglobulin construct provided herein. Figure 13B provides a western blot post-induction of expression of the immunoglobulin constructs Ab-bGCSF L0 and Ab-bGCSF LI . Figure 13C provides SDS-PAGE gel of purified Ab-bGCSF L0 and Ab-bGCSF LI expressed in Pichia at a yield of -70 μg per 100 mL culture.
[00211] Figure 14A-14C show vectors for expression of the immunoglobulin constructs described herein in free style HEK 293 cells. Figure 14A provides a vector of Ab-bGCSF L0 heavy chain for expression in free style HEK 293 cells. Figure 14B provides a vector of Ab-bGCSF LI heavy chain for expression in free style HEK 293 cells. Figure 14C provides a vector of Ab- bGCSF light chain for expression in free style HEK 293 cells.
[00212] Figure 15A shows SDS-PAGE gel of purified antibody fusions. Figure 15A SDS- PAGE gel of purified Ab-bGCSF L0 and Ab-bGCSF LI proteins from HEK 293 cells. Figure 15B provides a SDS PAGE of the immunoglobulin constructs Ab-Protoxin2 comprising a GGGGS linker attached to both ends of protoxin2.
[00213] Figure 16A-16B provide SDS PAGE and activities of the immunoglobulin constructs Ab-Mokal L0 (no linker) and Ab-Mokal LI (linker). Figure 16A provides a SDS PAGE of the immunoglobulin fusion proteins Ab-Mokal L0 and Ab-Mokal LI . Figure 16B provides BLVlH12-Mokal fusion proteins inhibitory activities on T cells activation
[00214] Figure 17 provides BLVlH12-Mokal fusion proteins inhibitory activities on human peripheral blood mononuclear cells (PBMCs)
[00215] Figure 18A-18C provide SDS PAGE and activities of the immunoglobulin constructs Ab-VM24 LI (GGGGS linker) and Ab-VM24 L2 (GGGSGGGGS and GGGGSGGGS linkers). Figure 18A provides a SDS PAGE of the immunoglobulin fusion proteins Ab-VM24 LI and Ab-VM24 L2. Figure 18B provides BLV1H12-VM24 LI fusion protein inhibitory activities on T cells activation. Figure 18C provides BLV1H12-VM24 L2 fusion protein inhibitory activities on T cells activation. [00216] Figure 19 provides a SDS PAGE of the immunoglobulin constructs Ab-GLP-1 and
Ab-Exendin-4.
[00217] Figure 20 provides activity of Ab-GLP-1 and Ab-Ex4 on HEK293 cells expressing
GLP-1 receptor.
[00218] Figure 21 provides proliferative activity of Ab-hEPO fusion proteins on TF1 cells.
[00219] Figure 22A-C depicts ultralong CDR3 sequences. (Top) Translation from the germline VHBUL, DR2, and JR. The 5 full length ultralong CDR H3s reported in the literature contain between four and eight cysteines and are not highly homologous to one another; however, some conservation of cysteine residues with DH2 could be found when the first cysteine of these CDR H3s was "fixed" prior to alignment. Four of the seven sequences (BLV1H12, BLV5D3, BLV8C 11, and BF4E9) contain four cysteines in the same positions as DR2, but also have additional cysteines. BLV5B8 has two cysteines in common with the germline DR2. This limited homology with some cysteine conservation suggests that mutation of DH2 could generate these sequences. B-Ll and B-L2 are from initial sequences from bovine spleen, and the remaining are selected ultralong CDR H3 sequences from deep sequencing data. The first group contains the longest CDR H3s identified, and appear clonally related. The * indicates a sequence represented 167 times, suggesting it was strongly selected for function. Several of the eight-cysteine sequences appear selected for function as they were represented multiple times, indicated in parentheses. Other representative sequences of various lengths are indicated in the last group. The framework cysteine and tryptophan residues that define the CDR H3 boundaries are double-underlined. The sequences BLV1H12 through UL-77 (left-most column) presented in Tables 2A-C are depicted broken apart into four segments to identify the segments of amino acid residues that are derived from certain germline sequences. Moving from left to right, the first segment is derived from the VH germline and is represented throughout the disclosure as a X1X2X3X4X5 motif. The second segment is a string of spacer amino acid residues designated throughout the disclosure as XN residues. The third segment is a string of amino acid residues derived from the germline DR2 region and the fourth segment is a string of amino acid residues derived from the germline ½1 region.
DETAILED DESCRIPTION
[00220] Disclosed herien are antibodies and fragments thereof. Generally, the antibodies and fragments thereof comprise at least a portion of an ultralong CDR3. The portion of the ultralong CDR3 may be derived from or based on an ultralong CDR3 sequence. The portion of the ultralong CDR3 may be derived from or based on a stalk domain of an ultralong CDR3 sequence. Alternatively, or additionally, the portion of the ultralong CDR3 may be derived from or based on a knob domain of an ultralong CDR3 sequence. The antibodies and fragments thereof may further comprise one or more therapeutic polypeptides. The therapeutic polypeptides may be inserted into the portion of the ultralong CDR3. The therapeutic polypeptides may replace one or more amino acid residues in the amino acid sequence of the portion of the ultralong CDR3. The therapeutic polypeptides may replace one or more nucleotides in the nucleic acid sequence of the portion of the ultralong CDR3. Alternatively, the therapeutic polypeptides may be conjugated or attached to the portion of the ultralong CDR3. The antibodies and fragments disclosed herein may further comprise one or more linkers. Additionally, the antibodies and fragments disclosed herein further comprise a cleavage site. A portion of the antibodies and fragments disclosed herien may be based on or derived from an antibody sequence from a different animal or specie from with the ultralong CDR3 is derived. For example, the ultralong CDR3 may be derived from or based on a bovine antibody sequence and the additional and another portion of the antibody sequence may be derived from or based on a non-bovine antibody sequence. Further details of the antibodies and fragments thereof are described herein.
Ultralong CDR3 Proteins
[00221] The present disclosure provides antibodies or immunoglobulin constructs comprising ultralong CDR3 sequences or portions thereof.
[00222] In an embodiment, the present disclosure provides an antibody comprising an ultralong CDR3. The ultralong CDR3 may be 35 amino acids in length or more (e.g., 40 or more, 45 or more, 50 or more, 55 or more, 60 or more). The ultralong CDR3 may comprise at least a portion of a knob domain of a CDR3, at least a portion of a stalk domain of a CDR3, or a combination thereof. The portion of the knob domain of the CDR3 may comprise one or more conserved motifs derived from the knob domain of the ultralong CDR3. The portion of the stalk domain of the CDR3 may comprise one or more conserved motis derived from the stalk domain of the ultralong CDR3. Such an antibody may comprise at least 3 cysteine residues or more (e.g., 4 or more, 6 or more, 8 or more) within the ultralong CDR3. The antibody may comprise one or more cysteine motifs. The antibody may comprise a non-antibody sequence within the ultralong CDR3. Alternatively, or additionally, the antibody comprises a non-bovine sequence. The non-bovine sequence can be linked to the ultralong CDR3 sequence. The antibody may further comprise a linker. The linker can comprise an amino acid sequence of (GGGGS)n wherein n = 1 to 5.
Alternatively, the linker comprises an amino acids sequence of (GSG)n, GGGSGGGGS or GGGGSGGGS. The antibody may comprise a non-bovine sequence within the ultralong CDR3. The antibody may further comprise an antibody sequence, wherein the antibody sequence does not comprise an ultralong CDR3 sequence. The antibody may further comprise an antibody sequence, wherein the amino acid sequence identitity of the antibody peptide sequence to the ultralong CDR3 peptide sequence is about 40% or less (e.g., about 35% or less, about 30%> or less, about 25% or less, about 20% or less, about 15% or lress, 10% or less, about 5% or less, about 3% or less, about 1% or less). The antibody may comprise a cytotoxic agent or therapeutic polypeptide. The cytotoxic agent or therapeutic polypeptide may be conjugated to the ultralong CDR3. The antibody may bind to a target. The target may be a protein target. The protein target may be a transmembrane protein target. The antibody may comprise at least a portion of a BLV1H12 and/or BLVCV1 antibody. Alternatively, or additionally, the antibody comprises at least a portion of a BLV5D3, BLV8C11, BF1H1, BLV5B8 and/or F18 antibody. The antibody may comprise at least a portion of a human antibody. The antibody may be a chimeric, recombinant, engineered, synthetic, humanized, fully human, or human engineered antibody. The antibody may comprise antibody sequences from two or more different antibodies. The two or more different antibodies may be from the same species. For example, the specie may be a bovine specie, human specie, or murine specie. The two or more different antibodies may be from the same type of animal. For example the two or more different antibodies may be from a cow. The two or more different antibodies may be from a human.
Alternatively, the two or more different antibodies are from different species. For example, the two or more different antibodies are from a human specie and bovine specie. In another example, the two or more diffent antibodies are from a bovine specie and a non-bovine specie. In another example, the two or more different antibodies are from a human specie and a non-human specie.
[00223] In another embodiment, the present disclosure provides an antibody comprising an ultralong CDR3, wherein the CDR3 is 35 amino acids in length or more and is derived from or based on a non-human sequence. The ultralong CDR3 sequence may be derived from any species that naturally produces ultralong CDR3 antibodies, including ruminants such as cattle (Bos taurus). The antibody may comprise at least a portion of a BLV1H12 and/or BLVCV1 antibody.
Alternatively, or additionally, the antibody comprises at least a portion of a BLV5D3, BLV8C11, BF1H1, BLV5B8 and/or F18 antibody. Alternatively, the ultralong CDR3 sequence may be derived from a camelid or shark CDR3 sequence.
[00224] In another embodiment, the present disclosure provides an antibody comprising an ultralong CDR3, wherein the CDR3 comprises a non-antibody sequence. The non-antibody sequence may be derived from any protein family including, but not limited to, chemokines, growth factors, peptides, cytokines, cell surface proteins, serum proteins, toxins, extracellular matrix proteins, clotting factors, secreted proteins, etc. The non-antibody sequence may be derived from a therapeutic polypeptide. The non-antibody sequence may be of human or non-human origin. The non-antibody sequence may comprise a synthetic sequence. The non-antibody sequence may comprise a portion of a non-antibody protein such as a peptide or domain. The non-antibody sequence of an ultralong CDR3 may contain mutations from its natural sequence, including amino acid changes (e.g., substitutions), insertions or deletions. Engineering additional amino acids at the junction between the non-antibody sequence may be done to facilitate or enhance proper folding of the non-antibody sequence within the antibody. The CDR3 may be 35 amino acids in length or more. The ultralong CDR3 may comprise at least a portion of a knob domain of a CDR3, at least a portion of a stalk domain of a CDR3, or a combination thereof. The portion of the knob domain of the CDR3 may comprise one or more conserved motifs derived from the knob domain of the ultralong CDR3. The portion of the stalk domain of the CDR3 may comprise one or more conserved motis derived from the stalk domain of the ultralong CDR3. Alternatively, or additionally, the antibody comprises at least 3 cysteine residues or more. The antibody can comprise one or more cysteine motifs. The antibody may comprise at least a portion of a BLV1H12 and/or BLVCV1 antibody. Alternatively, or additionally, the antibody comprises at least a portion of a BLV5D3, BLV8C1 1 , BF1H1 , BLV5B8 and/or F18 antibody.
[00225] In another embodiment, the present disclosure provides an antibody comprising an ultralong CDR3 and a non-bovine sequence. The ultralong CDR3 can be derived from a ruminant. The ruminant can be a bovine. The non-bovine sequence can be derived from or based on a non- bovine mammal sequence. For example, the non-bovine sequence can be derived from or based on a human, mouse, rat, sheep, dog, and/or goat sequence. The ultralong CDR3 sequence can comprise the non-bovine sequence. Alternatively, the non-bovine sequence is linked to the ultralong CDR3 sequence. The non-bovine sequence can be derived from or based on at least a portion of an antibody sequence. The antibody sequence can encode a variable region, constant region or a combination thereof. The CDR3 may be 35 amino acids in length or more. The ultralong CDR3 may comprise at least a portion of a knob domain of a CDR3, at least a portion of a stalk domain of a CDR3, or a combination thereof. The portion of the knob domain of the CDR3 may comprise one or more conserved motifs derived from the knob domain of the ultralong CDR3. The portion of the stalk domain of the CDR3 may comprise one or more conserved motis derived from the stalk domain of the ultralong CDR3. Alternatively, or additionally, the antibody comprises at least 3 cysteine residues or more. The antibody can comprise one or more cysteine motifs.
[00226] In another embodiment, the present disclosure provides an antibody comprising an ultralong CDR3, wherein the CDR3 is 35 amino acids in length or more and comprises at least 3 cysteine residues or more, including, for example, 4 or more, 6 or more, and 8 or more. [00227] In another embodiment, the present disclosure provides for an antibody comprising an ultralong CDR3 wherein the CDR3 is 35 amino acids in length or more and comprises at least 3 cysteine residues or more and wherein the ultralong CDR3 is a component of a multispecific antibody. The multispecific antibody may be bispecific or comprise greater valencies.
[00228] In another embodiment, the present disclosure provides an antibody comprising an ultralong CDR3, wherein the CDR3 is 35 amino acids in length or more and comprises at least 3 cysteine residues or more, wherein the ultralong CDR3 is a component of an immuno conjugate.
[00229] In another embodiment, the present disclosure provides an antibody comprising an ultralong CDR3, wherein the CDR3 is 35 amino acids in length or more and comprises at least 3 cysteine residues or more, wherein the antibody comprising an ultralong CDR3 binds to a transmembrane protein target. Such transmembrane targets may include, but are not limited to, GPCRs, ion channels, transporters, and cell surface receptors.
[00230] In another embodiment, the present disclosure provides an antibody comprising an ultralong CDR3, wherein the antibody comprising an ultralong CDR3 binds to a transmembrane protein target. Such transmembrane targets may include, but are not limited to, GPCRs, ion channels, transporters, and cell surface receptors. The CDR3 may be 35 amino acids in length or more. The ultralong CDR3 may comprise at least a portion of a knob domain of a CDR3, at least a portion of a stalk domain of a CDR3, or a combination thereof. The portion of the knob domain of the CDR3 may comprise one or more conserved motifs derived from the knob domain of the ultralong CDR3. The portion of the stalk domain of the CDR3 may comprise one or more conserved motis derived from the stalk domain of the ultralong CDR3. Alternatively, or additionally, the antibody comprises at least 3 cysteine residues or more. The antibody can comprise one or more cysteine motifs.
[00231] Provided herein is an immunoglobulin construct comprising a mammalian immunoglobulin heavy chain comprising at least a portion of complementarity- determining region 3 (CDR3H); and a therapeutic polypeptide, wherein the therapeutic polypeptide is inserted into or replaces at least a portion of the CDR3H. The immunoglobulin construct may comprise one or more linkers. The one or more linkers can connect the therapeutic polypeptide to the heavy chain. In some embodiments, the linker comprises an amino acid sequence of (GGGGS)n wherein n = 1 to 5. Alternatively, or additionally, the linker comprises an amino acid acid sequence of (GSG)n (SEQ ID NO: 342), GGGSGGGGS (SEQ ID NO: 337) or GGGGSGGGS. In some embodiments provided are immunoglobulin constructs described herein, wherein the therapeutic polypeptide is selected from a hormone, a lymphokine, an interleukin, a chemokines, a cytokine and combinations thereof. In certain embodiments, the therapeutic polypeptide is a cytokine. In some embodiments, the therapeutic polypeptide is a colony stimulating factor polypeptide. In certain embodiments, the colony stimulating factor is macrophage colony- stimulating factor (M-CSF), Granulocyte- macrophage colony- stimulating factor (GM-CSF), Granulocyte colony- stimulating factor (G-CSF) or fragment, or variant thereof. In an embodiment, the colony stimulating factor is mammalian G- CSF or derivative or variant thereof. In a certain embodiment, the colony stimulating factor is bovine G-CSF or derivative or variant thereof. In other instances, the therapeutic polypeptide is Mokal, Vm24, human GLP-1, Exendin-4, human EPO, human FGF21, human GMCSF, or human interferon-beta. Provided herein are immunoglobulin constructs comprising a mammalian immunoglobulin heavy chain comprising a knob domain in the complementarity- determining region 3 (CDR3H) or fragment thereof; and a therapeutic polypeptide attached to said knob domain of the CDR3H, wherein said mammalian immunoglobulin is a bovine immunoglobulin. In some embodiments, the bovine immunoglobulin is a BLV1H12 antibody. In some embodiments of the immunoglobulin constructs described herein, at least a portion of the knob domain is replaced by the therapeutic polypeptide. The knob domain of the CDR3H may comprise one or more conserved motifs derived from the knob domain of the ultralong CDR3H. The immunoglobulin construct may further comprise at least a portion of a stalk domain in the CDR3H. The portion of the stalk domain of the CDRH3 may comprise one or more conserved motis derived from the stalk domain of the ultralong CDR33H.
[00232] Further provided herein are antibodies or fragments thereof comprising a stalk domain in the complementarity-determining region 3 (CDR3H) or fragment thereof; and a therapeutic polypeptide. In some instances, the complementarity-determining region 3 (CDR3H) is derived from a bovine ultralong CDR3H. The therapeutic polypeptide can be any of the therapeutic polypeptides disclosed herein. For example, the therapeutic polypeptide is Mokal, Vm24, GLP-1, Exendin-4, human EPO, human FGF21, human GMCSF, or human interferon-beta. The therapeutic polypeptide can be attached to the stalk domain. In some instances, the antibody or fragment thereof further comprises a linker. The linker can attach the therapeutic polypeptide to the stalk domain. Alternatively, or additionally, the antibody or fragment thereof further comprises at least a portion of a knob domain in the CDR3H. In some instances, the linker attaches the therapeutic polypeptide to the knob domain. In some instances, the knob domain is attached to the stalk domain. The portion of the knob domain of the CDR3 may comprise one or more conserved motifs derived from the knob domain of the ultralong CDR3. The stalk domain of the CDR3 may comprise one or more conserved motis derived from the stalk domain of the ultralong CDR3.
[00233] In some instances, an antibody or fragment thereof is provided herein. The antibody or fragment thereof can comprise at least one immunoglobulin domain or fragment thereof; and a therapeutic polypeptide or derivative or variant thereof. The therapeutic polypeptide, or derivative or variant thereof can be attached to the immunoglobulin domain. In some instances, the therapeutic polypeptide is Mokal, Vm24, GLP-1, Exendin-4, human EPO, human FGF21, human GMCSF, human interferon-beta, or derivative or variant thereof. In some embodiments, the immunoglobulin domain is an immunoglobulin A, an immunoglobulin D, an immunoglobulin E, an immunoglobulin G, or an immunoglobulin M. The immunoglobulin domain can be an
immunoglobulin heavy chain region or fragment thereof. In some instances, the immunoglobulin domain is from a mammalian antibody. Alternatively, the immunoglobulin domain is from a chimeric antibody. In some instances, the immunoglobulin domain is from an engineered antibody or recombinant antibody. In other instances, the immunoglobulin domain is from a humanized, human engineered or fully human antibody. In certain embodiments, the mammalian antibody is a bovine antibody. In other instances, the mammalin antibody is a human antibody. In other instances, the mammalian antibody is a murine antibody. In some instances, the immunoglobulin domain is a heavy chain region comprising a knob domain in the complementarity- determining region 3 (CDR3H) or fragment thereof. The therapeutic polypeptide can be attached to the knob domain. Alternatively, or additionally, the immunoglobulin domain is a heavy chain region comprising a stalk domain in the complementarity-determining region 3 (CDR3H) or fragment thereof. In some instances, the therapeutic polypeptide is attached to the stalk domain. In some instances, the antibody or fragment thereof further comprises a linker. The linker can attach the therapeutic polypeptide to the immunoglobulin domain or fragment thereof. The knob domain of the CDR3 may comprise one or more conserved motifs derived from the knob domain of the ultralong CDR3. The stalk domain of the CDR3 may comprise one or more conserved motis derived from the stalk domain of the ultralong CDR3.
[00234] Provided herein is an immunoglobulin construct comprising at least one
immunoglobulin domain or fragment thereof; and a G-CSF polypeptide or derivative or variant thereof attached to said immunoglobulin domain. In some embodiments, the immunoglobulin domain is an immunoglobulin A, an immunoglobulin D, an immunoglobulin E, an immunoglobulin G, or an immunoglobulin M. In some embodiments, the immunoglobulin domain is an
immunoglobulin heavy chain region or fragment thereof. In an embodiment, the immunoglobulin domain is from a mammalian or chimeric antibody. In other instances, the immunoglobulin domain is from a humanized, human engineered or fully human antibody. In certain embodiments, the mammalian antibody is a bovine antibody. In some instances, the mammalian antibody is a human antibody. In other instances, the mammalian antibody is a murine antibody. In an embodiment, the immunoglobulin domain is a heavy chain region comprising a knob domain in the complementarity- determining region 3 (CDR3H) or fragment thereof. In an embodiment, the G- CSF polypeptide is attached to the knob domain. The immunoglobulin domain may be a heavy chain region comprising a stalk domain in the complementarity- determining region 3 (CDR3H) or fragment thereof. The G-CSF polypeptide may be attached to the stalk domain. The knob domain of the CDR3 may comprise one or more conserved motifs derived from the knob domain of the ultralong CDR3. The stalk domain of the CDR3 may comprise one or more conserved motis derived from the stalk domain of the ultralong CDR3.
[00235] In certain embodiments, provided is an immunoglobulin construct comprising at least one immunoglobulin domain or fragment thereof; and a G-CSF polypeptide or derivative or variant thereof attached to said immunoglobulin domain, wherein said G-CSF polypeptide is a bovine G-CSF polypeptide or derivative or variant thereof. In certain embodiments provided herein is a pharmaceutical composition comprising an immunoglobulin construct provided herein, and a pharmaceutically acceptable carrier. In certain embodiments is provided a method of preventing or treating a disease in a mammal in need thereof comprising administering a pharmaceutical composition described herein to said mammal. The immunoglobulin domain may be a heavy chain region comprising a knob domain in the complementarity- determining region 3 (CDR3H) or fragment thereof. The G-CSF polypeptide may be attached to the knob domain. The
immunoglobulin domain may be a heavy chain region comprising a stalk domain in the
complementarity- determining region 3 (CDR3H) or fragment thereof. The G-CSF polypeptide may be attached to the stalk domain. The knob domain of the CDR3 may comprise one or more conserved motifs derived from the knob domain of the ultralong CDR3. The stalk domain of the CDR3 may comprise one or more conserved motis derived from the stalk domain of the ultralong CDR3.
[00236] In some embodiments is an antibody or fragment thereof comprising: (a) a first antibody sequence, wherein at least a portion of the first antibody sequence is derived from at least a portion of an ultralong CDR3; and (b) a non-antibody sequence. The antibody or fragment thereof may further comprise a second antibody sequence, wherein at least a portion of the second antibody sequence is derived from at least a portion of an ultralong CDR3. The ultralong CDR3 from which the first antibody sequence and/or second antibody sequence may be derived from a ruminant. The ruminant can be a cow. At least a portion of the first antibody sequence and/or at least a portion of the second antibody sequence can be derived from a mammal. The mammal may be a bovine. Alternatively, the mammal is a non-bovine mammal, such as a human. The first and/or second antibody sequences may be 3 or more amino acids in length. The amino acids may be consecutive amino acids. Alternatively, the amino acids are non-consecutive amino acids. The first and/or second antibody sequences may comprise a bovine antibody sequence comprising 3 or more amino acids in length. The bovine antibody may be a BLVH12, BLV5B8, BLVCV1, BLV5D3,
BLV8C11, BF1H1, or F18 antibody. The first and/or second antibody sequences may comprise a human antibody sequence comprising 3 or moreore amino acids in length. The portion of the first antibody sequence derived from at least a portion of the ultralong CDR3 and/or the portion of the second antibody sequence derived from at least a portion of the ultralong CDR3 can be 20 or fewer amino acids in length. The portion of the first antibody sequence derived from at least a portion of the ultralong CDR3 and/or the portion of the second antibody sequence derived from at least a portion of the ultralong CDR3 may be 3 or more amino acids in length. The first and/or second antibody sequences can comprise 1 or more, 2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, 10 or more, 15 or more, 20 or more, 30 or more, or 40 or more amino acid residues derived from a knob domain of the ultralong CDR3. The 1 or more amino acid residues derived from the knob domain of the ultralong CDR3 may be a serine and/or cysteine residue. The first and/or second antibody sequences may comprise 1 or more, 2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, or 10 or more amino acid residues derived from a stalk domain of the ultralong CDR3. The first and/or second antibody sequences may comprise 1 or more, 2 or more, 3 or more, 4 or more, or 5 or more conserved motifs derived from a stalk domain of the ultralong CDR3. The one or more conserved motifs derived from the stalk domain of the ultralong CDR3 may comprise a sequence selected from any one of SEQ ID NOS: 157-307 and SEQ ID NOS: 333-336. The portion of the first antibody sequence derived from at least a portion of the ultralong CDR3 and/or the portion of the second antibody sequence derived from at least a portion of the ultralong CDR3 may comprise a sequence selected from any one of SEQ ID NOS: 157-307 and SEQ ID NOS: 333-336. The portion of the first antibody sequence derived from at least a portion of the ultralong CDR3 and/or the portion of the second antibody sequence derived from at least a portion of the ultralong CDR3 may comprise a sequence that is 50% or more homologous to a sequence selected from any one of SEQ ID NOS: 157-224 and 235- 295. The portion of the first antibody sequence derived from at least a portion of the ultralong CDR3 may comprise a sequence selected from any one of SEQ ID NOS: 157-234. The portion of the first antibody sequence derived from at least a portion of the ultralong CDR3 may comprise a sequence that is 50% or more homologous to a sequence selected from any one of SEQ ID NOS: 157-224. The portion of the first antibody sequence derived from at least a portion of the ultralong CDR3 may comprise a sequence that is 50%> or more homologous to a sequence selected from any one of SEQ ID NOS: 225-227. The portion of the second antibody sequence derived from at least a portion of the ultralong CDR3 may comprise a sequence selected from any one of SEQ ID NOS: 235-307 and SEQ ID NOS: 333-336. The portion of the second antibody sequence derived from at least a portion of the ultralong CDR3 may comprise a sequence that may be 50% or more homologous to a sequence selected from any one of SEQ ID NOS: 235-295. The portion of the first antibody sequence derived from at least a portion of the ultralong CDR3 and the portion of the second antibody sequence derived from at least a portion of the ultralong CDR3 may be derived from the same ultralong CDR3 sequence. The portion of the first antibody sequence derived from at least a portion of the ultralong CDR3 and the portion of the second antibody sequence derived from at least a portion of the ultralong CDR3 may be derived from two or more different ultralong CDR3 sequences. The portions of the ultralong CDR3 of the first and/or second antibody sequences may be based on or derived from a BLV1H12 ultralong CDR3 sequence. The portions of the ultralong CDR3 of the first and/or second antibody sequences may be based on or derived from a BLV5B8, BLVCV1, BLV5D3, BLV8C11, BF1H1, or F18 ultralong CDR3 sequence. The antibody may further comprise one or more linker sequences.
[00237] The present disclosure also provides antibodies that comprise a heavy chain polypeptide, wherein the heavy chain polypeptide comprises at least a portion of an ultralong CDR3 sequence. The heavy chain polypeptide may comprise a polypeptide sequence based on or derived from a polypeptide sequence of any one of SEQ ID NOS: 24-44. The heavy chain polypeptide may comprise a polypeptide sequence encoded by a DNA sequence based on or derived from the DNA sequence of any one of SEQ ID NOS: 2-22. Also provided are antibodies comprising a heavy chain polypeptide, wherein the heavy chain polypeptide comprises an ultralong CDR3 sequence and the heavy chain polypeptide sequences are substantially similar to those polypeptide sequences provided by any one of SEQ ID NOS: 24-44. A heavy chain polypeptide sequence may be considered substantially similar to a polypeptide sequence provided by any one of SEQ ID NOS: 24-44 where the heavy chain polypeptide sequence shares 60%, 70%, 80%, 90%, 95%), 99%), or more nucleic acid identity to a nucleotide sequence provided by any one of SEQ ID NOS: 24-44. The antibodies may further comprise a light chain polypeptide. The light chain polypeptide may comprise a polypeptide sequence based on or derived from a polypeptide sequence of SEQ ID NO: 23. The light chain polypeptide may comprise a polypeptide sequence encoded by a DNA sequence based on or derived from the DNA sequence of SEQ ID NO: 1. Also provided are antibodies further comprising a light chain polypeptide, wherein the light chain polypeptide comprises an ultralong CDR3 sequence and the light chain polypeptide sequences are substantially similar to those polypeptide sequences provided by SEQ ID NO: 23. A light chain polypeptide sequence may be considered substantially similar to a polypeptide sequence provided by SEQ ID NO: 1 where the light chain polypeptide sequence shares 60%, 70%, 80%, 90%, 95%, 99%, or more nucleic acid identity to a nucleotide sequence provided by any one of SEQ ID NO: 1. The antibody may have therapeutic activity in an animal. The antibody can have therapeutic activity in infectious disease in a subject. The antibody may comprise a monoclonal antibody, polyclonal antibody, chimeric antibody, recombinant antibody, engineered antibody, or synthetic antibody. The antibody may comprise a mammalian antibody. The antibody may comprise a bovine antibody. The antibody may comprise a G-CSF polypeptide, or derivative or variant thereof. The antibody may comprise a mammalian G-CSF polypeptide, or derivative or variant thereof. The antibody may comprise a bovine G-CSF, or derivative or variant thereof. In some embodiments, a pharmaceutical composition of therapeutic formulation comprises an antibody described herein and a pharmaceutically acceptable carrier. In certain embodiments, the antibody is used in a method of treating a subject in need thereof, with a therapeutically effective amount of the antibody or a pharmaceutical composition described herein. In some embodiments, a nucleic acid molecule or a complement therof encodes a therapeutic immunoglobulin described herein.
Genetic Sequences
[00238] The present disclosure provides genetic sequences (e.g., genes, nucleic acids, polynucleotides) encoding antibodies comprising ultralong CDR3 sequences or portions thereof. The present disclosure provides genetic sequences (e.g., genes, nucleic acids, polynucleotides) encoding antibodies comprising the knob domain and/or knob domain of ultralong CDR3 sequences. In another embodiment, the present disclosure provides genetic sequences encoding an antibody or immunoglobulin construct described herein.
[00239] The present disclosure also provides genetic sequences (e.g., genes, nucleic acids, polynucleotides) encoding an ultralong CDR3 or portion thereof. The present disclosure also provides genetic sequences (e.g., genes, nucleic acids, polynucleotides) encoding the knob domain and/or knob domain of an ultralong CDR3.
[00240] In an embodiment, the present disclosure provides genetic sequences encoding an antibody comprising an ultralong CDR3. The ultralong CDR3 may be 35 amino acids in length or more (e.g., 40 or more, 45 or more, 50 or more, 55 or more, 60 or more). The ultralong CDR3 may comprise at least a portion of a knob domain of a CDR3, at least a portion of a stalk domain of a CDR3, or a combination thereof. Such an antibody may comprise at least 3 cysteine residues or more (e.g., 4 or more, 6 or more, 8 or more) within the ultralong CDR3. The antibody may comprise one or more cysteine motifs. The antibody may comprise a non-antibody sequence within the ultralong CDR3. Alternatively, or additionally, the antibody comprises a non-bovine sequence. The antibody may further comprise an antibody sequence. The antibody may comprise a cytotoxic agent or therapeutic polypeptide. The cytotoxic agent or therapeutic polypeptide may be conjugated to the ultralong CDR3. The antibody may bind to a target. The target may be a protein target, such as a transmembrane protein target.
[00241] In another embodiment, the present disclosure provides genetic sequences encoding an antibody comprising an ultralong CDR3, wherein the CDR3 is 35 amino acids in length or more and is derived from or based on a non-human sequence. The genetic sequences encoding the ultralong CDR3 may be derived from any species that naturally produces ultralong CDR3 antibodies, including ruminants such as cattle (Bos taurus). Alternatively, the ultralong CDR3 sequence may be derived from a camelid or shark CDR3 sequence.
[00242] In another embodiment, the present disclosure provides genetic sequences encoding an antibody comprising an ultralong CDR3, wherein the CDR3 comprises a non-antibody protein sequence. The genetic sequences encoding the non-antibody protein sequences may be derived from any protein family including, but not limited to, chemokines, growth factors, peptides, cytokines, cell surface proteins, serum proteins, toxins, extracellular matrix proteins, clotting factors, secreted proteins, etc. The non-antibody sequence may be derived from a therapeutic polypeptide. The non-antibody protein sequence may be of human or non-human origin. The non- antibody sequence may comprise a synthetic sequence. The non-antibody sequencemay comprise a portion of a non-antibody protein such as a peptide or domain. The non-antibody protein sequence of an ultralong CDR3 may contain mutations from its natural sequence, including amino acid changes {e.g., substitutions), insertions or deletions. Engineering additional amino acids at the junction between the non-antibody sequence may be done to facilitate or enhance proper folding of the non-antibody sequence within the antibody. The CDR3 may be 35 amino acids in length or more. The ultralong CDR3 may comprise at least a portion of a knob domain of a CDR3, at least a portion of a stalk domain of a CDR3, or a combination thereof. Alternatively, or additionally, the antibody comprises at least 3 cysteine residues or more. The antibody can comprise one or more cysteine motifs.
[00243] In another embodiment, the present disclosure provides genetic sequences encoding an antibody comprising an ultralong CDR3 and a non-bovine sequence. The ultralong CDR3 can be derived from a ruminant. The ruminant can be a bovine. The non-bovine sequence can be derived from or based on a non-bovine mammal sequence. For example, the non-bovine sequence can be derived from or based on a human, mouse, rat, sheep, dog, and/or goat sequence. The non-bovine sequence can be within the ultralong CDR3. Alternatively, the non-bovine sequence is linked or attached to the ultralong CDR3 sequence. The non-bovine sequence can be derived from or based on at least a portion of an antibody sequence. The antibody sequence can encode a variable region, constant region or a combination thereof. The CDR3 may be 35 amino acids in length or more. The ultralong CDR3 may comprise at least a portion of a knob domain of a CDR3, at least a portion of a stalk domain of a CDR3, or a combination thereof. Alternatively, or additionally, the antibody comprises at least 3 cysteine residues or more. The antibody can comprise one or more cysteine motifs.
[00244] In another embodiment, the present disclosure provides genetic sequences encoding an antibody comprising an ultralong CDR3, wherein the CDR3 is 35 amino acids in length or more and comprises at least 3 cysteine residues or more, including, for example, 4 or more, 6 or more, and 8 or more.
[00245] In another embodiment, the present disclosure provides genetic sequences encoding an antibody comprising an ultralong CDR3 wherein the CDR3 is 35 amino acids in length or more and comprises at least 3 cysteine residues or more and wherein the ultralong CDR3 is a component of a multispecific antibody. The multispecific antibody may be bispecific or comprise greater valencies.
[00246] In another embodiment, the present disclosure provides genetic sequences encoding an antibody comprising an ultralong CDR3, wherein the CDR3 is 35 amino acids in length or more and comprises at least 3 cysteine residues or more, wherein the ultralong CDR3 is a component of an immunoconjugate.
[00247] In another embodiment, the present disclosure provides genetic sequences encoding an antibody comprising an ultralong CDR3 wherein the CDR3 is 35 amino acids in length or more and comprises at least 3 cysteine residues or more and wherein the antibody comprising an ultralong CDR3 binds to a transmembrane protein target. Such transmembrane targets may include, but are not limited to, GPCRs, ion channels, transporters, and cell surface receptors.
[00248] In another embodiment, the present disclosure provides genetic sequences encoding an antibody comprising an ultralong CDR3, wherein the antibody comprising an ultralong CDR3 binds to a transmembrane protein target. Such transmembrane targets may include, but are not limited to, GPCRs, ion channels, transporters, and cell surface receptors. The CDR3 may be 35 amino acids in length or more. The ultralong CDR3 may comprise at least a portion of a knob domain of a CDR3, at least a portion of a stalk domain of a CDR3, or a combination thereof.
Alternatively, or additionally, the antibody comprises at least 3 cysteine residues or more. The antibody can comprise one or more cysteine motifs.
[00249] In another embodiment, the present disclosure provides genetic sequences encoding an antibody or fragment thereof comprising: (a) a first antibody sequence, wherein at least a portion of the first antibody sequence is derived from at least a portion of an ultralong CDR3; and (b) a non-antibody sequence. The antibody or fragment thereof may further comprise a second antibody sequence, wherein at least a portion of the second antibody sequence is derived from at least a portion of an ultralong CDR3. The ultralong CDR3 from which the first antibody sequence and/or second antibody sequence may be derived from a ruminant. The ruminant can be a cow. At least a portion of the first antibody sequence and/or at least a portion of the second antibody sequence can be derived from a mammal. The mammal may be a bovine. Alternatively, the mammal is a non- bovine mammal, such as a human. The first and/or second antibody sequences may be 3 or more amino acids in length. The amino acids may be consecutive amino acids. Alternatively, the amino acids are non-consecutive amino acids. The first and/or second antibody sequences may comprise a bovine antibody sequence comprising 3 or more amino acids in length. The bovine antibody may be a BLVH12, BLV5B8, BLVCV1, BLV5D3, BLV8C11, BF1H1, or F18 antibody. The first and/or second antibody sequences may comprise a human antibody sequence comprising 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, 10 or more, 15 or more, 20 or more, 30 or more, 40 or more, 50 or more, 60 or more, or 70 or more amino acids in length. The portion of the first antibody sequence derived from at least a portion of the ultralong CDR3 and/or the portion of the second antibody sequence derived from at least a portion of the ultralong CDR3 can be 20 or fewer amino acids in length. The portion of the first antibody sequence derived from at least a portion of the ultralong CDR3 and/or the portion of the second antibody sequence derived from at least a portion of the ultralong CDR3 may be 3 or more amino, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, 10 or more, 15 or more, or 20 or more acids in length. The first and/or second antibody sequences can comprise 1 or more, 2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, 10 or more, 15 or more, 20 or more, 30 or more, or 40 or more amino acid residues derived from a knob domain of the ultralong CDR3. The 1 or more amino acid residues derived from the knob domain of the ultralong CDR3 may be a serine and/or cysteine residue. The first and/or second antibody sequences may comprise 1 or more, 2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, or 10 or more amino acid residues derived from a stalk domain of the ultralong CDR3. The first and/or second antibody sequences may comprise 1 or more, 2 or more, 3 or more, 4 or more, or 5 or more conserved motifs derived from a stalk domain of the ultralong CDR3. The one or more conserved motifs derived from the stalk domain of the ultralong CDR3 may comprise a sequence selected from any one of SEQ ID NOS: 157-307 and SEQ ID NOS: 333-336. The portion of the first antibody sequence derived from at least a portion of the ultralong CDR3 and/or the portion of the second antibody sequence derived from at least a portion of the ultralong CDR3 may comprise a sequence selected from any one of SEQ ID NOS: 157-307 and SEQ ID NOS: 333-336. The portion of the first antibody sequence derived from at least a portion of the ultralong CDR3 and/or the portion of the second antibody sequence derived from at least a portion of the ultralong CDR3 may comprise a sequence that is 50% or more homologous to a sequence selected from any one of SEQ ID NOS: 157-224 and 235-295. The portion of the first antibody sequence derived from at least a portion of the ultralong CDR3 may comprise a sequence selected from any one of SEQ ID NOS: 157-234. The portion of the first antibody sequence derived from at least a portion of the ultralong CDR3 may comprise a sequence that is 50% or more homologous to a sequence selected from any one of SEQ ID NOS: 157-224. The portion of the first antibody sequence derived from at least a portion of the ultralong CDR3 may comprise a sequence that is 50% or more homologous to a sequence selected from any one of SEQ ID NOS: 225-227. The portion of the second antibody sequence derived from at least a portion of the ultralong CDR3 may comprise a sequence selected from any one of SEQ ID NOS: 235-307 and SEQ ID NOS: 333-336. The portion of the second antibody sequence derived from at least a portion of the ultralong CDR3 may comprise a sequence that may be 50% or more homologous to a sequence selected from any one of SEQ ID NOS: 235- 295. The portion of the first antibody sequence derived from at least a portion of the ultralong CDR3 and the portion of the second antibody sequence derived from at least a portion of the ultralong CDR3 may be derived from the same ultralong CDR3 sequence. The portion of the first antibody sequence derived from at least a portion of the ultralong CDR3 and the portion of the second antibody sequence derived from at least a portion of the ultralong CDR3 may be derived from two or more different ultralong CDR3 sequences. The portions of the ultralong CDR3 of the first and/or second antibody sequences may be based on or derived from a BLV1H12 ultralong CDR3 sequence. The portions of the ultralong CDR3 of the first and/or second antibody sequences may be based on or derived from a BLV5B8, BLVCV1 , BLV5D3, BLV8C1 1 , BF1H1 , or F18 ultralong CDR3 sequence. The antibody may further comprise one or more linker sequences.
[00250] The present disclosure also provides isolated genetic sequences (e.g., genes, nucleic acids, polynucleotides, oligonucleotides) such as genetic sequences encoding antibodies that comprise an ultralong CDR sequence including, for example, a CDR3 sequence as provided by any one of SEQ ID NOS: 2-22. Also provided are ultralong CDR3 nucleic acid sequences that are substantially similar to those CDR3 sequences provided by any one of SEQ ID NOS: 2-22. A CDR3 sequence may be considered substantially similar to a CDR3 sequence provided by any one of SEQ ID NOS: 2-22 where the CDR3 sequence shares 80%, 85%, 90%, 95%, 99%, or more, nucleic acid sequence identity to a CDR3 sequence provided by any one of SEQ ID NOS: 2-22 or hybridizes to any one of SEQ ID NOS: 2-22 under stringent hybridization conditions. [00251] The present disclosure also provides isolated genetic sequences (e.g., genes, nucleic acids, polynucleotides, oligonucleotides) such as genetic sequences encoding antibodies that comprise a heavy chain polypeptide, wherein the heavy chain polypeptide comprises at least a portion of an ultralong CDR3 sequence. The heavy chain polypeptide may comprise a polypeptide sequence of any one of SEQ ID NOS: 24-44. The heavy chain polypeptide may comprise a polypeptide sequence encoded by the DNA of any one of SEQ ID NOS: 2-22. Also provided are isolated genetic sequences (e.g., genes, nucleic acids, polynucleotides, oligonucleotides) such as genetic sequences encoding antibodies comprising a heavy chain polypeptide, wherein the heavy chain polypeptide comprises an ultralong CDR3 sequence and the heavy chain polypeptide sequences are substantially similar to those polypeptide sequences provided by any one of SEQ ID NOS: 24-44. A heavy chain polypeptide sequence may be considered substantially similar to a polypeptide sequence provided by any one of SEQ ID NOS: 24-44where the heavy chain polypeptide sequence shares 60%, 70%, 80%>, 90%>, 95%, 99%, or more nucleic acid identity to a nucleotide sequence provided by any one of SEQ ID NOS: 24-44or hybridizes to any one of SEQ ID NOS: 24-44under stringent hybridization conditions. The isolated genetic sequences (e.g., genes, nucleic acids, polynucleotides, oligonucleotides) such as genetic sequences encoding antibodies may further comprise a light chain polypeptide. The light chain polypeptide may comprise a polypeptide sequence of SEQ ID NO: 23. The light chain polypeptide may comprise a polypeptide sequence encoded by the DNA of SEQ ID NO: 1. Also provided are isolated genetic sequences (e.g., genes, nucleic acids, polynucleotides, oligonucleotides) such as genetic sequences encoding antibodies further comprising a light chain polypeptide, wherein the light chain polypeptide comprises an ultralong CDR3 sequence and the light chain polypeptide sequences are substantially similar to those polypeptide sequences provided by SEQ ID NO: 23. A light chain polypeptide sequence may be considered substantially similar to a polypeptide sequence provided by SEQ ID NO: 1 where the light chain polypeptide sequence shares 60%, 70%, 80%, 90%, 95%, 99%), or more nucleic acid identity to a nucleotide sequence provided by any one of SEQ ID NO: 1 or hybridizes to SEQ ID NOS: 1 under stringent hybridization conditions.
Libraries and Arrays
[00252] The present disclosure provides collections, libraries and arrays of antibodies comprising ultralong CDR3 sequences. In some embodiments, members of the collections, libraries, or arrays may exhibit sequence diversity.
[00253] In an embodiment, the present disclosure provides a library or an array of antibodies comprising ultralong CDR3 sequences wherein at least two members of the library or array differ in the positions of at least one of the cysteines in the ultralong CDR3 sequence. Structural diversity may be enhanced through different numbers of cysteines in the ultralong CDR3 sequence (e.g., at least 3 or more cysteine residues such as 4 or more, 6 or more and 8 or more) and/or through different disulfide bond formation, and hence different loop structures.
[00254] In another embodiment, the present disclosure provides for a library or an array of antibodies comprising ultralong CDR3 sequences wherein at least two members of the library or the array differ in at least one amino acid located between cysteines in the ultralong CDR3. In this regard, members of the library or the array can contain cysteines in the same positions of CDR3, resulting in similar overall structural folds, but with fine differences brought about through different amino acid side chains. Such libraries or arrays may be useful for affinity maturation.
[00255] In another embodiment, the present disclosure provides libraries or arrays of antibodies comprising ultralong CDR3 sequences wherein at least two of the ultralong CDR3 sequences differ in length (e.g., 35 amino acids in length or more such as 40 or more, 45 or more, 50 or more, 55 or more and 60 or more). The amino acid and cysteine content may or may not be altered between the members of the library or the array. Different lengths of ultralong CDR3 sequences may provide for unique binding sites, including, for example, due to steric differences, as a result of altered length.
[00256] In another embodiment, the present disclosure provides libraries or arrays of antibodies comprising ultralong CDR3 sequences wherein at least two members of the library differ in the human framework used to construct the antibody comprising an ultralong CDR3.
[00257] In another embodiment, the present disclosure provides libraries or arrays of antibodies comprising ultralong CDR3 sequences wherein at least two members of the library or the array differ in having a non-antibody protein sequence that comprises a portion of the ultralong CDR3. Such libraries or arrays may contain multiple non-antibody protein sequences, including for chemokines, growth factors, peptides, cytokines, cell surface proteins, serum proteins, toxins, extracellular matrix proteins, clotting factors, secreted proteins, viral or bacterial proteins, etc. The non-antibody protein sequence may be of human or non-human origin and may be comprised of a portion of a non-antibody protein such as a peptide or domain. The non-antibody protein sequence of the ultralong CDR3 may contain mutations from its natural sequence, including amino acid changes (e.g., substitutions), or insertions or deletions. Engineering additional amino acids at the junction between the non-antibody sequence within the ultralong CDR3 may be done to facilitate or enhance proper folding of the non-antibody sequence within the antibody.
[00258] In another embodiment, the present disclosure provides libraries or arrays of antibodies comprising ultralong CDR3 sequences wherein at least two members of the library or the array differ in having a non-bovine sequence. The non-bovine sequence can be derived from or based on a non-bovine mammal sequence. For example, the non-bovine sequence can be derived from or based on a human, mouse, rat, sheep, dog, and/or goat sequence. The non-bovine sequence can be within the ultralong CDR3. Alternatively, the non-bovine sequence is linked or attached to the ultralong CDR3 sequence. The non-bovine sequence can be derived from or based on at least a portion of an antibody sequence. The antibody sequence can encode a variable region, constant region or a combination thereof.
[00259] In another embodiment, the present disclosure provides libraries or arrays of antibodies comprising ultralong CDR3 sequences wherein at least two members of the library or array differ in having a cytoxic agent or therapeutic polypeptide that is conjugated to the ultralong CDR3. The cytoxic agent or therapeutic polypeptide may include, but is not limited to, a chemotherapeutic agent, a drug, a growth inhibitory agent, a toxin (e.g., an enzymatically active toxin of bacterial, fungal, plant, or animal origin, or fragments thereof), or a radioactive isotope (e.g., a radio conjugate). The cytotoxic agent or therapeutic polypeptide can be encoded by a non- antibody sequence.
[00260] In another embodiment, the present disclosure provides libraries or arrays of antibodies comprising ultralong CDR3 sequences wherein at least two members of the library or array differ in binding to targets. The target can be a protein target. The protein target can be a transmembrane protein target. Such transmembrane targets may include, but are not limited to, GPCRs, ion channels, transporters, and cell surface receptors.
[00261] The libraries or the arrays of the present disclosure may be in several formats well known in the art. The library or the array may be an addressable library or an addressable array. The library or array may be in display format, for example, the antibody sequences may be expressed on phage, ribosomes, mRNA, yeast, or mammalian cells.
Cells
[00262] The present disclosure provides cells comprising genetic sequences encoding antibodies comprising ultralong CDR3 sequences or portions thereof. The present disclosure provides cells comprising genetic sequences encoding antibodies comprising at least a portion of a knob domain or at least a portion of a knob domain of an ultralong CDR3 sequence.
[00263] The present disclosure provides cells comprising genetic sequences (e.g., genes, nucleic acids, polynucleotides) encoding an ultralong CDR3 or portion thereof. The present disclosure also provides cells comprising genetic sequences (e.g., genes, nucleic acids, polynucleotides) encoding the knob domain and/or knob domain of an ultralong CDR3. [00264] In an embodiment, the present disclosure provides cells expressing an antibody comprising an ultralong CDR3. The cells may be prokaryotic or eukaryotic, and an antibody comprising an ultralong CDR3 may be expressed on the cell surface or secreted into the media. When displayed on the cell surface an antibody preferentially contains a motif for insertion into the plasmid membrane such as a membrane spanning domain at the C-terminus or a lipid attachment site. For bacterial cells, an antibody comprising an ultralong CDR3 may be secreted into the periplasm. When the cells are eukaryotic, they may be transiently transfected with genetic sequences encoding an antibody comprising an ultralong CDR3. Alternatively, a stable cell line or stable pools may be created by transfecting or transducing genetic sequences encoding an antibody comprising an ultralong CDR3 by methods well known to those of skill in the art. Cells can be selected by fluorescence activated cell sorting (FACS) or through selection for a gene encoding drug resistance. Cells useful for producing antibodies comprising ultralong CDR3 sequences include prokaryotic cells like E. coli, eukaryotic cells like the yeasts Saccharomyces cerevisiae and Pichia pastoris, insect cells (e.g., Sf9, Hi5), Chinese hamster ovary (CHO) cells, monkey cells like COS-1, or human cells like HEK-293, HeLa, SP-1.
Library Methods
[00265] The present disclosure provides methods for making libraries comprising antibodies comprising ultralong CDR3 sequences. Methods for making libraries of spatially addressed libraries are described in WO 2010/054007. Methods of making libraries in yeast, phage, E. coli, or mammalian cells are well known in the art.
[00266] The present disclosure also provides methods of screening libraries of antibodies comprising ultralong CDR3 sequences.
Definitions
[00267] The terms "a," "an," "the" and similar referents used in the context of describing the exemplary embodiments (especially in the context of the following claims) are to be construed to cover both the singular and the plural, unless otherwise indicated herein or clearly contradicted by context. Recitation of ranges of values herein is merely intended to serve as a shorthand method of referring individually to each separate value falling within the range. Unless otherwise indicated herein, each individual value is incorporated into the specification as if it were individually recited herein. All methods described herein can be performed in any suitable order unless otherwise indicated herein or otherwise clearly contradicted by context. The use of any and all examples, or exemplary language {e.g., "such as") provided herein is intended merely to better illuminate the exemplary embodiments and does not pose a limitation on the scope of the exemplary embodiments otherwise claimed. No language in the specification should be construed as indicating any non- claimed element essential to the practice of the exemplary embodiments.
[00268] An "ultralong CDR3" or an "ultralong CDR3 sequence", used interchangeably herein, comprises a CDR3 or CDR3 sequence that is not derived from a human antibody sequence. An ultralong CDR3 may be 35 amino acids in length or longer, for example, 40 amino acids in length or longer, 45 amino acids in length or longer, 50 amino acids in length or longer, 55 amino acids in length or longer, or 60 amino acids in length or longer. The length of the ultralong CDR3 may include a non-antibody sequence. An ultralong CDR3 may comprise at least a portion of a knob domain and/or knob domain. An ultralong CDR3 may comprise a non-antibody sequence, including, for example, a cytokine, chemokine, growth factor or hormone sequence. Preferably, the ultralong CDR3 is a heavy chain CDR3 (CDR-H3 or CDRH3). Preferably, the ultralong CDR3 is a sequence derived from or based on a ruminant (e.g., bovine) sequence. An ultralong CDR3 may comprise at least 3 or more cysteine residues, for example, 4 or more cysteine residues, 6 or more cysteine residues, or 8 or more cysteine residues. An ultralong CDR3 may comprise one or more cysteine motifs. An ultralong CDR3 may comprise an amino acid sequence that is derived from or based on SEQ ID NOS: 23-44 or is encoded by a DNA sequence that is derived from or based on SEQ ID NOS: 2-22. A variable region that comprises an ultralong CDR3 may include an amino acid sequence that is derived from or based on SEQ ID NOS: 23-44 or is encoded by a DNA sequence that is derived from or based on SEQ ID NOS: 2-22. Such a sequence may be derived from or based on a bovine germline VH gene sequence. An ultralong CDR3 may comprise a sequence derived from or based on a non-human DH gene sequence (see, e.g., Koti, et al. (2010) Mol. Immunol. 47: 2119-2128). An ultralong CDR3 may comprise a sequence derived from or based on a JH sequence, (see e.g., Hosseini, et al. (2004) Int. Immunol. 16: 843-852). In an embodiment, an ultralong CDR3 may comprise a sequence derived from or based on a non-human VH sequence and/or a sequence derived from or based on a non-human DH sequence and/or a sequence derived from or based on a JH sequence, and optionally an additional sequence comprising two to six amino acids or more such as, for example, between the VH derived sequence and the DH derived sequence. In another embodiment, an ultralong CDR3 may comprise a sequence that is about 50% or more homologous to a sequence derived from or based on SEQ ID NOS: 23-44. For example, the ultralong CDR3 may comprise a sequence that is about 60%, 70%>, 80%), 85%o, 90%), 95%o, 97% or more homologous to a sequence derived from or based on SEQ ID NOS: 23-44. In another embodiment, an ultralong CDR3 may comprise a sequence that aligns to 5 or more amino acids to a sequence derived from or based SEQ ID NOS: 23-44. For example, the ultralong CDR3 may comprise a sequence that aligns to 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60 or more amino acids to a sequence derived from or based SEQ ID NOS: 23-44. In another embodiment, an ultralong CDR3 may comprise a sequence that comprises 5 or more consecutive amino acids to a sequence derived from or based SEQ ID NOS: 23-44. For example, the ultralong CDR3 may comprise a sequence that comprises 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60 or more consecutive amino acids to a sequence derived from or based SEQ ID NOS: 23-44. In another embodiment, an ultralong CDR3 may comprise a sequence that is about 50% or more homologous to a DNA sequence that is derived from or based on a SEQ ID NOS: 2-22. For example, the ultralong CDR3 may comprise a sequence that is about 60%, 70%, 80%, 85%, 90%, 95%, 97% or more homologous to a DNA sequence that is derived from or based on SEQ ID NOS: 2-22. In another embodiment, an ultralong CDR3 may comprise a sequence that aligns to 5 or more nucleic acids to a DNA sequence that is derived from or based SEQ ID NOS: 2-22. For example, the ultralong CDR3 may comprise a sequence that aligns to 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 80, 100, 120, 140, 150, 175, 200, 225, 250, 275, 300, 350, 400, 450, 500, 550, 600 or more nucleic acids to a DNA sequence that is derived from or based SEQ ID NOS: 2-22. In another embodiment, an ultralong CDR3 may comprise a sequence that comprises 5 or more consecutive nucleic acids to a DNA sequence that is derived from or based SEQ ID NOS: 2-22. For example, the ultralong CDR3 may comprise a sequence that comprises 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 80, 100, 120, 140, 150, 175, 200, 225, 250, 275, 300, 350, 400, 450, 500, 550, 600 or more consecutive amino acids to a DNA sequence that is derived from or based SEQ ID NOS: 2-22. In another embodiment, an ultralong CDR3 may comprise a sequence that is about 50% or more homologous to a sequence derived from or based on a knob domain sequence. For example, the ultralong CDR3 may comprise a sequence that is about 60%, 70%, 80%, 85%, 90%, 95%, 97% or more
homologous to a sequence derived from or based on a knob domain sequence. In another embodiment, an ultralong CDR3 may comprise a sequence that aligns to 5 or more amino acids to a sequence derived from or based a knob domain sequence. For example, the ultralong CDR3 may comprise a sequence that aligns to 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60 or more amino acids to a sequence derived from or based a knob domain sequence In another embodiment, an ultralong CDR3 may comprise a sequence that comprises 5 or more consecutive amino acids to a sequence derived from or based a knob domain sequence For example, the ultralong CDR3 may comprise a sequence that comprises 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60 or more consecutive amino acids to a sequence derived from or based a knob domain sequence. In another embodiment, an ultralong CDR3 may comprise a sequence that is about 50%> or more homologous to a sequence derived from or based on a knob domain sequence. For example, the ultralong CDR3 may comprise a sequence that is about 60%, 70%, 80%>, 85%, 90%, 95%, 97% or more homologous to a sequence derived from or based on a knob domain sequence. In another embodiment, an ultralong CDR3 may comprise a sequence that aligns to 5 or more amino acids to a sequence derived from or based a knob domain sequence For example, the ultralong CDR3 may comprise a sequence that aligns to 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60 or more amino acids to a sequence derived from or based a knob domain sequence In another embodiment, an ultralong CDR3 may comprise a sequence that comprises 5 or more consecutive amino acids to a sequence derived from or based a stalk domain sequence For example, the ultralong CDR3 may comprise a sequence that comprises 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60 or more consecutive amino acids to a sequence derived from or based a stalk domain sequence. The antibodies disclosed herein may comprise at least a portion of an ultralong CDR3 derived from or based on a sequence of any of the ultralong CDR3s disclosed herein. The sequence of the ultralong CDR3 or a portion thereof may be modified or altered to contain one or more non-bovine antibody-based nucleotides and/or amino acids. The modifications and/or alterations in the sequence of the ultralong CDR3 or portion therof may improve one or more features of the expressed antibody. For example, the modifications and/or alterations may improve expression, folding, half-life, activity and/or solubility of the antibody.
[00269] An "isolated" biological molecule, such as the various polypeptides,
polynucleotides, and antibodies disclosed herein, refers to a biological molecule that has been identified and separated and/or recovered from at least one component of its natural environment.
[00270] "Antagonist" refers to any molecule that partially or fully blocks, inhibits, or neutralizes an activity (e.g., biological activity) of a polypeptide. Also encompassed by
"antagonist" are molecules that fully or partially inhibit the transcription or translation of mRNA encoding the polypeptide. Suitable antagonist molecules include, e.g., antagonist antibodies or antibody fragments; fragments or amino acid sequence variants of a native polypeptide; peptides; antisense oligonucleotides; small organic molecules; and nucleic acids that encode polypeptide antagonists or antagonist antibodies. Reference to "an" antagonist encompasses a single antagonist or a combination of two or more different antagonists.
[00271] "Agonist" refers to any molecule that partially or fully mimics a biological activity of a polypeptide. Also encompassed by "agonist" are molecules that stimulate the transcription or translation of mRNA encoding the polypeptide. Suitable agonist molecules include, e.g., agonist antibodies or antibody fragments; a native polypeptide; fragments or amino acid sequence variants of a native polypeptide; peptides; antisense oligonucleotides; small organic molecules; and nucleic acids that encode polypeptides agonists or antibodies. Reference to "an" agonist encompasses a single agonist or a combination of two or more different agonists. [00272] An "isolated" antibody refers to one which has been identified and separated and/or recovered from a component of its natural environment. Contaminant components of its natural environment are materials which would interfere with diagnostic or therapeutic uses for the antibody, and may include enzymes, hormones, and other proteinaceous or nonproteinaceous solutes. In preferred embodiments, the antibody will be purified (1) to greater than 95% by weight of antibody (e.g., as determined by the Lowry method), and preferably to more than 99% by weight, (2) to a degree sufficient to obtain at least 15 residues of N-terminal or internal amino acid sequence (e.g., by use of a spinning cup sequenator), or (3) to homogeneity by SDS-PAGE under reducing or nonreducing conditions (e.g., using Coomassie™ blue or, preferably, silver stain). Isolated antibody includes the antibody in situ within recombinant cells since at least one component of the antibody's natural environment will not be present. Similarly, isolated antibody includes the antibody in medium around recombinant cells. An isolated antibody may be prepared by at least one purification step.
[00273] An "isolated" nucleic acid molecule refers to a nucleic acid molecule that is identified and separated from at least one contaminant nucleic acid molecule with which it is ordinarily associated in the natural source of the antibody nucleic acid. An isolated nucleic acid molecule is other than in the form or setting in which it is found in nature. Isolated nucleic acid molecules therefore are distinguished from the nucleic acid molecule as it exists in natural cells. However, an isolated nucleic acid molecule includes a nucleic acid molecule contained in cells that express an antibody where, for example, the nucleic acid molecule is in a chromosomal location different from that of natural cells.
[00274] Variable domain residue numbering as in Kabat or amino acid position numbering as in Kabat, and variations thereof, refers to the numbering system used for heavy chain variable domains or light chain variable domains of the compilation of antibodies in Kabat et al, Sequences of Proteins of Immunological Interest, 5th Ed. Public Health Service, National Institutes of Health, Bethesda, Md. (1991). Using this numbering system, the actual linear amino acid sequence may contain fewer or additional amino acids corresponding to a shortening of, or insertion into, a FR or CDR of the variable domain. For example, a heavy chain variable domain may include a single amino acid insert (e.g., residue 52a according to Kabat) after residue 52 of H2 and inserted residues (e.g., residues 82a, 82b, and 82c, etc according to Kabat) after heavy chain FR residue 82. The Kabat numbering of residues may be determined for a given antibody by alignment at regions of homology of the sequence of the antibody with a "standard" Kabat numbered sequence.
[00275] "Substantially similar," or "substantially the same", refers to a sufficiently high degree of similarity between two numeric values (generally one associated with an antibody disclosed herein and the other associated with a reference/comparator antibody) such that one of skill in the art would consider the difference between the two values to be of little or no biological and/or statistical significance within the context of the biological characteristic measured by said values (e.g., Kd values). The difference between said two values is preferably less than about 50%, preferably less than about 40%>, preferably less than about 30%>, preferably less than about 20%>, preferably less than about 10% as a function of the value for the reference/comparator antibody.
[00276] "Binding affinity" generally refers to the strength of the sum total of noncovalent interactions between a single binding site of a molecule (e.g., an antibody) and its binding partner (e.g., an antigen). Unless indicated otherwise, "binding affinity" refers to intrinsic binding affinity which reflects a 1 : 1 interaction between members of a binding pair (e.g., antibody and antigen). The affinity of a molecule X for its partner Y can generally be represented by the dissociation constant. Affinity can be measured by common methods known in the art, including those described herein. Low-affinity antibodies generally bind antigen slowly and tend to dissociate readily, whereas high-affinity antibodies generally bind antigen faster and tend to remain bound longer. A variety of methods of measuring binding affinity are known in the art, any of which can be used for purposes of the present disclosure.
[00277] An "on-rate" or "rate of association" or "association rate" or "kon" can be determined with a surface plasmon resonance technique such as Biacore (e.g., Biacore A100, Biacore™-2000, Biacore™-3000, Biacore, Inc., Piscataway, N.J.) carboxymethylated dextran biosensor chips (CM5, Biacore Inc.) and according to the supplier's instructions.
[00278] "Vector" refers to a nucleic acid molecule capable of transporting another nucleic acid to which it has been linked. One type of vector is a "plasmid", which refers to a circular double stranded DNA loop into which additional DNA segments may be ligated. Another type of vector is a phage vector. Another type of vector is a viral vector, wherein additional DNA segments may be ligated into the viral genome. Certain vectors are capable of autonomous replication in a host cell into which they are introduced (e.g., bacterial vectors having a bacterial origin of replication and episomal mammalian vectors). Other vectors (e.g., non-episomal mammalian vectors) can be integrated into the genome of a host cell upon introduction into the host cell, and thereby are replicated along with the host genome. Moreover, certain vectors are capable of directing the expression of genes to which they are operatively linked. Such vectors are referred to herein as "recombinant expression vectors" (or simply, "recombinant vectors"). In general, expression vectors of utility in recombinant DNA techniques are often in the form of plasmids. Accordingly, "plasmid" and "vector" may, at times, be used interchangeably as the plasmid is a commonly used form of vector. [00279] "Gene" refers to a nucleic acid (e.g., DNA) sequence that comprises coding sequences necessary for the production of a polypeptide, precursor, or R A (e.g., mR A, rR A, tR A). The polypeptide can be encoded by a full length coding sequence or by any portion of the coding sequence so long as the desired activity or functional properties (e.g., enzymatic activity, ligand binding, signal transduction, immunogenicity, etc.) of the full-length or fragment are retained. The term also encompasses the coding region of a structural gene and the sequences located adjacent to the coding region on both the 5' and 3' ends for a distance of about 1 kb or more on either end such that the gene corresponds to the length of the full-length mRNA. Sequences located 5' of the coding region and present on the mRNA are referred to as 5' non-translated sequences. Sequences located 3' or downstream of the coding region and present on the mRNA are referred to as 3' non-translated sequences. The term "gene" encompasses both cDNA and genomic forms of a gene. A genomic form or clone of a gene contains the coding region interrupted with non-coding sequences termed "introns" or "intervening regions" or "intervening sequences." Introns are segments of a gene that are transcribed into nuclear RNA (hnRNA); introns can contain regulatory elements such as enhancers. Introns are removed or "spliced out" from the nuclear or primary transcript; introns therefore are absent in the messenger RNA (mRNA) transcript. The mRNA functions during translation to specify the sequence or order of amino acids in a nascent polypeptide. In addition to containing introns, genomic forms of a gene can also include sequences located on both the 5' and 3' end of the sequences that are present on the RNA transcript. These sequences are referred to as "flanking" sequences or regions (these flanking sequences are located 5 ' or 3' to the non-translated sequences present on the mRNA transcript). The 5' flanking region can contain regulatory sequences such as promoters and enhancers that control or influence the transcription of the gene. The 3' flanking region can contain sequences that direct the termination of transcription, post transcriptional cleavage and polyadenylation.
[00280] "Polynucleotide," or "nucleic acid," as used interchangeably herein, refers to polymers of nucleotides of any length, and include DNA and RNA. The nucleotides can be deoxyribonucleotides, ribonucleotides, modified nucleotides or bases, and/or their analogs, or any substrate that can be incorporated into a polymer by DNA or RNA polymerase, or by a synthetic reaction. A polynucleotide may comprise modified nucleotides, such as methylated nucleotides and their analogs. If present, modification to the nucleotide structure may be imparted before or after assembly of the polymer. The sequence of nucleotides may be interrupted by non-nucleotide components. A polynucleotide may be further modified after synthesis, such as by conjugation with a label. Other types of modifications include, for example, "caps", substitution of one or more of the naturally occurring nucleotides with an analog, internucleotide modifications such as, for example, those with uncharged linkages (e.g., methyl phosphonates, phosphotriesters, phosphoamidates, carbamates, etc.) and with charged linkages (e.g., phosphorothioates, phosphorodithioates, etc.), those containing pendant moieties, such as, for example, proteins (e.g., nucleases, toxins, antibodies, signal peptides, poly-L-lysine, etc.), those with intercalators (e.g., acridine, psoralen, etc.), those containing chelators (e.g., metals, radioactive metals, boron, oxidative metals, etc.), those containing alkylators, those with modified linkages (e.g., alpha anomeric nucleic acids, etc.), as well as unmodified forms of the polynucleotide(s). Further, any of the hydroxyl groups ordinarily present in the sugars may be replaced, for example, by phosphonate groups, phosphate groups, protected by standard protecting groups, or activated to prepare additional linkages to additional nucleotides, or may be conjugated to solid or semi-solid supports. The 5' and 3' terminal OH can be phosphorylated or substituted with amines or organic capping group moieties of from 1 to 20 carbon atoms. Other hydroxyls may also be derivatized to standard protecting groups. Polynucleotides can also contain analogous forms of ribose or deoxyribose sugars that are generally known in the art, including, for example, 2'-0-methyl-, 2'-0-allyl, 2'- fluoro-or 2'-azido-ribose, carbocyclic sugar analogs, alpha-anomeric sugars, epimeric sugars such as arabinose, xyloses or lyxoses, pyranose sugars, furanose sugars, sedoheptuloses, acyclic analogs and a basic nucleoside analogs such as methyl riboside. One or more phosphodiester linkages may be replaced by alternative linking groups. These alternative linking groups include, but are not limited to, embodiments wherein phosphate is replaced by P(0)S("thioate"), P(S)S ("dithioate"), "(0)NR2 ("amidate"), P(0)R, P(0)OR*, CO or CH2 ("formacetal"), in which each R or R is independently H or substituted or unsubstituted alkyl (1-20 C) optionally containing an ether (-0-) linkage, aryl, alkenyl, cycloalkyl, cycloalkenyl or araldyl. Not all linkages in a polynucleotide need be identical. The preceding description applies to all polynucleotides referred to herein, including RNA and DNA.
[00281] "Oligonucleotide" refers to short, generally single stranded, generally synthetic polynucleotides that are generally, but not necessarily, less than about 200 nucleotides in length. The terms "oligonucleotide" and "polynucleotide" are not mutually exclusive. The description above for polynucleotides is equally and fully applicable to oligonucleotides.
[00282] "Stringent hybridization conditions" refer to conditions under which a probe will hybridize to its target subsequence, typically in a complex mixture of nucleic acids, but to no other sequences. Stringent conditions are sequence-dependent and will be different in different circumstances. Longer sequences hybridize specifically at higher temperatures. An extensive guide to the hybridization of nucleic acids is found in Tijssen, Techniques in Biochemistry and Molecular Biology—Hybridization with Nucleic Probes, "Overview of principles of hybridization and the strategy of nucleic acid assays" (1993). Generally, stringent conditions are selected to be about 5- 10°C lower than the thermal melting point (Tm) for the specific sequence at a defined ionic strength pH. The Tm is the temperature (under defined ionic strength, pH, and nucleic concentration) at which 50% of the probes complementary to the target hybridize to the target sequence at equilibrium (as the target sequences are present in excess, at Tm, 50% of the probes are occupied at equilibrium). Stringent conditions may also be achieved with the addition of destabilizing agents such as formamide. For selective or specific hybridization, a positive signal is at least two times background, preferably 10 times background hybridization. Exemplary stringent hybridization conditions can be as following: 50%> formamide, 5xSSC, and 1% SDS, incubating at 42° C, or, 5xSSC, 1% SDS, incubating at 65° C, with wash in 0.2xSSC, and 0.1% SDS at 65° C.
[00283] "Recombinant" when used with reference to a cell, nucleic acid, protein, antibody or vector indicates that the cell, nucleic acid, protein or vector has been modified by the introduction of a heterologous nucleic acid or protein, the alteration of a native nucleic acid or protein, or that the cell is derived from a cell so modified. For example, recombinant cells express genes that are not found within the native (non-recombinant) form of the cell or express native genes that are overexpressed or otherwise abnormally expressed such as, for example, expressed as non-naturally occurring fragments or splice variants. By the term "recombinant nucleic acid" herein is meant nucleic acid, originally formed in vitro, in general, by the manipulation of nucleic acid, e.g., using polymerases and endonucleases, in a form not normally found in nature. In this manner, operably linkage of different sequences is achieved. Thus an isolated nucleic acid, in a linear form, or an expression vector formed in vitro by ligating DNA molecules that are not normally joined, are both considered recombinant for the purposes of this disclosure. It is understood that once a recombinant nucleic acid is made and introduced into a host cell or organism, it will replicate non- recombinantly, e.g., using the in vivo cellular machinery of the host cell rather than in vitro manipulations; however, such nucleic acids, once produced recombinantly, although subsequently replicated non-recombinantly, are still considered recombinant for the purposes disclosed herein. Similarly, a "recombinant protein" is a protein made using recombinant techniques, e.g., through the expression of a recombinant nucleic acid as depicted herein.
[00284] "Percent (%) amino acid sequence identity" with respect to a peptide or polypeptide sequence refers to 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 MegAlign (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.
[00285] "Polypeptide," "peptide," "protein," and "protein fragment" may be used
interchangeably to refer to a polymer of amino acid residues. The terms apply to amino acid polymers in which one or more amino acid residue is an artificial chemical mimetic of a
corresponding naturally occurring amino acid, as well as to naturally occurring amino acid polymers and non-naturally occurring amino acid polymers.
[00286] "Amino acid" refers to naturally occurring and synthetic amino acids, as well as amino acid analogs and amino acid mimetics that function similarly to the naturally occurring amino acids. Naturally occurring amino acids are those encoded by the genetic code, as well as those amino acids that are later modified, e.g., hydroxyproline, gamma-carboxyglutamate, and O- phospho serine. Amino acid analogs refers to compounds that have the same basic chemical structure as a naturally occurring amino acid, e.g., an alpha carbon that is bound to a hydrogen, a carboxyl group, an amino group, and an R group, e.g., homoserine, norleucine, methionine sulfoxide, methionine methyl sulfonium. Such analogs can have modified R groups {e.g., norleucine) or modified peptide backbones, but retain the same basic chemical structure as a naturally occurring amino acid. Amino acid mimetics refers to chemical compounds that have a structure that is different from the general chemical structure of an amino acid, but that functions similarly to a naturally occurring amino acid.
[00287] "Conservatively modified variants" applies to both amino acid and nucleic acid sequences. "Amino acid variants" refers to amino acid sequences. With respect to particular nucleic acid sequences, conservatively modified variants refers to those nucleic acids which encode identical or essentially identical amino acid sequences, or where the nucleic acid does not encode an amino acid sequence, to essentially identical or associated {e.g., naturally contiguous) sequences. Because of the degeneracy of the genetic code, a large number of functionally identical nucleic acids encode most proteins. For instance, the codons GCA, GCC, GCG and GCU all encode the amino acid alanine. Thus, at every position where an alanine is specified by a codon, the codon can be altered to another of the corresponding codons described without altering the encoded polypeptide. Such nucleic acid variations are "silent variations," which are one species of conservatively modified variations. Every nucleic acid sequence herein which encodes a
polypeptide also describes silent variations of the nucleic acid. One of skill will recognize that in certain contexts each codon in a nucleic acid (except AUG, which is ordinarily the only codon for methionine, and TGG, which is ordinarily the only codon for tryptophan) can be modified to yield a functionally identical molecule. Accordingly, silent variations of a nucleic acid which encodes a polypeptide is implicit in a described sequence with respect to the expression product, but not with respect to actual probe sequences. As to amino acid sequences, one of skill will recognize that individual substitutions, deletions or additions to a nucleic acid, peptide, polypeptide, or protein sequence which alters, adds or deletes a single amino acid or a small percentage of amino acids in the encoded sequence is a "conservatively modified variant" including where the alteration results in the substitution of an amino acid with a chemically similar amino acid. Conservative substitution tables providing functionally similar amino acids are well known in the art. Such conservatively modified variants are in addition to and do not exclude polymorphic variants, interspecies homo logs, and alleles disclosed herein. Typically conservative substitutions include: 1) Alanine (A), Glycine (G); 2) Aspartic acid (D), Glutamic acid (E); 3) Asparagine (N), Glutamine (Q); 4) Arginine (R), Lysine (K); 5) Isoleucine (I), Leucine (L), Methionine (M), Valine (V); 6)
Phenylalanine (F), Tyrosine (Y), Tryptophan (W); 7) Serine (S), Threonine (T); and 8) Cysteine (C), Methionine (M) (see, e.g., Creighton, Proteins (1984)).
[00288] "Antibodies" (Abs) and "immunoglobulins" (Igs) are glycoproteins having similar structural characteristics. While antibodies may exhibit binding specificity to a specific antigen, immunoglobulins may include both antibodies and other antibody-like molecules which generally lack antigen specificity. Polypeptides of the latter kind are, for example, produced at low levels by the lymph system and at increased levels by myelomas.
[00289] "Antibody", "immunoglobulin" and "immunoglobulin construct" are used interchangeably in the broadest sense and include monoclonal antibodies {e.g., full length or intact monoclonal antibodies), polyclonal antibodies, multivalent antibodies, multispecific antibodies {e.g., bispecific antibodies so long as they exhibit the desired biological activity) and may also include certain antibody fragments (as described in greater detail herein). The term "antibody" can refer to a full length antibody or a portion thereof. An antibody can refer to a peptide comprising at least one antibody sequence. The antibody sequence can comprise 5 or more amino acids of an antibody sequence. For example the antibody sequence can comprise 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more amino acids of an antibody sequence. The 5 or more amino acids may be consecutive amino acids of an antibody sequence. Alternatively, the 5 or more amino acids are non-consecutive amino acids of an antibody sequence. For example, the 5 or more amino acids may comprise a conserved motif within the antibody sequence. For example, the 5 or more amino acids may comprise a conserved motif within an ultralong CDR3 sequence. An antibody can be human, humanized, fully human and/or affinity matured. An antibody can be a chimeric antibody. An antibody can be a recombinant, engineered, or synthetic antibody. An antibody may be a bovine, bovine engineered, fully bovine and/or affinity matured. The bovine engineered antibody may comprise one or more nucleotides or peptides derived from a bovine antibody sequence. A fully bovine antibody may comprise replacing one or more nucleotides or peptides from a non- bovine antibody sequence with one or more nucleotides or peptides based on a bovine antibody sequence. An antibody may refer to immunoglobulins and immunoglobulin portions, whether natural or partially or wholly synthetic, such as recombinantly produced, including any portion thereof containing at least a portion of the variable region of the immunoglobulin molecule that is sufficient to form an antigen binding site. Hence, an antibody or portion thereof includes any protein having a binding domain that is homologous or substantially homologous to an
immunoglobulin antigen binding site. For example, an antibody may refer to an antibody that contains two heavy chains (which can be denoted H and FT) and two light chains (which can be denoted L and L'), where each heavy chain can be a full-length immunoglobulin heavy chain or a portion thereof sufficient to form an antigen binding site (e.g. heavy chains include, but are not limited to, VH, chains VH-CH1 chains and VH-CH1-CH2-CH3 chains), and each light chain can be a full-length light chain or a thereof sufficient to form an antigen binding site (e.g. light chains include, but are not limited to, VL chains and VL-CL chains). Each heavy chain (H and FT) pairs with one light chain (L and L', respectively). Typically, antibodies minimally include all or at least a portion of the variable heavy (VH) chain and/or the variable light (VL) chain. The antibody also can include all or a portion of the constant region. For example, a full-length antibody is an antibody having two full-length heavy chains (e.g. VH-CH 1 -CH2-CH3 or VH-CH1-CH2-CH3- CH4) and two full-length light chains (VL-CL) and hinge regions, such as antibodies produced by antibody secreting B cells and antibodies with the same domains that are produced synthetically. Additionally, an "antibody" refers to a protein of the immunoglobulin family or a polypeptide comprising fragments of an immunoglobulin that is capable of noncovalently, reversibly, and in a specific manner binding a corresponding antigen. An exemplary antibody structural unit comprises a tetramer. Each tetramer is composed of two identical pairs of polypeptide chains, each pair having one "light" (about 25 kD) and one "heavy" chain (about 50-70 kD), connected through a disulfide bond. The recognized immunoglobulin genes include the κ, λ, α, γ, δ, ε, and μ constant region genes, as well as the myriad immunoglobulin variable region genes. Light chains are classified as either κ or λ. Heavy chains are classified as γ, μ, α, δ, or ε, which in turn define the
immunoglobulin classes, IgG, IgM, IgA, IgD, and IgE, respectively. The N-terminus of each chain defines a variable region of about 100 to 1 10 or more amino acids primarily responsible for antigen recognition. The terms variable light chain (VL) and variable heavy chain (VH) refer to these regions of light and heavy chains respectively. In some instances, the antibodies provided herein comprise at least one immunoglobulin domain from an avian antibody, reptilian antibody, amphibian antibody, insect antibody, or chimeric combinations thereof. The antibodies can comprise at least one immunoglobulin domain from a chimeric antibody. The chimeric antibody can be derived from two or more different species (e.g., mouse and human, bovine and human). The antibodies can comprise at least one immunoglobulin domain from an engineered, recombinant or synthetic antibody. In some instances, engineered, recombinant or synthetic antibodies are created using antibody genes made in a laboratory or taken from cells. The antibody genes can be derived from one or more mammals. For example, the antibody genes are derived from a human. The antibody genes may be derived from a bovine. Alternatively, or additionally, the antibodies disclosed herein comprise at least one immunoglobulin domain from a humanized, human engineered or fully human antibody. The antibody may comprise antibody sequences from two or more different antibodies. The two or more different antibodies may be from the same species. For example, the specie may be a bovine specie, human specie, or murine specie. The two or more different antibodies may be from the same type of animal. For example the two or more different antibodies may be from a cow. The two or more different antibodies may be from a human.
Alternatively, the two or more different antibodies are from different species. For example, the two or more different antibodies are from a human specie and bovine specie. In another example, the two or more diffent antibodies are from a bovine specie and a non-bovine specie. In another example, the two or more different antibodies are from a human specie and a non-human specie. The two or more different antibodies may be from different animals. For example, the two different animals are a human and a cow. The different animals may be from the same specie. For example, the different animals may be a cow and a water buffalo.
[00290] "Variable" refers to the fact that certain portions of the variable domains (also referred to as variable regions) differ extensively in sequence among antibodies and are used in the binding and specificity of each particular antibody for its particular antigen. However, the variability is not evenly distributed throughout the variable domains of antibodies. It is
concentrated in three segments called complementarity-determining regions (CDRs) or
hypervariable regions (HVRs) both in the light-chain and the heavy-chain variable domains. CDRs include those specified as Kabat, Chothia, and IMGT as shown herein within the variable region sequences. The more highly conserved portions of variable domains are called the framework (FR). The variable domains of native heavy and light chains each comprise four FR regions, largely adopting a β-sheet configuration, connected by three CDRs, which form loops connecting, and in some cases forming part of, the β-sheet structure. The CDRs in each chain are held together in close proximity by the FR regions and, with the CDRs from the other chain, contribute to the formation of the antigen-binding site of antibodies (see Kabat et al., Sequences of Proteins of Immunological Interest. Fifth Edition, National Institute of Health, Bethesda, Md. (1991)). The constant domains are not involved directly in binding an antibody to an antigen, but exhibit various effector functions, such as participation of the antibody in antibody-dependent cellular toxicity.
[00291] Papain digestion of antibodies produces two identical antigen-binding fragments, called "Fab" fragments, each with a single antigen-binding site, and a residual "Fc" fragment, whose name reflects its ability to crystallize readily. Pepsin treatment yields an F(ab')2 fragment that has two antigen-combining sites and is still capable of cross-linking antigen.
[00292] "Fv" refers to an antibody fragment which contains an antigen-recognition and antigen-binding site. In a two-chain Fv species, this region consists of a dimer of one heavy and one light chain variable domain in non-covalent association. In a single chain Fv (scFv) species, one heavy chain and one light chain variable domain can be covalently linked by a flexible peptide linker such that the light and heavy chains can associate in a "dimeric" structure analogous to that in a two-chain Fv (scFv) species. It is in this configuration that the three CDRs of each variable domain interact to define an antigen-binding site on the surface of the VH-VL dimer. Collectively, the six CDRs confer antigen-binding specificity to the antibody. However, even a single variable domain (or half of an Fv comprising only three CDRs specific for an antigen) has the ability to recognize and bind antigen, although at a lower affinity than the entire binding site.
[00293] The Fab fragment also contains the constant domain of the light chain and the first constant domain (CHI) of the heavy chain. Fab' fragments differ from Fab fragments by the addition of a few residues at the carboxy terminus of the heavy chain CHI domain including one or more cysteines from the antibody hinge region. Fab'-SH is the designation herein for Fab' in which the cysteine residue(s) of the constant domains bear a free thiol group. F(ab')2 antibody fragments originally were produced as pairs of Fab' fragments which have hinge cysteines between them. Other chemical couplings of antibody fragments are also known.
[00294] The "light chains" of antibodies (immunoglobulins) from any vertebrate species can be assigned to one of two clearly distinct types, called kappa (κ) and lambda (λ), based on the amino acid sequences of their constant domains.
[00295] Depending on the amino acid sequence of the constant domain of their heavy chains, immunoglobulins can be assigned to different classes. There are five major classes of
immunoglobulins: IgA, IgD, IgE, IgG, and IgM, and several of these can be further divided into subclasses (isotypes), e.g., IgGi, IgG2, IgG3, IgG4, IgAi, and IgA2. The heavy-chain constant domains that correspond to the different classes of immunoglobulins are called α, δ, ε, γ, and μ, respectively. The subunit structures and three-dimensional configurations of different classes of immunoglobulins are well known.
[00296] "Antibody fragments" comprise only a portion of an intact antibody, wherein the portion preferably retains at least one, preferably most or all, of the functions normally associated with that portion when present in an intact antibody. Examples of antibody fragments include Fab, Fab', F(ab')2, single-chain Fvs (scFv), Fv, dsFv, diabody (e.g., (ds Fv)2), Fd and Fd' fragments Fab fragments, Fd fragments, scFv fragments, linear antibodies, single-chain antibody molecules, minibodies, flex minibodies, bispecific fragments, and multispecific antibodies formed from antibody fragments (see, for example, Methods in Molecular Biology, Vol 207: Recombinant Antibodies for Cancer Therapy Methods and Protocols (2003); Chapter 1; p 3-25, Kipriyanov). Other known fragments include, but are not limited to, scFab fragments (Hust et al, BMC
Biotechnology (2007), 7: 14). In one embodiment, an antibody fragment comprises an antigen binding site of the intact antibody and thus retains the ability to bind antigen. In another
embodiment, an antibody fragment, for example one that comprises the Fc region, retains at least one of the biological functions normally associated with the Fc region when present in an intact antibody, such as FcRn binding, antibody half life modulation, ADCC function and complement binding. In one embodiment, an antibody fragment is a monovalent antibody that has an in vivo half life substantially similar to an intact antibody. For example, such an antibody fragment may comprise on antigen binding arm linked to an Fc sequence capable of conferring in vivo stability to the fragment. For another example, an antibody fragment or antibody portion refers to any portion of a full-length antibody that is less than full length but contains at least a portion of the variable region of the antibody sufficient to form an antigen binding site (e.g. one or more CDRs) and thus retains the a binding specificity and/or an activity of the full-length antibody; antibody fragments include antibody derivatives produced by enzymatic treatment of full-length antibodies, as well as synthetically, e.g. recombinantly produced derivatives.
[00297] A "dsFv" refers to an Fv with an engineered intermolecular disulfide bond, which stabilizes the VH-VL pair.
[00298] A "Fd fragment" refers to a fragment of an antibody containing a variable domain
(VH) and one constant region domain (CHI) of an antibody heavy chain.
[00299] A "Fab fragment" refers to an antibody fragment that contains the portion of the full-length antibody that would results from digestion of a full-length immunoglobulin with papain, or a fragment having the same structure that is produced synthetically, e.g. recombinantly. A Fab fragment contains a light chain (containing a VL and CL portion) and another chain containing a variable domain of a heavy chain (VH) and one constant region domain portion of the heavy chain (CHI); it can be recombinantly produced.
[00300] A "F(ab')2 fragment" refers to an antibody fragment that results from digestion of an immunoglobulin with pepsin at pH 4.0-4.5, or a synthetically, e.g. recombinantly, produced antibody having the same structure. The F(ab')2 fragment contains two Fab fragments but where each heavy chain portion contains an additional few amino acids, including cysteine residues that form disulfide linkages joining the two fragments; it can be recombinantly produced.
[00301] A "Fab' fragment" refers to a fragment containing one half (one heavy chain and one light chain) of the F(ab')2 fragment.
[00302] A "Fd' fragment refers to a fragment of an antibody containing one heavy chain portion of a F(ab')2 fragment.
[00303] A "Fv' fragment" refers to a fragment containing only the VH and VL domains of an antibody molecule.
[00304] A "scFv fragment" refers to an antibody fragment that contains a variable light chain
(VL) and variable heavy chain (VH), covalently connected by a polypeptide linker in any order. The linker is of a length such that the two variable domains are bridged without substantial interference. Exemplary linkers are (Gly-Ser)n residues with some Glu or Lys residues dispersed throughout to increase solubility.
[00305] Diabodies are dimeric scFv; diabodies typically have shorter peptide linkers than scFvs, and they preferentially dimerize.
[00306] "HsFv" refers to antibody fragments in which the constant domains normally present in a Fab fragment have been substituted with a heterodimeric coiled-coil domain (see, e.g., Arndt et al. (2001) J Mol Biol. 7:312:221-228).
[00307] "Hypervariable region", "HVR", or "HV", as well as "complementary determing region" or "CDR", may refer to the regions of an antibody variable domain which are hypervariable in sequence and/or form structurally defined loops. Generally, antibodies comprise six
hypervariable or CDR regions; three in the VH (HI, H2, H3), and three in the VL (LI, L2, L3). A number of hypervariable region or CDR delineations are in use and are encompassed herein. The Kabat Complementarity Determining Regions (Kabat CDRs) are based on sequence variability and are the most commonly used (Kabat et al., Sequences of Proteins of Immunological Interest. 5th Ed. Public Health Service, National Institutes of Health, Bethesda, Md. (1991)). Chothia refers instead to the location of the structural loops (Chothia and Lesk, J. Mol. Biol. 196:901-917 (1987)). The AbM hypervariable regions represent a compromise between the Kabat CDRs and Chothia structural loops, (Chothia "CDRs") and are used by Oxford Molecular's AbM antibody modeling software. The "contact" hypervariable regions are based on an analysis of the available complex crystal structures. The residues from each of these hypervariable regions are noted below. (See also, for example, Figure 1 and bold, italicized text for Kabat CDRs and underlined text for Chothia CDRs for 12.3 ICI antibody).
Loop Kabat AbM Chothia Contact
LI L24-L34 L24-L34 L26-L32 L30-L36
L2 L50-L56 L50-L56 L50-L52 L46-L55
L3 L89-L97 L89-L97 L91-L96 L89-L96
HI H31-H35B H26-H35B H26-H32 H30-H35B
(Kabat Numbering)
HI H31-H35 H26-H35 H26-H32 H30-H35
(Chothia Numbering)
H2 H50-H65 H50-H58 H53-H55 H47-H58
H3 H95-H102 H95-H102 H96-H101 H93-H101
[00308] IMGT referes to the international ImMunoGeneTics Information System, as described by Lefrace et ah, Nucl. Acids, Res. 37; D1006-D1012 (2009), including for example, IMGT designated CDRs for antibodies (see also, for example, Figure 1 and bracketed text for 12.3 1C1 antibody).
[00309] Hypervariable regions may comprise "extended hypervariable regions" as follows:
24-36 or 24-34 (LI), 46-56 or 50-56 (L2) and 89-97 (L3) in the VL and 26-35 (HI), 50-65 or 49-65 (H2) and 93-102, 94-102 or 95-102 (H3) in the VH. The variable domain residues are numbered according to Kabat et ah, Supra for each of these definitions.
[00310] "Framework" or "FR" residues are those variable domain residues other than the hypervariable region residues as herein defined. "Framework regions" (FRs) are the domains within the antibody variable region domains comprising framework residues that are located within the beta sheets; the FR regions are comparatively more conserved, in terms of their amino acid sequences, than the hypervariable regions.
[00311] "Monoclonal antibody" refers to an antibody from a population of substantially homogeneous antibodies, that is, for example, the individual antibodies comprising the population are identical and/or bind the same epitope(s), except for possible variants that may arise during production of the monoclonal antibody, such variants generally being present in minor amounts. Such monoclonal antibody typically includes an antibody comprising a polypeptide sequence that binds a target, wherein the target-binding polypeptide sequence was obtained by a process that includes the selection of a single target binding polypeptide sequence from a plurality of polypeptide sequences. For example, the selection process can be the selection of a unique clone from a plurality of clones, such as a pool of hybridoma clones, phage clones or recombinant DNA clones. It should be understood that the selected target binding sequence can be further altered, for example, to improve affinity for the target, to humanize the target binding sequence, to improve its production in cell culture, to reduce its immunogenicity in vivo, to create a multispecific antibody, etc., and that an antibody comprising the altered target binding sequence is also a monoclonal antibody of this disclosure. In contrast to polyclonal antibody preparations which typically include different antibodies directed against different determinants {e.g., epitopes), each monoclonal antibody of a monoclonal antibody preparation is directed against a single determinant on an antigen. In addition to their specificity, the monoclonal antibody preparations are advantageous in that they are typically uncontaminated by other immunoglobulins. 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. For example, the monoclonal antibodies to be used in accordance with the present disclosure may be made by a variety of techniques, including, for example, the hybridoma method {e.g., Kohler et al, Nature, 256:495 (1975); Harlow et al, Antibodies: A Laboratory Manual, (Cold Spring Harbor Laboratory Press, 2nd ed. 1988); Hammerling et al., in: Monoclonal Antibodies and T-Cell Hybridomas 563-681, (Elsevier, N.Y., 1981)), recombinant DNA methods (see, e.g., U.S. Patent No. 4,816,567), phage display technologies (see, e.g., Clackson et al, Nature, 352:624-628 (1991); Marks et al, J. Mol. Biol, 222:581-597 (1991); Sidhu et al, J. Mol. Biol. 338(2):299-310 (2004); Lee et al, J. Mol. Biol. 340(5): 1073-1093 (2004); Fellouse, Proc. Nat. Acad. Sci. USA 101(34): 12467-12472 (2004); and Lee et al. J. Immunol. Methods 284(1-2): 119- 132 (2004), and technologies for producing human or human- like antibodies in animals that have parts or all of the human immunoglobulin loci or genes encoding human immunoglobulin sequences (see, e.g., WO 1998/24893; WO 1996/34096; WO 1996/33735; WO 1991/10741; Jakobovits et al, Proc. Natl. Acad. Sci. USA, 90:2551 (1993); Jakobovits et al, Nature, 362:255- 258 (1993); Bruggemann et al, Year in Immuno., 7:33 (1993); U.S. Patent Nos. 5,545,806;
5,569,825; 5,591,669; 5,545,807; WO 1997/17852; U.S. Patent Nos. 5,545,807; 5,545,806;
5,569,825; 5,625,126; 5,633,425; and 5,661,016; Marks et al, Bio/Technology, 10: 779-783 (1992); Lonberg et al, Nature, 368: 856-859 (1994); Morrison, Nature, 368: 812-813 (1994);
Fishwild et al, Nature Biotechnology, 14: 845-851 (1996); Neuberger, Nature Biotechnology, 14: 826 (1996); and Lonberg and Huszar, Intern. Rev. Immunol, 13: 65-93 (1995)).
[00312] "Humanized" or "Human engineered" forms of non- human {e.g., murine, bovine) antibodies are chimeric antibodies that contain amino acids represented in human immunoglobulin sequences, including, for example, wherein minimal sequence is derived from non-human immunoglobulin. For example, humanized antibodies may be human antibodies in which some hypervariable region residues and possibly some FR residues are substituted by residues from analogous sites in non-human {e.g., rodent) antibodies. Alternatively, humanized or human engineered antibodies may be non-human {e.g., rodent) antibodies in which some residues are substituted by residues from analogious sites in human antibodies (see, e.g., U.S. Patent No.
5,766,886). Humanized antibodies include human immunoglobulins (recipient antibody) in which residues from a hypervariable region of the recipient are replaced by residues from a hypervariable region of a non-human species (donor antibody) such as mouse, rat, rabbit or nonhuman primate having the desired specificity, affinity, and capacity. In some instances, framework region (FR) residues of the human immunoglobulin are replaced by corresponding non-human residues.
Furthermore, humanized antibodies may comprise residues that are not found in the recipient antibody or in the donor antibody, including, for example non-antibody sequences such as a chemokine, growth factor, peptide, cytokine, cell surface protein, serum protein, toxin, extracellular matrix protein, clotting factor, or secreted protein sequence. These modifications may be made to further refine antibody performance. Humanized antibodies include human engineered antibodies, for example, as described by U.S. Patent No. 5,766,886, including methods for preparing modified antibody variable domains. A humanized antibody may comprise substantially all of at least one, and typically two, variable domains, in which all or substantially all of the hypervariable loops correspond to those of a non-human immunoglobulin and all or substantially all of the FRs are those of a human immunoglobulin sequence. A humanized antibody optionally may also comprise at least a portion of an immunoglobulin constant region (Fc), typically that of a human
immunoglobulin. For further details, see Jones et al, Nature 321 :522-525 (1986); Riechmann et al, Nature 332:323-329 (1988); and Presta, Curr. Op. Struct. Biol. 2:593-596 (1992). See also the following review articles and references cited therein: Vaswani and Hamilton, Ann. Allergy, Asthma & Immunol. 1 : 105-115 (1998); Harris, Biochem. Soc. Transactions 23: 1035-1038 (1995); Hurle and Gross, Curr. Op. Biotech. 5:428-433 (1994).
[00313] "Hybrid antibodies" refer to immunoglobulin molecules in which pairs of heavy and light chains from antibodies with different antigenic determinant regions are assembled together so that two different epitopes or two different antigens can be recognized and bound by the resulting tetramer.
[00314] "Chimeric" antibodies (immunoglobulins) have a portion of the heavy and/or light chain identical with or homologous to corresponding sequences in antibodies derived from a particular species or belonging to a particular antibody class or subclass, while the remainder of the chain(s) is identical with or homologous to corresponding sequences in antibodies derived from another species or belonging to another antibody class or subclass, as well as fragments of such antibodies, so long as they exhibit the desired biological activity (see e.g., Morrison et ah, Proc. Natl. Acad. Sci. USA 81 :6851-6855 (1984)). Humanized antibody refers to a subset of chimeric antibodies.
[00315] "Single-chain Fv" or "scFv" antibody fragments may comprise the VH and VL domains of antibody, wherein these domains are present in a single polypeptide chain. Generally, the scFv polypeptide further comprises a polypeptide linker between the VH and VL domains which enables the scFv to form the desired structure for antigen binding. For a review of scFv, see e.g., Pluckthun, in The Pharmacology of Monoclonal Antibodies, vol. 113, Rosenburg and Moore eds., Springer- Verlag, New York, pp. 269-315 (1994).
[00316] An "antigen" refers to a predetermined antigen to which an antibody can selectively bind. The target antigen may be polypeptide, carbohydrate, nucleic acid, lipid, hapten or other naturally occurring or synthetic compound. Preferably, the target antigen is a polypeptide.
[00317] "Epitope" or "antigenic determinant", used interchangeably herein, refer to that portion of an antigen capable of being recognized and specifically bound by a particular antibody. When the antigen is a polypeptide, epitopes can be formed both from contiguous amino acids and noncontiguous amino acids juxtaposed by tertiary folding of a protein. Epitopes formed from contiguous amino acids are typically retained upon protein denaturing, whereas epitopes formed by tertiary folding are typically lost upon protein denaturing. An epitope typically includes at least 3, and more usually, at least 5 or 8-10 amino acids in a unique spatial conformation. Antibodies may bind to the same or a different epitope on an antigen. Antibodies may be characterized in different epitope bins. Whether an antibody binds to the same or different epitope as another antibody {e.g., a reference antibody or benchmark antibody) may be determined by competition between antibodies in assays {e.g., competitive binding assays). [00318] Competition between antibodies may be determined by an assay in which the immunoglobulin under test inhibits specific binding of a reference antibody to a common antigen. Numerous types of competitive binding assays are known, for example: solid phase direct or indirect radioimmunoassay (RIA), solid phase direct or indirect enzyme immunoassay or enzyme- linked immunosorbent assay (EIA or ELISA), sandwich competition assay including an ELISA assay (see Stahli et al, Methods in Enzymology 9:242-253 (1983)); solid phase direct biotin-avidin EIA (see Kirkland et al., J. Immunol. 137:3614-3619 (1986)); solid phase direct labeled assay, solid phase direct labeled sandwich assay (see Harlow and Lane, "Antibodies, A Laboratory Manual," Cold Spring Harbor Press (1988)); solid phase direct label RIA using 1-125 label (see Morel et al., Molec. Immunol. 25(1):7-15 (1988)); solid phase direct biotin-avidin EIA (Cheung et al., Virology 176:546-552 (1990)); and direct labeled RIA (Moldenhauer et al, Scand. J. Immunol, 32:77-82 (1990)). Competition binding assays may be performed using Surface Plasmon Resonance (SPR), for example, with a Biacore® instrument for kinetic analysis of binding interactions. In such an assay, an antibody comprising an ultralong CDR3 of unknown epitope specificity may be evaluated for its ability to compete for binding against a comparator antibody (e.g., a BA1 or BA2 antibody as described herein). An assay may involve the use of purified antigen bound to a solid surface or cells bearing either of these, an unlabeled test immunoglobulin and a labeled reference
immunoglobulin. Competitive inhibition may be measured by determining the amount of label bound to the solid surface or cells in the presence of the test immunoglobulin. Usually the test immunoglobulin is present in excess. An assay (competing antibodies) may include antibodies binding to the same epitope as the reference antibody and antibodies binding to an adjacent epitope sufficiently proximal to the epitope bound by the reference antibody for steric hindrance to occur. Usually, when a competing antibody is present in excess, it will inhibit specific binding of a reference antibody to a common antigen by at least 50%, or at least about 70%, or at least about 80%), or least about 90%>, or at least about 95%>, or at least about 99%> or about 100% for a competitor antibody.
[00319] That an antibody "selectively binds" or "specifically binds" means that the antibody reacts or associates more frequently, more rapidly, with greater duration, with greater affinity, or with some combination of the above to an antigen or an epitope than with alternative substances, including unrelated proteins. "Selectively binds" or "specifically binds" may mean, for example, that an antibody binds to a protein with a KD of at least about 0.1 mM, or at least about 1 μΜ or at least about 0.1 μΜ or better, or at least about 0.01 μΜ or better. Because of the sequence identity between homologous proteins in different species, specific binding can include an antibody that recognizes a given antigen in more than one species. [00320] "Non-specific binding" and "background binding" when used in reference to the interaction of an antibody and a protein or peptide refer to an interaction that is not dependent on the presence of a particular structure (e.g., the antibody is binding to proteins in general rather that a particular structure such as an epitope).
[00321] "Diabodies" refer to small antibody fragments with two antigen-binding sites, which fragments comprise a heavy-chain variable domain (VH) connected to a light-chain variable domain (VL) in the same polypeptide chain (VH-VL). By using a linker that is too short to allow pairing between the two domains on the same chain, the domains are forced to pair with the complementary domains of another chain and create two antigen-binding sites. Diabodies are described more fully in, for example, EP 404,097; WO 93/11161 ; and Hollinger et. al, Proc. Natl. Acad. Sci. USA, 90:6444-6448 (1993).
[00322] A "human antibody" refers to one which possesses an amino acid sequence which corresponds to that of an antibody produced by a human and/or has been made using any of the techniques for making human antibodies as disclosed herein. This definition of a human antibody specifically excludes a humanized antibody comprising non-human antigen-binding residues.
[00323] An "affinity matured" antibody refers to one with one or more alterations in one or more CDRs thereof which result in an improvement in the affinity of the antibody for antigen, compared to a parent antibody which does not possess those alteration(s). Preferred affinity matured antibodies will have nanomolar or even picomolar affinities for the target antigen. Affinity matured antibodies are produced by procedures known in the art. Marks et al, Bio/Technology 10:779-783 (1992) describes affinity maturation by VH and VL domain shuffling. Random mutagenesis of CDR and/or framework residues is described by: Barbas et al, Proc Nat. Acad. Sci. USA 91 :3809-3813 (1994); Schier et al, Gene 169: 147-155 (1995); Yelton et al, J. Immunol. 155: 1994-2004 (1995); Jackson et al, J. Immunol. 154(7):3310-9 (1995); and Hawkins et al, J. Mol. Biol. 226:889-896 (1992).
[00324] Antibody "effector functions" refer to those biological activities attributable to the
Fc region (a native sequence Fc region or amino acid sequence variant Fc region) of an antibody, and vary with the antibody isotype. Examples of antibody effector functions include: Clq binding and complement dependent cytotoxicity; Fc receptor binding; antibody-dependent cell-mediated cytotoxicity (ADCC); phagocytosis; down regulation of cell surface receptors (e.g. B cell receptor); and B cell activation.
[00325] "Antibody-dependent cell-mediated cytotoxicity" or "ADCC" refers to a form of cytotoxicity in which secreted Ig bound onto Fc receptors (FcRs) present on certain cytotoxic cells (e.g., Natural Killer (NK) cells, neutrophils, and macrophages) enable these cytotoxic effector cells to bind specifically to an antigen-bearing target cell and subsequently kill the target cell with cytotoxins. The antibodies "arm" the cytotoxic cells and are absolutely required for such killing. The primary cells for mediating ADCC, NK cells, express FcyRIII only, whereas monocytes express FcyRI, FcyRII and FcyRIII. FcR expression on hematopoietic cells is summarized in Table 3 on page 464 of Ravetch and Kinet, Annu. Rev. Immunol 9:457-92 (1991). To assess ADCC activity of a molecule of interest, an in vitro ADCC assay, may be performed. Useful effector cells for such assays include peripheral blood mononuclear cells (PBMC) and Natural Killer (NK) cells. Alternatively, or additionally, ADCC activity of the molecule of interest may be assessed in vivo, e.g., in a animal model such as that disclosed in Clynes et al Proc. Natl. Acad. Sci. USA 95:652- 656 (1998).
[00326] "Effector cells" are leukocytes which express one or more FcRs and perform effector functions. Preferably, the cells express at least FcyRIII and perform ADCC effector function. Examples of human leukocytes which mediate ADCC include peripheral blood mononuclear cells (PBMC), natural killer (NK) cells, monocytes, cytotoxic T cells and neutrophils; with PBMCs and NK cells being preferred. The effector cells may be isolated from a native source, e.g., from blood.
[00327] "Fc receptor" or "FcR" describes a receptor that binds to the Fc region of an antibody. The preferred FcR is a native sequence human FcR. Moreover, a preferred 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 these 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 tyro sine-based activation motif (IT AM) in its cytoplasmic domain. Inhibiting receptor FcyRIIB contains an immunoreceptor tyro sine-based inhibition motif (ITIM) in its cytoplasmic domain, (see review M. in Daeron, Annu. Rev. Immunol. 15:203-234 (1997)). FcRs are reviewed in Ravetch and Kinet, Annu. Rev. Immunol 9:457-92 (1991); Capel et al, Immunomethods 4:25-34 (1994); and de Haas et al, J. Lab. Clin. Med.
126:330-41 (1995). Other FcRs, including those to be identified in the future, are encompassed by the term "FcR" herein. The term also includes the neonatal receptor, FcRn, which is responsible for the transfer of maternal IgGs to the fetus (Guyer et al, J. Immunol. 117:587 (1976) and Kim et al, J. Immunol. 24:249 (1994)) and regulates homeostasis of immunoglobulins. For example, antibody variants with improved or diminished binding to FcRs have been described (see, e.g., Shields et al J. Biol. Chem. 9(2): 6591-6604 (2001)). [00328] Methods of measuring binding to FcRn are known (see, e.g., Ghetie 1997, Hinton
2004). Binding to human FcRn in vivo and serum half life of human FcRn high affinity binding polypeptides can be assayed, e.g., in transgenic mice or transfected human cell lines expressing human FcRn, or in primates administered with the Fc variant polypeptides.
[00329] "Complement dependent cytotoxicity" or "CDC" refers to the lysis of a target cell in the presence of complement. Activation of the classical complement pathway is initiated by the binding of the first component of the complement system (Clq) to antibodies (of the appropriate subclass) which are bound to their cognate antigen. To assess complement activation, a CDC assay, for example, as described in Gazzano-Santoro et al, J. Immunol. Methods 202: 163 (1996), may be performed.
[00330] Polypeptide variants with altered Fc region amino acid sequences and increased or decreased Clq binding capability have been described {e.g., see, also, Idusogie et al. J. Immunol. 164: 4178-4184 (2000)).
[00331] "Fc region-comprising polypeptide" refers to a polypeptide, such as an antibody or immunoadhesin (see definitions below), which comprises an Fc region. The C-terminal lysine (residue 447 according to the EU numbering system) of the Fc region may be removed, for example, during purification of the polypeptide or by recombinant engineering the nucleic acid encoding the polypeptide.
[00332] "Blocking" antibody or an "antagonist" antibody refers to one which inhibits or reduces biological activity of the antigen it binds. Preferred blocking antibodies or antagonist antibodies substantially or completely inhibit the biological activity of the antigen.
[00333] "Agonist" antibody refers to an antibody which mimics {e.g., partially or fully) at least one of the functional activities of a polypeptide of interest.
[00334] "Acceptor human framework" refers to a framework comprising the amino acid sequence of a VL or VH framework derived from a human immunoglobulin framework, or from a human consensus framework. An acceptor human framework "derived from" a human
immunoglobulin framework or human consensus framework may comprise the same amino acid sequence thereof, or may contain pre-existing amino acid sequence changes. Where pre-existing amino acid changes are present, preferably no more than 5 and preferably 4 or less, or 3 or less, pre-existing amino acid changes are present.
[00335] A "human consensus framework" refers to a framework which represents the most commonly occurring amino acid residues in a selection of human immunoglobulin VL or VH framework sequences. Generally, the selection of human immunoglobulin VL or VH sequences is from a subgroup of variable domain sequences. Generally, the subgroup of sequences is a subgroup as in Kabat et al, Sequences of Proteins of Immunological Interest, Fifth Edition, NIH Publication 91-3242, Bethesda Md. (1991), vols. 1-3. In one embodiment, for the VL, the subgroup is subgroup kappa I as in Kabat et al, supra. In one embodiment, for the VH, the subgroup is subgroup III as in Kabat et al, supra.
[00336] "Disorder" or "disease" refers to any condition that would benefit from treatment with a substance/molecule {e.g., an antibody comprising an ultralong CDR3 as disclosed herein) or method disclosed herein. This includes chronic and acute disorders or diseases including those pathological conditions which predispose the mammal to the disorder in question.
[00337] "Treatment" refers to clinical intervention in an attempt to alter the natural course of the individual or cell being treated, and can be performed either for prophylaxis or during the course of clinical pathology. Desirable effects of treatment include preventing occurrence or recurrence of disease, alleviation of symptoms, diminishment of any direct or indirect pathological consequences of the disease, preventing metastasis, decreasing the rate of disease progression, amelioration or palliation of the disease state, and remission or improved prognosis. In some embodiments, antibodies disclosed herein are used to delay development of a disease or disorder.
[00338] "Individual" {e.g., a "subject") refers to a vertebrate, preferably a mammal, more preferably a human. Mammals include, but are not limited to, farm animals (such as cows), sport animals, pets (such as cats, dogs and horses), primates, mice and rats.
[00339] "Mammal" for purposes of treatment refers to any animal classified as a mammal, including humans, rodents {e.g., mice and rats), and monkeys; domestic and farm animals; and zoo, sports, laboratory, or pet animals, such as dogs, cats, cattle, horses, sheep, pigs, goats, rabbits, etc.
In some embodiments, the mammal is selected from a human, rodent, or monkey.
[00340] "Pharmaceutically acceptable" refers to approved or approvable by a regulatory agency of the Federal or a state government or listed in the U.S. Pharmacopeia or other generally recognized pharmacopeia for use in animals, including humans.
[00341] "Pharmaceutically acceptable salt" refers to a salt of a compound that is
pharmaceutically acceptable and that possesses the desired pharmacological activity of the parent compound.
[00342] "Pharmaceutically acceptable excipient, carrier or adjuvant" refers to an excipient, carrier or adjuvant that can be administered to a subject, together with at least one antibody of the present disclosure, and which does not destroy the pharmacological activity thereof and is nontoxic when administered in doses sufficient to deliver a therapeutic amount of the compound.
[00343] "Pharmaceutically acceptable vehicle" refers to a diluent, adjuvant, excipient, or carrier with which at least one antibody of the present disclosure is administered. [00344] "Providing a prognosis", "prognostic information", or "predictive information" refer to providing information, including for example the presence of cancer cells in a subject's tumor, regarding the impact of the presence of cancer (e.g., as determined by the diagnostic methods of the present disclosure) on a subject's future health (e.g., expected morbidity or mortality, the likelihood of getting cancer, and the risk of metastasis).
[00345] Terms such as "treating" or "treatment" or "to treat" or "alleviating" or "to alleviate" refer to both 1) therapeutic measures that cure, slow down, lessen symptoms of, and/or halt progression of a diagnosed pathologic condition or disorder and 2) prophylactic or preventative measures that prevent and/or slow the development of a targeted pathologic condition or disorder. Thus those in need of treatment include those already with the disorder; those prone to have the disorder; and those in whom the disorder is to be prevented.
[00346] "Providing a diagnosis" or "diagnostic information" refers to any information, including for example the presence of cancer cells, that is useful in determining whether a patient has a disease or condition and/or in classifying the disease or condition into a phenotypic category or any category having significance with regards to the prognosis of or likely response to treatment (either treatment in general or any particular treatment) of the disease or condition. Similarly, diagnosis refers to providing any type of diagnostic information, including, but not limited to, whether a subject is likely to have a condition (such as a tumor), whether a subject's tumor comprises cancer stem cells, information related to the nature or classification of a tumor as for example a high risk tumor or a low risk tumor, information related to prognosis and/or information useful in selecting an appropriate treatment. Selection of treatment can include the choice of a particular chemotherapeutic agent or other treatment modality such as surgery or radiation or a choice about whether to withhold or deliver therapy.
[00347] A "human consensus framework" refers to a framework which represents the most commonly occurring amino acid residues in a selection of human immunoglobulin VL or VH framework sequences. Generally, the selection of human immunoglobulin VL or VH sequences is from a subgroup of variable domain sequences. Generally, the subgroup of sequences is a subgroup as in Kabat et al, Sequences of Proteins of Immunological Interest, Fifth Edition, NIH Publication 91-3242, Bethesda Md. (1991), vols. 1-3. In one embodiment, for the VL, the subgroup is subgroup kappa I as in Kabat et al, supra. In one embodiment, for the VH, the subgroup is subgroup III as in Kabat et al, supra.
[00348] An "acceptor human framework" for the purposes herein refers to a framework comprising the amino acid sequence of a light chain variable domain (VL) framework or a heavy chain variable domain (VH) framework derived from a human immunoglobulin framework or a human consensus framework, as defined below. An acceptor human framework "derived from" a human immunoglobulin framework or a human consensus framework may comprise the same amino acid sequence thereof, or it may contain amino acid sequence changes. In some
embodiments, the number of amino acid changes are 10 or less, 9 or less, 8 or less, 7 or less, 6 or less, 5 or less, 4 or less, 3 or less, or 2 or less. In some embodiments, the VL acceptor human framework is identical in sequence to the VL human immunoglobulin framework sequence or human consensus framework sequence.
[00349] "Antigen-binding site" refers to the interface formed by one or more complementary determining regions. An antibody molecule has two antigen combining sites, each containing portions of a heavy chain variable region and portions of a light chain variable region. The antigen combining sites can contain other portions of the variable region domains in addition to the CDRs.
[00350] An "antibody light chain" or an "antibody heavy chain" refers to a polypeptide comprising the VL or VH, respectively. The VL is encoded by the minigenes V (variable) and J (junctional), and the VH by minigenes V, D (diversity), and J. Each of VL or VH includes the CDRs as well as the framework regions. In this application, antibody light chains and/or antibody heavy chains may, from time to time, be collectively referred to as "antibody chains." These terms encompass antibody chains containing mutations that do not disrupt the basic structure of VL or VH, as one skilled in the art will readily recognize.
[00351] "Native antibodies" refer to naturally occurring immunoglobulin molecules with varying structures. For example, native IgG antibodies are heterotetrameric glycoproteins of about 150,000 daltons, composed of two identical light chains and two identical heavy chains that are disulfide bonded. From N-to C-terminus, each heavy chain has a variable region (V H), also called a variable heavy domain or a heavy chain variable domain, followed by three constant domains (CHI, CH2, and CH3). Similarly, from N-to C-terminus, each light chain has a variable region (V L), also called a variable light domain or a light chain variable domain, followed by a constant light (CL) domain. The light chain of an antibody may be assigned to one of two types, called kappa (K) and lambda (K), based on the amino acid sequence of its constant domain.
[00352] "Combinatorial library" refers to collections of compounds formed by reacting different combinations of interchangeable chemical "building blocks" to produce a collection of compounds based on permutations of the building blocks. For an antibody combinatorial library, the building blocks are the component V, D and J regions (or modified forms thereof) from which antibodies are formed. For purposes herein, the terms "library" or "collection" are used
interchangeably. [00353] A "combinatorial antibody library" refers to a collection of antibodies (or portions thereof, such as Fabs), where the antibodies are encoded by nucleic acid molecules produced by the combination of V, D and J gene segments, particularly human V, D and J germline segments. The combinatorial libraries herein typically contain at least 50 different antibody (or antibody portions or fragment) members, typically at or about 50, 100, 500, 103, 1 x 103, 2 x 103, 3 x 103, 4x 103, 5 x 103, 6 x 103, 7 x 103, 8 x 103, 9 x 103, 1 x 104, 2 x 104, 3 x 104, 4x 104, 5 x 104, 6 x 104, 7 x
104, 8 x 104, 9 x 104 , 1 x 105, 2 x 105, 3 x 105, 4x 105, 5 x 105, 6 x 105, 7 x 105, 8 x 105, 9 x
105, 106, 107, 108, 109, 1010, or more different members. The resulting libraries or collections of antibodies or portions thereof, can be screened for binding to a target protein or modulation of a functional activity.
[00354] A "human combinatorial antibody library" refers to a collection of antibodies or portions thereof, whereby each member contains a VL and VH chains or a sufficient portion thereof to form an antigen binding site encoded by nucleic acid containing human germline segments produced as described herein.
[00355] A "variable germline segment" refers to V, D and J groups, subgroups, genes or alleles thereof. Gene segment sequences are accessible from known database (e.g. , National Center for Biotechnology Information (NCBI), the international ImMunoGeneTics information system® (IMGT), the Kabat database and the Tomlinson's VBase database (Lefranc (2003) Nucleic Acids Res., 31 :307-310; Martin et al. , Bioinformatics Tools for Antibody Engineering in Handbook of Therapeutic Antibodies, Wiley- VCH (2007), pp. 104-107). Tables 3-5 list exemplary human variable germline segments. Sequences of exemplary VH, DH, JH, VK, JK, νλ and or JX, germline segments are set forth in SEQ ID NOS: 10-451 and 868. For purposes herein, a germline segment includes modified sequences thereof, that are modified in accord with the rules of sequence compilation provided herein to permit practice of the method. For example, germline gene segments include those that contain one amino acid deletion or insertion at the 5 ' or 3 ' end compared to any of the sequences of nucleotides set forth in SEQ ID NOS: 10-451 , 868.
[00356] "Compilation," "compile," "combine," "combination," "rearrange,"
"rearrangement," or other similar terms or grammatical variations thereof refers to the process by which germline segments are ordered or assembled into nucleic acid sequences representing genes. For example, variable heavy chain germline segments are assembled such that the VH segment is 5 ' to the DH segment which is 5 ' to the JH segment, thereby resulting in a nucleic acid sequence encoding a VH chain. Variable light chain germline segments are assembled such that the VL segment is 5 ' to the JL segment, thereby resulting in a nucleic acid sequence encoding a VL chain. A constant gene segment or segments also can be assembled onto the 3 ' end of a nucleic acid encoding a VH or VL chain.
[00357] "Linked," or "linkage" or other grammatical variations thereof with reference to germline segments refers to the joining of germline segments. Linkage can be direct or indirect. Germline segments can be linked directly without additional nucleotides between segments, or additional nucleotides can be added to render the entire segment in- frame, or nucleotides can be deleted to render the resulting segment in- frame. It is understood that the choice of linker nucleotides is made such that the resulting nucleic acid molecule is in-frame and encodes a functional and productive antibody.
[00358] "In- frame" or "linked in- frame" with reference to linkage of human germline segments means that there are insertions and/or deletions in the nucleotide germline segments at the joined junctions to render the resulting nucleic acid molecule in- frame with the 5 ' start codon (ATG), thereby producing a "productive" or functional full-length polypeptide. The choice of nucleotides inserted or deleted from germline segments, particularly at joints joining various VD, DJ and VJ segments, is in accord with the rules provided in the method herein for V(D)J joint generation. For example, germline segments are assembled such that the VH segment is 5 ' to the DH segment which is 5 ' to the JH segment. At the junction joining the VH and the DH and at the junction joining the DH and JH segments, nucleotides can be inserted or deleted from the individual VH, DH or JH segments, such that the resulting nucleic acid molecule containing the joined VDJ segments are in- frame with the 5 ' start codon (ATG).
[00359] A portion of an antibody includes sufficient amino acids to form an antigen binding site.
[00360] A "reading frame" refers to a contiguous and non-overlapping set of three- nucleotide codons in DNA or RNA. Because three codons encode one amino acid, there exist three possible reading frames for given nucleotide sequence, reading frames 1 , 2 or 3. For example, the sequence ACTGGTCA will be ACT GGT CA for reading frame 1 , A CTG GTC A for reading frame 2 and AC TGG TCA for reading frame 3. Generally for practice of the method described herein, nucleic acid sequences are combined so that the V sequence has reading frame 1.
[00361] A "stop codon" refers to a three-nucleotide sequence that signals a halt in protein synthesis during translation, or any sequence encoding that sequence (e.g. a DNA sequence encoding an RNA stop codon sequence), including the amber stop codon (UAG or TAG)), the ochre stop codon (UAA or TAA)) and the opal stop codon (UGA or TGA)). It is not necessary that the stop codon signal termination of translation in every cell or in every organism. For example, in suppressor strain host cells, such as amber suppressor strains and partial amber suppressor strains, translation proceeds through one or more stop codon (e.g. the amber stop codon for an amber suppressor strain), at least some of the time.
[00362] A "variable heavy" (VH) chain or a "variable light" (VL) chain (also termed VH domain or VL domain) refers to the polypeptide chains that make up the variable domain of an antibody. For purposes herein, heavy chain germline segments are designated as VH, DH and JH, and compilation thereof results in a nucleic acid encoding a VH chain. Light chain germline segments are designated as VL or JL, and include kappa and lambda light chains (VK and JK; νλ and Ιλ.) and compilation thereof results in a nucleic acid encoding a VL chain. It is understood that a light chain is either a kappa or lambda light chain, but does not include a kappa/lambda combination by virtue of compilation of a VK and Ιλ.
[00363] A "degenerate codon" refers to three-nucleotide codon that specifies the same amino acid as a codon in a parent nucleotide sequence. One of skill in the art is familiar with degeneracy of the genetic code and can identify degenerate codons.
[00364] "Diversity" with respect to members in a collection refers to the number of unique members in a collection. Hence, diversity refers to the number of different amino acid sequences or nucleic acid sequences, respectively, among the analogous polypeptide members of that collection. For example, a collection of polynucleotides having a diversity of 104 contains 104 different nucleic acid sequences among the analogous polynucleotide members. In one example, the provided collections of polynucleotides and/or polypeptides have diversities of at least at or about 102, 103, 104, 105, 106, 107, 108, 109, 1010 or more.
[00365] "Sequence diversity" refers to a representation of nucleic acid sequence similarity and is determined using sequence alignments, diversity scores, and/or sequence clustering. Any two sequences can be aligned by laying the sequences side-by-side and analyzing differences within nucleotides at every position along the length of the sequences. Sequence alignment can be assessed in silico using Basic Local Alignment Search Tool (BLAST), an NCBI tool for comparing nucleic acid and/or protein sequences. The use of BLAST for sequence alignment is well known to one of skill in the art. The Blast search algorithm compares two sequences and calculates the statistical significance of each match (a Blast score). Sequences that are most similar to each other will have a high Blast score, whereas sequences that are most varied will have a low Blast score.
[00366] A "polypeptide domain" refers to a part of a polypeptide (a sequence of three or more, generally 5 or 7 or more amino acids) that is a structurally and/or functionally distinguishable or definable. Exemplary of a polypeptide domain is a part of the polypeptide that can form an independently folded structure within a polypeptide made up of one or more structural motifs (e.g. combinations of alpha helices and/or beta strands connected by loop regions) and/or that is recognized by a particular functional activity, such as enzymatic activity or antigen binding. A polypeptide can have one, typically more than one, distinct domains. For example, the polypeptide can have one or more structural domains and one or more functional domains. A single polypeptide domain can be distinguished based on structure and function. A domain can encompass a contiguous linear sequence of amino acids. Alternatively, a domain can encompass a plurality of non-contiguous amino acid portions, which are non-contiguous along the linear sequence of amino acids of the polypeptide. Typically, a polypeptide contains a plurality of domains. For example, each heavy chain and each light chain of an antibody molecule contains a plurality of
immunoglobulin (Ig) domains, each about 110 amino acids in length.
[00367] An "Ig domain" refers to a domain, recognized as such by those in the art, that is distinguished by a structure, called the Immunoglobulin (Ig) fold, which contains two beta-pleated sheets, each containing anti-parallel beta strands of amino acids connected by loops. The two beta sheets in the Ig fold are sandwiched together by hydrophobic interactions and a conserved intra- chain disulfide bond. Individual immunoglobulin domains within an antibody chain further can be distinguished based on function. For example, a light chain contains one variable region domain (VL) and one constant region domain (CL), while a heavy chain contains one variable region domain (VH) and three or four constant region domains (CH). Each VL, CL, VH, and CH domain is an example of an immunoglobulin domain.
[00368] A "variable domain" with reference to an antibody refers to a specific Ig domain of an antibody heavy or light chain that contains a sequence of amino acids that varies among different antibodies. Each light chain and each heavy chain has one variable region domain (VL, and, VH). The variable domains provide antigen specificity, and thus are responsible for antigen recognition. Each variable region contains CDRs that are part of the antigen binding site domain and framework regions (FRs).
[00369] A "constant region domain" refers to a domain in an antibody heavy or light chain that contains a sequence of amino acids that is comparatively more conserved among antibodies than the variable region domain. Each light chain has a single light chain constant region (CL) domain and each heavy chain contains one or more heavy chain constant region (CH) domains, which include, CHI, CH2, CH3 and CH4. Full-length IgA, IgD and IgG isotypes contain CHI, CH2 CH3 and a hinge region, while IgE and IgM contain CHI, CH2 CH3 and CH4. CHI and CL domains extend the Fab arm of the antibody molecule, thus contributing to the interaction with antigen and rotation of the antibody arms. Antibody constant regions can serve effector functions, such as, but not limited to, clearance of antigens, pathogens and toxins to which the antibody specifically binds, e.g. through interactions with various cells, biomolecules and tissues. [00370] An "antibody or portion thereof that is sufficient to form an antigen binding site" means that the antibody or portion thereof contains at least 1 or 2, typically 3, 4, 5 or all 6 CDRs of the VH and VL sufficient to retain at least a portion of the binding specificity of the corresponding full-length antibody containing all 6 CDRs. Generally, a sufficient antigen binding site at least requires CDR3 of the heavy chain (CDRH3). It typically further requires the CDR3 of the light chain (CDRL3). As described herein, one of skill in the art knows and can identify the CDRs based on Kabat or Chothia numbering (see, e.g., Kabat, E.A. et al. (1991) Sequences of Proteins of Immunological Interest, Fifth Edition, U.S. Department of Health and Human Services, NIH Publication No. 91-3242, and Chothia, C. et al. (1987) J. Mol. Biol. 196:901-917). For example, based on Kabat numbering, CDR-LI corresponds to residues L24-L34; CDR-L2 corresponds to residues L50-L56; CDR-L3 corresponds to residues L89-L97; CDR-H1 corresponds to residues H31 - H35, 35a or 35b depending on the length; CDR-H2 corresponds to residues H50-H65; and CDR-H3 corresponds to residues H95-H102.
[00371] A "peptide mimetic" refers to a peptide that mimics the activity of a polypeptide.
For example, an erythropoietin (EPO) peptide mimetic is a peptide that mimics the activity of Epo, such as for binding and activation of the EPO receptor.
[00372] An "address" refers to a unique identifier for each locus in a collection whereby an addressed member {e.g. an antibody) can be identified. An addressed moiety is one that can be identified by virtue of its locus or location. Addressing can be effected by position on a surface, such as a well of a microplate. For example, an address for a protein in a microwell plate that is F9 means that the protein is located in row F, column 9 of the microwell plate. Addressing also can be effected by other identifiers, such as a tag encoded with a bar code or other symbology, a chemical tag, an electronic, such RF tag, a color-coded tag or other such identifier.
[00373] An "array" refers to a collection of elements, such as antibodies, containing three or more members.
[00374] A "spatial array" refers to an array where members are separated or occupy a distinct space in an array. Hence, spatial arrays are a type of addressable array. Examples of spatial arrays include micro titer plates where each well of a plate is an address in the array. Spacial arrays include any arrangement wherein a plurality of different molecules, e.g., polypeptides, are held, presented, positioned, situated, or supported. Arrays can include microtiter plates, such as 48-well, 96-well, 144-well, 192-well, 240-well, 288-well, 336-well, 384-well, 432-well, 480-well, 576-well, 672-well, 768-well, 864-well, 960-well, 1056-well, 1152-well, 1248-well, 1344-well, 1440-well, or 1536-well plates, tubes, slides, chips, flasks, or any other suitable laboratory apparatus.
Furthermore, arrays can also include a plurality of sub-arrays. A plurality of sub-arrays encompasses an array where more than one arrangement is used to position the polypeptides. For example, multiple 96-well plates could constitute a plurality of sub-arrays and a single array.
[00375] An "addressable library" or "spatially addressed library" refers to a collection of molecules such as nucleic acid molecules or protein agents, such as antibodies, in which each member of the collection is identifiable by virtue of its address.
[00376] An "addressable array" refers to one in which the members of the array are identifiable by their address, the position in a spatial array, such as a well of a microtiter plate, or on a solid phase support, or by virtue of an identifiable or detectable label, such as by color, fluorescence, electronic signal (i.e. RF, microwave or other frequency that does not substantially alter the interaction of the molecules of interest), bar code or other symbology, chemical or other such label. Hence, in general the members of the array are located at identifiable loci on the surface of a solid phase or directly or indirectly linked to or otherwise associated with the identifiable label, such as affixed to a microsphere or other particulate support (herein referred to as beads) and suspended in solution or spread out on a surface.
[00377] "An addressable combinatorial antibody library" refers to a collection of antibodies in which member antibodies are identifiable and all antibodies with the same identifier, such as position in a spatial array or on a solid support, or a chemical or RF tag, bind to the same antigen, and generally are substantially the same in amino acid sequence. For purposes herein, reference to an "addressable arrayed combinatorial antibody library" means that the antibody members are addressed in an array.
[00378] "In silico" refers to research and experiments performed using a computer. In silico methods include, but are not limited to, molecular modeling studies, biomolecular docking experiments, and virtual representations of molecular structures and/or processes, such as molecular interactions. For purposes herein, the antibody members of a library can be designed using a computer program that selects component V, D and J germline segments from among those input into the computer and joins them in- frame to output a list of nucleic acid molecules for synthesis. Thus, the recombination of the components of the antibodies in the collections or libraries provided herein, can be performed in silico by combining the nucleotide sequences of each building block in accord with software that contains rules for doing so. The process could be performed manually without a computer, but the computer provides the convenience of speed.
[00379] A "database" refers to a collection of data items. For purposes herein, reference to a database is typically with reference to antibody databases, which provide a collection of sequence and structure information for antibody genes and sequences. Exemplary antibody databases include, but are not limited to, IMGT®, the international ImMunoGeneTics information system (imgt.cines.fr; see e.g., Lefranc et al. (2008) Briefings in Bioinformatics, 9:263-275), National Center for Biotechnology Information (NCBI), the Kabat database and the Tomlinson's VBase database (Lefranc (2003) Nucleic Acids Res., 31 :307-310; Martin et al, Bioinformatics Tools for Antibody Engineering in Handbook of Therapeutic Antibodies, Wiley- VCH (2007), pp. 104-107). A database also can be created by a user to include any desired sequences. The database can be created such that the sequences are inputted in a desired format (e.g., in a particular reading frame; lacking stop codons; lacking signal sequences). The database also can be created to include sequences in addition to antibody sequences.
[00380] "Screening" refers to identification or selection of an antibody or portion thereof from a collection or library of antibodies and/or portions thereof, based on determination of the activity or property of an antibody or portion thereof. Screening can be performed in any of a variety of ways, including, for example, by assays assessing direct binding (e.g. binding affinity) of the antibody to a target protein or by functional assays assessing modulation of an activity of a target protein.
[00381] "Activity towards a target protein" refers to binding specificity and/or modulation of a functional activity of a target protein, or other measurements that reflects the activity of an antibody or portion thereof towards a target protein.
[00382] A "target protein" or "protein target" refers to candidate proteins or peptides that are specifically recognized by an antibody or portion thereof and/or whose activity is modulated by an antibody or portion thereof. Modulating the activity can comprise increasing, decreasing, stimulating, or preventing the activity or expression of the target protein. A target protein includes any peptide or protein that contains an epitope for antibody recognition. Target proteins include proteins involved in the etiology of a disease or disorder by virtue of expression or activity.
Exemplary target proteins are described herein. In some instances, the target protein is a transmembrane protein target. Transmembrane protein targets include, but are not limited to, GPCRs, ion channels, transporters, and cell surface receptors. Ion channels may be potassium ion channels, sodium ion channels, calcium ion channels, and voltage gated channels. In some instances, the antibodies disclosed herein modulate a Kvl .3 ion channel, Navl .7 ion channel, or acid sensing ion channel (ASIC). The antibodies disclosed herein may modulate cell surface receptors such as GLP1R, GCGR, EPO receptor, FGFR, FGF21R, CSFR, GMCSFR, and GCSFR. Additional target proteins include, but are not limited to, cytokines, kinases, interferons, hormones, and growth factors. The target proteins can be from a mammal or non-mammal. The target proteins can be from a human. Alternatively, the target proteins are from a bovine. [00383] "Hit" refers to an antibody or portion thereof identified, recognized or selected as having an activity in a screening assay.
[00384] "Iterative" with respect to screening means that the screening is repeated a plurality of times, such as 2, 3, 4, 5 or more times, until a "Hit" is identified whose activity is optimized or improved compared to prior iterations.
[00385] "High-throughput" refers to a large-scale method or process that permits
manipulation of large numbers of molecules or compounds, generally tens to hundreds to thousands of compounds. For example, methods of purification and screening can be rendered high- throughput. High-throughput methods can be performed manually. Generally, however, high- throughput methods involve automation, robotics or software.
[00386] Basic Local Alignment Search Tool (BLAST) is a search algorithm developed by
Altschul et al. (1990) to separately search protein or DNA databases, for example, based on sequence identity. For example, blastn is a program that compares a nucleotide query sequence against a nucleotide sequence database {e.g. GenBank). BlastP is a program that compares an amino acid query sequence against a protein sequence database.
[00387] A BLAST bit score is a value calculated from the number of gaps and substitutions associated with each aligned sequence. The higher the score, the more significant the alignment.
[00388] A "human protein" refers to a protein encoded by a nucleic acid molecule, such as
DNA, present in the genome of a human, including all allelic variants and conservative variations thereof. A variant or modification of a protein is a human protein if the modification is based on the wildtype or prominent sequence of a human protein.
[00389] "Naturally occurring amino acids" refer to the 20 L-amino acids that occur in polypeptides. The residues are those 20 a-amino acids found in nature which are incorporated into protein by the specific recognition of the charged tRNA molecule with its cognate mRNA codon in humans.
[00390] "Non-naturally occurring amino acids" refer to amino acids that are not genetically encoded. For example, a non-natural amino acid is an organic compound that has a structure similar to a natural amino acid but has been modified structurally to mimic the structure and reactivity of a natural amino acid. Non-naturally occurring amino acids thus include, for example, amino acids or analogs of amino acids other than the 20 naturally-occurring amino acids and include, but are not limited to, the D-isostereomers of amino acids. Exemplary non-natural amino acids are known to those of skill in the art.
[00391] "Nucleic acids" include DNA, RNA and analogs thereof, including peptide nucleic acids (PNA) and mixtures thereof. Nucleic acids can be single or double-stranded. When referring to probes or primers, which are optionally labeled, such as with a detectable label, such as a fluorescent or radio label, single-stranded molecules are contemplated. Such molecules are typically of a length such that their target is statistically unique or of low copy number (typically less than 5, generally less than 3) for probing or priming a library. Generally a probe or primer contains at least 14, 16 or 30 contiguous nucleotides of sequence complementary to or identical to a gene of interest. Probes and primers can be 10, 20, 30, 50, 100 or more nucleic acids long.
[00392] A "peptide" refers to a polypeptide that is from 2 to 40 amino acids in length.
[00393] The amino acids which occur in the various sequences of amino acids provided herein are identified according to their known, three-letter or one-letter abbreviations (Table 1). The nucleotides which occur in the various nucleic acid fragments are designated with the standard single-letter designations used routinely in the art.
[00394] An "amino acid" is an organic compound containing an amino group and a carboxylic acid group. A polypeptide contains two or more amino acids. For purposes herein, amino acids include the twenty naturally-occurring amino acids, non-natural amino acids and amino acid analogs (i.e., amino acids wherein the a-carbon has a side chain).
[00395] "Amino acid residue" refers to an amino acid formed upon chemical digestion
(hydrolysis) of a polypeptide at its peptide linkages. The amino acid residues described herein are presumed to be in the "L" isomeric form. Residues in the "D" isomeric form, which are so designated, can be substituted for any L-amino acid residue as long as the desired functional property is retained by the polypeptide. NH2 refers to the free amino group present at the amino terminus of a polypeptide. COOH refers to the free carboxy group present at the carboxyl terminus of a polypeptide. In keeping with standard polypeptide nomenclature described in J. Biol. Chem., 243: 3552-3559 (1969), and adopted 37 C.F.R.□§§ 1.821-1.822, abbreviations for amino acid residues are shown below:
Figure imgf000081_0001
SYMBOL
1-Letter 3-Letter AMINO ACID
T Thr Threonine
V Val Valine
P Pro Proline
K Lys Lysine
H His Histidine
Q Gin Glutamine
E Glu Glutamic acid
Z Glx Glu and/or Gin
W Trp Tryptophan
R Arg Arginine
D Asp Aspartic acid
N Asn Asparagine
B Asx Asn and/or Asp
C Cys Cysteine
X Xaa Unknown or other
[00396] It should be noted that all amino acid residue sequences represented herein by formulae have a left to right orientation in the conventional direction of amino -terminus to carboxyl-terminus. In addition, the phrase "amino acid residue" is broadly defined to include the amino acids listed in the Table of Correspondence (Table 1) and modified and unusual amino acids, such as those referred to in 37 C.F.R. §§ 1.821-1.822, and incorporated herein by reference.
Furthermore, it should be noted that a dash at the beginning or end of an amino acid residue sequence indicates a peptide bond to a further sequence of one or more amino acid residues, to an amino -terminal group such as NH2 or to a carboxyl-terminal group such as COOH. The
abbreviations for any protective groups, amino acids and other compounds, are, unless indicated otherwise, in accord with their common usage, recognized abbreviations, or the IUPAC-IUB Commission on Biochemical Nomenclature (see, (1972) Biochem. 11 : 1726). Each naturally occurring L-amino acid is identified by the standard three letter code (or single letter code) or the standard three letter code (or single letter code) with the prefix "L-"; the prefix "D-" indicates that the stereoisomeric form of the amino acid is D.
[00397] An "immuno conjugate" refers to an antibody conjugated to one or more
heterologous molecule(s), including but not limited to a cytotoxic agent, non-antibody peptide or therapeutic polypeptide. An immuno conjugate may include non-antibody sequences. The non- antibody sequence can be conjugated to the antibody. Alternatively, the non-antibody sequence can be within the antibody sequence.
[00398] A "non-antibody peptide" refers to a peptide encoded by a non-antibody antibody sequence. For example, a non-antibody peptide may be a hormone, a lymphokine, an interleukin, a chemokines, a cytokine or a peptide toxin.
[00399] As used herein, the terms "therapeutic polypeptide," "therapeutic peptides," and therapeutic immunoglobulin construct" mean one or more peptides having demonstrated or potential use in treating, preventing, or ameliorating one or more diseases, disorders, or conditions in a subject in need thereof, as well as related peptides. Therapeutic peptides include peptides found to have use in treating, preventing, or ameliorating one or more diseases, disorders, or conditions after the time of filing of this application. Related peptides include fragments of therapeutic peptides, therapeutic peptide variants, and therapeutic peptide derivatives that retain some or all of the therapeutic activities of the therapeutic peptide. As will be known to one of skill in the art, as a general principle, modifications may be made to peptides that do not alter, or only partially abrogate, the properties and activities of those peptides. In some instances, modifications result in an increase in therapeutic activities. The terms "therapeutic polypeptide" or "therapeutic peptides" encompass modifications to the therapeutic peptides defined and/or disclosed herein. In certain embodiments, the therapeutic polypeptide is selected from a hormone, a lymphokine, an
interleukin, a chemokines, a cytokine, a peptide toxin, and combinations thereof. Therapeutic polypeptides can be peptides encoded by non-antibody sequences.
[00400] A derivative or a variant of a polypeptide is said to share "homology" or be
"homologous" with the peptide if the amino acid sequences of the derivative or variant has at least 50% identity with the original peptide. In certain embodiments, the derivative or variant is at least 75% the same as that of either the peptide or a fragment of the peptide having the same number of amino acid residues as the derivative. In certain embodiments, the derivative or variant is at least 85% the same as that of either the peptide or a fragment of the peptide having the same number of amino acid residues as the derivative. In certain embodiments, the amino acid sequence of the derivative is at least 90% the same as the peptide or a fragment of the peptide having the same number of amino acid residues as the derivative. In some embodiments, the amino acid sequence of the derivative is at least 95% the same as the peptide or a fragment of the peptide having the same number of amino acid residues as the derivative. In certain embodiments, the derivative or variant is at least 99% the same as that of either the peptide or a fragment of the peptide having the same number of amino acid residues as the derivative. [00401] Groupings of alternative elements or embodiments disclosed herein are not to be construed as limitations. Each group member can be referred to and claimed individually or in any combination with other members of the group or other elements found herein. It is anticipated that one or more members of a group can be included in, or deleted from, a group for reasons of convenience and/or patentability. When any such inclusion or deletion occurs, the specification is deemed to contain the group as modified thus fulfilling the written description of all Markush groups used in the appended claims.
[00402] Certain embodiments are described herein, including the best mode known to the inventors for carrying out the exemplary embodiments. Of course, variations on these described embodiments will become apparent to those of ordinary skill in the art upon reading the foregoing description. The inventor expects skilled artisans to employ such variations as appropriate, and the inventors intend for the embodiments to be practiced otherwise than specifically described herein. Accordingly, this disclosure includes all modifications and equivalents of the subject matter recited in the claims appended hereto as permitted by applicable law. Moreover, any combination of the above-described elements in all possible variations thereof is encompassed by the disclosure unless otherwise indicated herein or otherwise clearly contradicted by context.
[00403] Furthermore, numerous references have been made to patents and printed publications. Each of the above-cited references is individually incorporated herein by reference in their entirety.
[00404] Specific embodiments disclosed herein can be further limited in the claims using consisting of or and consisting essentially of language. When used in the claims, whether as filed or added per amendment, the transition term "consisting of excludes any element, step, or ingredient not specified in the claims. The transition term "consisting essentially of limits the scope of a claim to the specified materials or steps and those that do not materially affect the basic and novel characteristic(s). Exemplary embodiments so claimed are inherently or expressly described and enabled herein.
[00405] In closing, it is to be understood that the exemplary embodiments disclosed herein are illustrative of the principles of the present disclosure. Other modifications that can be employed are within the scope of the disclosure. Thus, by way of example, but not of limitation, alternative configurations of the present exemplary embodiments can be utilized in accordance with the teachings herein. Accordingly, the present exemplary embodiments are not limited to that precisely as shown and described. General techniques
[00406] The present disclosure relies on routine techniques in the field of recombinant genetics. Basic texts disclosing the general methods of use in this present disclosure include Sambrook and Russell, Molecular Cloning: A Laboratory Manual 3d ed. (2001); Kriegler, Gene Transfer and Expression: A Laboratory Manual (1990); and Ausubel et al, Current Protocols in Molecular Biology (1994).
[00407] For nucleic acids, sizes are given in either kilobases (Kb) or base pairs (bp). These are estimates derived from agarose or polyacrylamide gel electrophoresis, from sequenced nucleic acids, or from published DNA sequences. For proteins, sizes are given in kilo-Daltons (kD) or amino acid residue numbers. Proteins sizes are estimated from gel electrophoresis, from sequenced proteins, from derived amino acid sequences, or from published protein sequences.
[00408] Oligonucleotides that are not commercially available can be chemically synthesized according to the solid phase phosphoramidite triester method first described by Beaucage and Caruthers, Tetrahedron Letters, 22: 1859-1862 (1981), using an automated synthesizer, as described in Van Devanter et al, Nucleic Acids Res., 12:6159-6168 (1984). Purification of oligonucleotides is by either native polyacrylamide gel electrophoresis or by anion-exchange chromatography as described in Pearson & Reanier, J. Chrom., 255: 137-149 (1983). The sequence of the cloned genes and synthetic oligonucleotides can be verified after cloning using, e.g., the chain termination method for sequencing double-stranded templates of Wallace et al, Gene, 16:21-26 (1981).
[00409] The nucleic acids encoding recombinant polypeptides of the present disclosure may be cloned into an intermediate vector before transformation into prokaryotic or eukaryotic cells for replication and/or expression. The intermediate vector may be a prokaryote vector such as a plasmid or shuttle vector.
Antibodies with Ultralong CDR3 Sequences
[00410] To date, cattle are the only species where ultralong CDR3 sequences have been identified. However, other species, for example other ruminants, may also possess antibodies with ultralong CDR3 sequences.
[00411] Exemplary antibody variable region sequences comprising an ultralong CDR3 sequence identified in cattle include those designated as: BLV1H12 {see, SEQ ID NO: 22), BLV5B8 (see, SEQ ID NO: 23), BLV5D3 (see, SEQ ID NO: 24) and BLV8C11 (see, SEQ ID NO: 25) (see, e.g., Saini, et al (1999) Eur. J. Immunol 29: 2420-2426; and Saini and Kaushik (2002) Scand. J. Immunol. 55: 140-148); BF4E9 (see, SEQ ID NO: 26) and BF1H1 (see, SEQ ID NO: 27) (see, e.g., Saini and Kaushik (2002) Scand. J. Immunol. 55: 140-148); and F18 (see, SEQ ID NO: 28) (see, e.g., Berens, et al. (1997) Int. Immunol. 9: 189-199).
[00412] In an embodiment, bovine antibodies are identified and/or produced. Multiple techniques exist to identify and/or produce antibodies.
[00413] Antibodies of the present disclosure may be isolated by screening including, high- throughput screening, of combinatorial libraries for antibodies with the desired activity or activities. For example, a variety of methods are known in the art for generating phage display libraries and screening such libraries for antibodies possessing the desired binding characteristics. Such methods are reviewed, e.g., in Hoogenboom et al. in Methods in Molecular Biology 178: 1-37 (O'Brien et al, ed., Human Press, Totowa, N.J., 2001) and further described, e.g., in the McCafferty et al, Nature 348:552-554; Clackson et al, Nature 352: 624-628 (1991); Marks et al, J. Mol. Biol. 222: 581-597 (1992); Marks and Bradbury, in Methods in Molecular Biology 248: 161-175 (Lo, ed., Human Press, Totowa, N.J., 2003); Sidhu et al, J. Mol. Biol. 338(2): 299-310 (2004); Lee et al, J. Mol. Biol. 340(5): 1073-1093 (2004); Fellouse, Proc. Natl. Acad. Sci. USA 101(34): 12467-12472 (2004); and Lee et al, J. Immunol. Methods 284(1-2): 119-132 (2004). Such screening may be iterative until a hit is obtained.
[00414] In certain phage display methods, repertoires of VH and VL genes are separately cloned by polymerase chain reaction (PCR) and recombined randomly in phage libraries, which can then be screened for antigen-binding phage as described in Winter et al, Ann. Rev. Immunol, 12: 433-455 (1994). Phage typically display antibody fragments, either as single-chain Fv (scFv) fragments or as Fab fragments. Libraries from immunized sources provide high-affinity antibodies to the immunogen without the requirement of constructing hybridomas. Phage display libraries of bovine antibodies may be a source of bovine antibody gene sequences, including ultralong CDR3 sequences.
[00415] Typically, a non-human antibody is humanized to reduce imrnunogenicity to humans, while retaining the specificity and affinity of the parental non-human antibody. Generally, 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. In some embodiments, some FR residues in a humanized antibody are substituted with corresponding residues from a non-human antibody (e.g., the antibody from which the CDR residues are derived), e.g., to restore or improve antibody specificity or affinity.
[00416] Humanized antibodies and methods of making them are reviewed, e.g., in Almagro and Fransson, Front. Biosci. 13: 1619-1633 (2008), and are further described, e.g., in Riechmann et al, Nature 332:323-329 (1988); Queen et al, Proc. Nafl Acad. Sci. USA 86: 10029-10033 (1989); U.S. Pat. Nos. 5,821,337, 7,527,791, 6,982,321, and 7,087,409; Kashmiri et al, Methods 36:25-34 (2005) (describing SDR (a-CDR) grafting); Padlan, Mol. Immunol. 28:489-498 (1991) (describing "resurfacing"); DallAcqua et al, Methods 36:43-60 (2005) (describing "FR shuffling"); and Osbourn et al, Methods 36:61-68 (2005); Klimka et al, Br. J. Cancer, 83:252-260 (2000) (describing the "guided selection" approach to FR shuffling); and Studnicka et al, U.S. Patent No. 5,766,886.
[00417] Human framework regions that may be used for humanization include but are not limited to: framework regions selected using the "best-fit" method (see, e.g., Sims et al J.
Immunol. 151 :2296 (1993)); framework regions derived from the consensus sequence of human antibodies of a particular subgroup of light or heavy chain variable regions (see, e.g., Carter et al Proc. Natl. Acad. Sci. USA, 89:4285 (1992); and Presta et al. J. Immunol, 151 :2623 (1993)); human mature (somatically mutated) framework regions or human germline framework regions (see, e.g., Almagro and Fransson, Front. Biosci. 13: 1619-1633 (2008)); and framework regions derived from screening FR libraries (see, e.g., Baca et al, Biol. Chem. 272: 10678-10684 (1997) and Rosok et al, J. Biol. Chem. 271 :22611-22618 (1996)).
[00418] Antibodies with ultralong CDR3 sequences may also include non-antibody sequences, such as cytokines, therapeutic polypeptides or growth factors, into the CDR3 region. The resultant antibody can be effective in treating or preventing a disease or condition. For example, an antibody comprising an ultralong CDR3 inhibits tumor metastasis. In some embodiments, the cytokine, therapeutic polypeptide or growth factor may be shown to have an antiproliferative effect on at least one cell population. Alternatively, or additionally, the resultant antibody modulates the expression or activity of a target (e.g., protein target, transmembrane protein target). For example, an antibody comprising an ultralong CDR3 inhibits or blocks an ion channel. The non-antibody sequence may be a hormone, a lymphokine, an interleukin, a chemokines, a cytokine, a peptide toxin, and combinations thereof. Such cytokines, therapeutic polypeptides, toxins, lymphokines, growth factors, or other hematopoietic factors include
Granulocyte colony- stimulating factor (G-CSF), macrophage colony-stimulating factor (M-CSF), Granulocyte-macrophage colony- stimulating factor (GM-CSF), Meg-CSF, TNF, IL-1, IL-2, IL-3, IL-4, IL-5, IL-6, IL-7, IL-8, IL-9, IL-10, IL-11, IL-12, IL-13, IL-14, IL-15, IL-16, IL-17, IL-18, IFN (e.g., a-interferon, β-interferon, a λ-interferon), TNF-alpha, TNF1, TNF2, thrombopoietin, stem cell factor, and erythropoietin (EPO). Additional growth factors for use in the antibodies and/or pharmaceutical compositions of the present disclosure include: angiogenin, bone morp biogenic protein- 1, bone morphogenic protein-2, bone morphogenic protein-3, bone morphogenic protein-4, bone morphogenic protein-5, bone morphogenic protein-6, bone morphogenic protein-7, bone morphogenic protein-8, bone morphogenic protein-9, bone morphogenic protein- 10, bone morphogenic protein- 11, bone morphogenic protein- 12, bone morphogenic protein- 13, bone morphogenic protein- 14, bone morphogenic protein- 15, bone morphogenic protein receptor IA, bone morphogenic protein receptor IB, brain derived
neurotrophic factor, ciliary neutrophic factor, ciliary neutrophic factor receptor, cytokine-induced neutrophil chemotactic factor 1 , cytokine-induced neutrophil, chemotactic factor 2, cytokine- induced neutrophil chemotactic factor 2, endothelial cell growth factor, endothelin 1 , epidermal growth factor, epithelial-derived neutrophil attractant, fibroblast growth factor 4, fibroblast growth factor 5, fibroblast growth factor 6, fibroblast growth factor 7, fibroblast growth factor 8, fibroblast growth factor 8b, fibroblast growth factor 8c, fibroblast growth factor 9, fibroblast growth factor 10, fibroblast growth factor 21 (FGF21)fibroblast growth factor acidic, fibroblast growth factor basic, glial cell line-derived neutrophic factor receptor- 1, glial cell line-derived neutrophic factor receptor-2, growth related protein, growth related protein- 1, growth related protein-2, growth related protein-3, heparin binding epidermal growth factor, hepatocyte growth factor, hepatocyte growth factor receptor, insulin-like growth factor I, insulin-like growth factor receptor, insulin-like growth factor II, insulin- like growth factor binding protein, keratinocyte growth factor, leukemia inhibitory factor, leukemia inhibitory factor receptor- 1, nerve growth factor nerve growth factor receptor, neurotrophin-3, neurotrophin-4, placenta growth factor, placenta growth factor 2, platelet- derived endothelial cell growth factor, platelet derived growth factor, platelet derived growth factor A chain, platelet derived growth factor AA, platelet derived growth factor AB, platelet derived growth factor B chain, platelet derived growth factor BB, platelet derived growth factor receptor- 1, platelet derived growth factor receptor-2, pre-B cell growth stimulating factor, stem cell factor, stem cell factor receptor, transforming growth factor- 1, transforming growth factor-2, transforming growth factor- 1, transforming growth factor- 1.2, transforming growth factor-2, transforming growth factor-3, transforming growth factor-S, latent transforming growth factor-1, transforming growth factor-1 binding protein I, transforming growth factor-1 binding protein II, transforming growth factor-1 binding protein III, tumor necrosis factor receptor type I, tumor necrosis factor receptor type II, urokinase-type plasminogen activator receptor, vascular endothelial growth factor, and chimeric proteins and biologically or immunologically active fragments thereof. In some embodiments, the therapeutic polypeptide is a mammalian G-CSF, a growth hormone, a leptin, a a- interferon, a β-interferon, a λ-interferon, a GM-CSF, a IL-11, a IL-10, a mokal (e.g., Moka, mokatoxin-1), or a VM-24. In some embodiments, the therapeutic polypeptide is a glucagon-like peptide 1 (GLP-1), exendin-4 (Ex-4), erythropoietin (EPO), fibroblast growth factor (FGF21), IL8, ziconotide, somatostatin, chlorotoxin, SDF1 (alpha), IL21, or derivative or variant thereof. The G- CSF may be a bovine G-CSF. The G-CSF, GM-CSF, EPO, FGF21, β-interferon and GLP-1 may be from a human.
[00419] The non-antibody sequence may comprise an amino acid sequence based on or derived from any of SEQ ID NOS: 317-332. The non-antibody sequence may comprise an amino acid sequence that is 50%, 60%, 70% 80%, 90%, 95%, 97%, 99% identical to any of SEQ ID NOS: 317-332. The non-antibody sequence may comprise an amino acid sequence that comprises 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or more amino acid residues of SEQ ID NOS: 317-332. The amino acid residues may be consecutive. Alternatively, the amino acid residues are non-consecutive. The non-antibody sequence may comprise at least a portion of any of SEQ ID NOS: 317-332.
[00420] The antibodies disclosed herein may comprise one or more sequences based on or derived from a mammalian, avian, reptilian, amphibian, fish, insect, bug, or arachnid sequence. Mammals include, but are not limited to, cows, bison, buffalo, humans, mice, dogs, cats, sheep, goats, or rabbits. Avians include, but are not limited to, chicken, geese, doves, eagles, sparrows, and pidgeons. Reptiles include, but are not limited to, lizards, gators, snakes, and turtles.
Amphibians include, but are not limited to, frogs, salamanders, toads, and newts. Fish include, but are not limited to, tuna, salmon, whales, and sharks. Insects, bugs, and arachnids include, but are not limited to, flies, mosquitos, spiders, and scorpions. The non-antibody sequence may be based on or derived from a bovine or human sequence. Alternatively, the non-antibody sequence is based on or derived from a lizard, snail, snake or scorpion sequence. The lizard may be a gila monster. The snail may be a cone snail.
[00421] In some embodiments, the non-antibody sequence is linked to an end of an ultralong
CDR3 sequence. For example, the non-antibody sequence can be linked to the 5' end or 3' end of the ultralong CDR3 nucleotide sequence. In another example, the non-antibody sequence can be linked to the N-terminus or C-terminus of the ultralong CDR3 peptide sequence.
[00422] In another embodiment, the non-antibody sequence is inserted within an ultralong
CDR3 sequence. For example, the non-antibody sequence is inserted between the stalk domain of an ultralong CDR3 sequence. The non-antibody sequence can be inserted within the stalk domain of an ultralong CDR3 sequence. In another example, the non-antibody sequence is inserted between the stalk domain and the knob domain of an ultralong CDR3 sequence. Alternatively, the non- antibody sequence is inserted within the knob domain of an ultralong CDR3 sequence.
[00423] In some embodiments, the non-antibody sequence replaces at least a portion of an ultralong CDR3 sequence. The non-antibody sequence can replace about 1 or more, 2 or more, 3 or more, 4 or more, 5 or more, 10 or more, 15 or more, 20 or more, 25 or more, 30 or more, 35 or more, 40 or more, 45 or more, 50 or more, 55 or more amino acids of the ultralong CDR3 peptide sequence. The non-antibody sequence can replace about 10% or more, 20% or more, 30%> or more, 40%) or more, 50%> or more, 55% or more, 60%> or more, 65%> or more, 70%> or more, 75% or more, 80%) or more, 85% or more, 90%> or more, 95% or more of the ultralong CDR3 peptide sequence. The non-antibody sequence can replace at least a portion of a knob domain of an ultralong CDR3. The non-antibody sequence can replace about 5 or more, 10 or more, 15 or more, 20 or more, 25 or more, 30 or more, 35 or more, 40 or more, 45 or more amino acids of the knob domain of an ultralong CDR3 peptide sequence. The non-antibody sequence can replace about 10% or more, 20%) or more, 30% or more, 40% or more, 50% or more, 55% or more, 60% or more, 65% or more, 70%) or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% or more of the knob domain of the ultralong CDR3 peptide sequence. The non-antibody sequence can replace at least a portion of a stalk domain of an ultralong CDR3. The non-antibody sequence can replace about 1 or more, 2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, 10 or more, 11 or more, 12 or more, 13 or more, 14 or more, 15 or more, 20 or more amino acids of the stalk domain of an ultralong CDR3 peptide sequence. The non-antibody sequence can replace about 10%) or more, 20% or more, 30% or more, 40% or more, 50% or more, 55% or more, 60% or more, 65%) or more, 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% or more of the stalk domain of the ultralong CDR3 peptide sequence. The amino acids may be consecutive amino acids. Alternatively, the amino acids are non-consecutive amino acids. The ultralong CDR3 may comprise one or more conserved motifs. The conserved motifs may be stalk domain conserved motifs as disclosed herein. Alternatively, the conserved motifs may be knob domain conserved motifs as disclosed herein.
[00424] In some embodiments, the non-antibody sequence replaces at least a portion of an ultralong CDR3 sequence. The non-antibody sequence can replace about 5 or more, 10 or more, 15 or more, 20 or more, 25 or more, 30 or more, 40 or more, 50 or more, 55 or more, 60 or more, 70 or more, 80 or more, 90 or more, 100 or more, 110 or more, 120 or more, 130 or more, 140 or more, 150 or more, 160 or more, 170 or more nucleotides of the ultralong CDR3 nucleotide sequence. The non-antibody sequence can replace about 10% or more, 20% or more, 30% or more, 40% or more, 50% or more, 55% or more, 60% or more, 65% or more, 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% or more of the ultralong CDR3 nucleotide sequence. The non-antibody sequence can replace at least a portion of a knob domain of an ultralong CDR3. The non-antibody sequence can replace about 5 or more, 10 or more, 15 or more, 20 or more, 25 or more, 30 or more, 40 or more, 50 or more, 55 or more, 60 or more, 70 or more, 80 or more, 90 or more, 100 or more, 110 or more, 120 or more, 130 or more, 140 or more nucleotides of the knob domain of an ultralong CDR3 nucleotide sequence. The non-antibody sequence can replace about 10% or more, 20% or more, 30%> or more, 40%> or more, 50%> or more, 55% or more, 60% or more, 65%) or more, 70%> or more, 75% or more, 80%> or more, 85% or more, 90%> or more, 95% or more of the knob domain of the ultralong CDR3 nucleotide sequence. The non-antibody sequence can replace at least a portion of a stalk domain of an ultralong CDR3. The non-antibody sequence can replace about 5 or more, 10 or more, 15 or more, 20 or more, 25 or more, 30 or more, 35 or more, 40 or more, 45 or more, 50 or more, 55 or more, 60 or more, 65 or more, 70 or more nucleotides of the stalk domain of an ultralong CDR3 nucleotide sequence. The non-antibody sequence can replace about 10% or more, 20% or more, 30% or more, 40% or more, 50% or more, 55% or more, 60%) or more, 65% or more, 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% or more of the stalk domain of the ultralong CDR3 nucleotide sequence. The nucleotides may be consecutive nucleotides. Alternatively, the nucleotides are non-consecutive nucleotides. The ultralong CDR3 may comprise one or more conserved motifs. The conserved motifs may be stalk domain conserved motifs as disclosed herein. Alternatively, the conserved motifs may be knob domain conserved motifs as disclosed herein.
[00425] An antibody comprising an ultralong CDR3 sequence and a non-antibody sequence may further comprise one or more cleavage sites between the ultralong CDR3 sequence and the non-antibody sequence. The one or more cleavage sites may be in front of the N-terminus of the non-antibody peptide sequence. For example, a cleavage site is inserted at the N-terminus of the non-antibody peptide sequence and at the C-terminus of the ultralong CDR3 peptide sequence. Alternatively, the one or more cleave sites are behind the C-terminus of the non-antibody peptide sequence. For example the cleavage site is inserted at the C-terminus of the non-antibody peptide sequence and at the N-terminus of the ultralong CDR3 peptide sequence. The one or more cleavage sites may flank both the N-terminus and the C-terminus of the non-antibody peptide sequence. The one or more cleavage sites may be upstream of the non-antibody nucleotide sequence. For example, the one or more cleavage sites may be at the 5' end of the non-antibody nucleotide sequence and at the 3' end of the ultralong CDR3 nucleotide sequence. The one or more cleavage sites may be downstream of the non-antibody nucleotide sequence. For example, the one or more cleavage sites may be at the 3' end of the non-antibody nucleotide sequence and at the 5' end of the ultralong CDR3 nucleotide sequence. The one or more cleavage sites may flank both the 5' end and the 3' end of the non-antibody nucleotide sequence. The one or more cleavage sites may directly flank the non-antibody sequence. For example, there are zero nucleotides or amino acids between the cleavage site sequence and the non-antibody sequence. Alternatively, the one or more cleavage sites may indirectly flank the non-antibody sequence. For example, there are one or more nucleotides between the cleavage site nucleotide sequence and the non-antibody nucleotide sequence. There may be 2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, 10 or more, 12 or more, 15 or more, 20 or more nucleotides between the cleavage site nucleotide sequence and the non-antibody nucleotide sequence. In another example, there are one or more amino acids between the cleavage site peptide sequence and the non-antibody peptide sequence. There may be 2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, 10 or more, 12 or more, 15 or more, 20 or more amino acids between the cleavage site peptide sequence and the non-antibody peptide sequence. The cleavage site may be adjacent to the sequence based on or derived from the ultralong CDR3 sequence, linker sequence, non- antibody sequence, non-bovine sequence, or a combination thereof. The cleavage site may be between the sequence based on or derived from the ultralong CDR3 sequence and the linker sequence. The cleavage site may be between the sequence based on or derived from the ultralong CDR3 sequence and the non-antibody sequence. The cleavage site may be between the linker sequence and the non-antibody sequence. The cleavage site may be for a protease. The protease may be a serine protease, threonine protease, cysteine protease, aspartate protease, or
metalloprotease. The protease may include, but is not limited to, Factor Xa protease, chymotrypsin- like protease, trypsin-like protease, elastase-like protease, subtilisin-like protease, actinidain, bromelain, calpains, caspases, cathepsins, Mir 1 -CP, papain, HIV-1 protease, chymosin, renin, cathepsin D, pepsin, plasmepsin, nepenthesin, metalloexopeptidases, and metalloendopeptidases. The cleavage site may be a cleavage site for Factor Xa or thrombin. For example, the cleavage site may comprise the amino acid sequence of IEGR. Alternatively, the cleavage site is for a nuclease. The antibody comprising the ultralong CDR3 sequence and non-antibody sequence may be cleaved by one or more proteases. Cleavage of the antibody by the one or more protease can result in release of one or more ends of the non-antibody peptide from the ultralong CDR3 region of the antibody. For example, cleavage of the antibody results in release of the N-terminus of the non- antibody peptide from the ultralong CDR3 region. Alternatively, cleavage of the antibody results in release of the C-terminus of the non-antibody peptide from the ultralong CDR3 region.
[00426] The non-antibody sequence may be linked to the ultralong CDR3 sequence via one or more linkers. The non-antibody sequence may be inserted with an ultralong CDR3 sequence. In some instances, two or more linkers are used to link the non-antibody sequence to the ultralong CDR3 sequence. The two or more linkers may comprise the same sequence. Alternatively, the two or more linkers comprise different sequences. The one or more linker sequences may be the same length. The one or more linker sequences may be different lengths. The one or more linker sequences may be 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more or 10 or more amino acids in length. The one or more linker sequences may comprise 1 or more, 2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, or 10 or more glycine residues. The one or more linker sequences may comprise 2 or more, 3 or more, 4 or more, or 5 or more consecutive glycine residues. The one or more linker sequences may comprise 1 or more serine residues. The one or more linker sequences may comprise 1 or more, 2 or more, 3 or more, 4 or more, or 5 or more polar amino acid residues. The polar amino acid residues may be selected from serine, threonine, asparagine, or glutamine. The polar amino acid residues may comprise uncharged side chains. The linkers may be attached to the N-terminal, C-terminal, or both N-and C-termini of the non-antibody peptide sequence. The linkers may be attached to the 5 '-end, 3 '-end, or both the 5 '-and 3 'ends of the non-antibody nucleotide sequence. In some embodiments, the linker may comprise amino acid residues. Exemplary amino acid linker components include a dipeptide, a tripeptide, a tetrapeptide or a pentapeptide. Exemplary dipeptides include: valine- citrulline (vc or val-cit), alanine-phenylalanine (af or ala-phe). Exemplary tripeptides include: glycine-valine-citrulline (gly-val-cit) and glycine-glycine-glycine (gly-gly-gly). Alternatively, the linker comprises an amino acid sequence of (GGGGS)n (SEQ ID NO: 339) wherein n = 1 to 5. The linker may comprise an amino acid sequence of GGGSGGGGS (SEQ ID NO: 337) or
GGGGSGGGS (SEQ ID NO: 338). Amino acid residues which comprise an amino acid linker component include those occurring naturally, as well as minor amino acids and non-naturally occurring amino acids including analogs, such as citrulline. Amino acid linker components can be designed and optimized in their selectivity for enzymatic cleavage by a particular enzymes, for example, a tumor-associated protease, cathepsin B, C and D, or a plasmin protease.
[00427] The ultralong CDR3 may be based on or derived from a single ultralong CDR3 sequence. Alternatively, the ultralong CDR3 is based on or derived from two or more ultralong CDR3 sequences. The two or more ultralong CDR3 sequences may be from the same animal. Alternatively, the two or more ultralong CDR3 sequences are from two or more different animals.
[00428] The ultralong CDR3 may comprise at least a portion of a stalk domain of an ultralong CDR3. The antibodies disclosed herein may comprise 1 or more, 2 or more, 3 or more, 4 or more, 5 or more, 6 or more 7 or more, 8 or more, 9 or more, or 10 or more amino acids derived from or based on the stalk domain of the ultralong CDR3. The antibodies disclosed herien may comprise 20 or fewer, 19 or fewer, 18 or fewer, 17 or fewer, 16 or fewer, 15 or fewer, 14 or fewer, 13 or fewer, 12 or fewer, 11 or fewer, 10 or fewer, 9 or fewer, 8 or fewer, 7 or fewer, 6 or fewer, 5 or fewer, 4 or fewer, 3 or fewer, or 2 or fewer amino acids derived from or based the stalk domain of the ultralong CDR3. The amino acids may be consecutive amino acids. Alternatively, the amino acids are non-consecutive amino acids. The antibodies disclosed herein may comprise a sequence that is 50% or more, 60%> or more, 70%> or more, 80%> or more, 85% or more, 90%> or more, 95% or more, 97% or more, 99% or more, or 100% homologous the sequence of the stalk domain of the ultralong CDR3. The ultralong CDR3 may comprise one or more conserved motifs derived from or based on a stalk domain of the ultralong CDR3. The antibodies disclosed herein may comprise 1 or more, 2 or more, 3 or more, 4 or more, or 5 or more conserved motifs derived from or based on the stalk domain of the ultralong CDR3. The one or more conserved motifs derived from or based on the stalk domain of the ultralong CDR3 may comprise a sequence selected from any one of SEQ ID NOS: 157-307 and SEQ ID NOS: 333-336. The antibodies disclosed herein may comprise a sequence that is 50% or more, 60% or more, 70% or more, 80% or more, 85% or more, 90% or more, 95% or more, 97% or more, 99% or more, or 100%) homologous to a sequence selected from any one of SEQ ID NOS: 157-224 and 235-295. The antibodies disclosed herein may comprise a sequence that is 50% or more, 60% or more, 70% or more, 80% or more, 85% or more, 90% or more, 95% or more, 97% or more, 99% or more, or 100%) homologous to a sequence selected from any one of SEQ ID NOS: 225-227.
[00429] The one or more conserved motifs derived from or based on the stalk domain of the ultralong CDR3 may comprise a CT(T/S)VHQ motif. Alternatively, the one or more conserved motifs derived from or based on the stalk domain of the ultralong CDR3 comprise a
CT(T/S)VHQXn motif. In some instances, n is between 1 to 8, between 1 to 7, between 1 to 6, between 1 to 5, between 1 to 4, or between 1 to 3. The one or more conserved motifs derived from or based on the stalk domain of the ultralong CDR3 may comprise a CX1 X2 X3 X4Q motif. X1 may be a T, S, A, or G residue. X2 may be a T, S, A, P, or I residue. X3 may be a V or K residue. X4 may be an H, K, or Y residue. The one or more conserved motifs derived from or based on the stalk domain of the ultralong CDR3 may comprise an X1 X2VHQ motif. X1 may be a T, S, A, or G residue. X2 may be a T, S, A, P or I residue. The one or more conserved motifs derived from or based on the stalk domain of the ultralong CDR3 may comprise a CX1 X2VHQ motif. X1 may be a T, S, A, or G residue. X2 may be a T, S, A, P or I residue. The one or more conserved motifs derived from or based on the stalk domain of the ultralong CDR3 may comprise an X1 X2VX3Q motif. X1 may be a T, S, A, or G residue. X2 may be a T, S, A, P or I residue. X3 may be an H, Y or K residue. The one or more conserved motifs derived from or based on the stalk domain of the ultralong CDR3 may comprise a CX1 X2VX3Q motif. X1 may be a T, S, A, or G residue. X2 may be a T, S, A, P or I residue. X3 may be an H, Y or K residue. The one or more conserved motifs derived from or based on the stalk domain of the ultralong CDR3 may comprise an X1 X2K Q motif. X1 may be a T, S, A, or G residue. X2 may be a T, S, A, P or I residue. The one or more conserved motifs derived from or based on the stalk domain of the ultralong CDR3 may comprise a CX1 X2K Q motif X1 may be a T, S, A, or G residue. X2 may be a T, S, A, P or I residue.
[00430] The one or more conserved motifs derived from or based on the stalk domain of the ultralong CDR3 may comprise an YX1 YX2 motif. X1 may be a T, S, N, or I residue. X2 may be an E or D residue. The one or more conserved motifs derived from or based on the stalk domain of the ultralong CDR3 may comprise an YX1 YX2Y motif. X1 may be an L, S, T, or R residue. X2 may be a T, S, N or I residue. The one or more conserved motifs derived from or based on the stalk domain of the ultralong CDR3 may comprise an YX1 YX2YX3 motif. X1 may be an L, S, T, or R residue. X2 may be a T, S, N or I residue. X3 may be an E or D residue. The one or more conserved motifs derived from or based on the stalk domain of the ultralong CDR3 may comprise an YXJYX2YX3X4 motif. X1 may be an L, S, T, or R residue. X2 may be a T, S, N or I residue. X3 may be an E or D residue. X4 may be an H, W, N, F, I or Y residue. The one or more conserved motifs derived from or based on the stalk domain of the ultralong CDR3 may comprise an Y(E/D)X motif. X may be an H, W, N, F, I or Y residue. The one or more conserved motifs derived from or based on the stalk domain of the ultralong CDR3 may comprise an XY(E/D) motif. X may be a T, S, N or I residue. The one or more conserved motifs derived from or based on the stalk domain of the ultralong CDR3 may comprise an Y(E/D)X1XnW motif. X1 may be an H, W, N, F, I or Y residue. In some instances, n is between 1 to 4, between 1 to 3, or between 1 to 2. The one or more conserved motifs derived from or based on the stalk domain of the ultralong CDR3 may comprise an Y(E/D)X1X2 X3X4X5W motif. X1 may be an H, W, N, F, I or Y residue. X2 may be an Y, H, G, or N residue. X3 may be a V, I, or A residue. X4 may be a D, N, T, or E residue. X5 may be an A, V, S, or T residue.
[00431] The antibodies disclosed herein may comprise a first conserved motif derived from or based on the stalk domain of the ultralong CDR3 selected from any of SEQ ID NOS: 157-234 and a second conserved motif derived from or based on the stalk domain of the ultralong CDR3 selected from any of SEQ ID NOS: 235-307 and SEQ ID NOS: 333-336. The antibodies disclosed herein may comprise a first conserved motif derived from or based on the stalk domain of the ultralong CDR3 selected from a group comprising CT(T/S)VHQXn, CX!X2 X3X4Q, X1X2VHQ, CX!X2 VHQ, X1X2VX3Q, CX1X2VX3Q, X!X2KKQ, and CX1X2K Q and a second conserved motif derived from or based on the stalk domain of the ultralong CDR3 selected from the group comprising YX!YX2, YX!YX2Y, YX!YX2YX3, YX!YX2YX3X4, Y(E/D)X, XY(E/D),
Y(E/D)X1XnW, and Y(E/D)X1X2 X3X4X5W.
[00432] The ultralong CDR3 may comprise at least a portion of a knob domain of an ultralong CDR3. The antibodies disclosed herein may comprise 1 or more, 2 or more, 3 or more, 4 or more, 5 or more, 6 or more 7 or more, 8 or more, 9 or more, or 10 or more amino acids derived from or based on the knob domain of the ultralong CDR3. The antibodies disclosed herien may comprise 20 or fewer, 19 or fewer, 18 or fewer, 17 or fewer, 16 or fewer, 15 or fewer, 14 or fewer, 13 or fewer, 12 or fewer, 1 1 or fewer, 10 or fewer, 9 or fewer, 8 or fewer, 7 or fewer, 6 or fewer, 5 or fewer, 4 or fewer, 3 or fewer, or 2 or fewer amino acids derived from or based the knob domain of the ultralong CDR3. The amino acids may be consecutive amino acids. Alternatively, the amino acids are non-consecutive amino acids. The antibodies disclosed herein may comprise a sequence that is 50% or more, 60%> or more, 70%> or more, 80%> or more, 85% or more, 90%> or more, 95% or more, 97% or more, 99% or more, or 100% homologous the sequence of the knob domain of the ultralong CDR3. The ultralong CDR3 may comprise one or more conserved motifs derived from or based on a knob domain of the ultralong CDR3. The antibodies disclosed herein may comprise 1 or more, 2 or more, 3 or more, 4 or more, or 5 or more conserved motifs derived from or based on the knob domain of the ultralong CDR3. The one or more conserved motifs derived from or based on the knob domain may comprise a cysteine motif as disclosed herein. Alternatively, or additionally, one or more conserved motifs derived from or based on the knob domain comprises a C(P/S)DG motif.
[00433] The antibodies disclosed herein may comprise a sequence based on or derived from a mammal. The mammal may be a bovine. Alternatively, the mammal is a non-bovine mammal, such as a human. The antibody sequences may be 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, 10 or more, 1 1 or more, 12 or more, 15 or more, 20 or more, 25 or more, 30 or more, 35 or more, 40 or more 45 or more, 50 or more, 55 or more, 60 or more, 65 or more 70 or more, 80 or more, 90 or more, 100 or more, 1 10 or more, 120 or more, 130 or more, 140 or more, 150 or more, 160 or more, 170 or more, 180 or more 190 or more, 200 or more, 220 or more, 230 or more, 240 or more 250 or more 260 or more, 270 or more, 280 or more, 290 or more or 300 or more amino acids in length. The amino acids may be consecutive amino acids.
Alternatively, the amino acids are non-consecutive amino acids.
[00434] The antibody sequences may comprise a bovine antibody sequence comprising 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, 10 or more, 1 1 or more, 12 or more, 15 or more, 20 or more, 25 or more, 30 or more, 35 or more, 40 or more 45 or more, 50 or more, 55 or more, 60 or more, 65 or more 70 or more, 80 or more, 90 or more, 100 or more, 1 10 or more, 120 or more, 130 or more, 140 or more, 150 or more, 160 or more, 170 or more, 180 or more 190 or more, 200 or more, 220 or more, 230 or more, 240 or more 250 or more 260 or more, 270 or more, 280 or more, 290 or more or 300 or more amino acids in length. The bovine antibody may be a BLVH12, BLV5B8, BLVCV1 , BLV5D3, BLV8C1 1 , BF1H1 , or F18 antibody. The antibody sequences may comprise a human antibody sequence comprising 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, 10 or more, 11 or more, 12 or more, 15 or more, 20 or more, 25 or more, 30 or more, 35 or more, 40 or more 45 or more, 50 or more, 55 or more, 60 or more, 65 or more 70 or more, 80 or more, 90 or more, 100 or more, 110 or more, 120 or more, 130 or more, 140 or more, 150 or more, 160 or more, 170 or more, 180 or more 190 or more, 200 or more, 220 or more, 230 or more, 240 or more 250 or more 260 or more, 270 or more, 280 or more, 290 or more or 300 or more amino acids in length. The amino acids may be consecutive amino acids. Alternatively, the amino acids are non-consecutive amino acids.
[00435] The antibody sequence based on or derived from at least a portion of the ultralong
CDR3 can be 20 or fewer, 19 or fewer, 18 or fewer, 17 or fewer, 16 or fewer, 15 or fewer, 14 or fewer, 13 or fewer, 12 or fewer, 11 or fewer, 10 or fewer, 9 or fewer, 8 or fewer, 7 or fewer, 6 or fewer, or 5 or fewer amino acids in length. The antibody sequence based on or derived from at least a portion of the ultralong CDR3 may be 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, 10 or more, 11 or more, 12 or more, 13 or more, 14 or more, or 15 or more amino acids in length. The amino acids may be consecutive amino acids. Alternatively, the amino acids are non-consecutive amino acids.
[00436] The antibody sequence based on or derived from at least a portion of the ultralong
CDR3 can contain 1 or more, 2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, 10 or more, 15 or more, 20 or more, 25 or more, 30 or more, 35 or more, 40 or more, 50 or more, 60 or more, 70 or more, 80 or more, 90 or more, or 100 or more nucleic acid modifications or alterations in the nucleotide sequence of the ultralong CDR3 from which it is based on or derived from. The modifications and/or alterations may comprise substitutions, deletions, and/or insertions. Substitutions may comprise replacing one nucleic acid with another nucleic acid. The nucleic acid may be a natural nucleic acid or a non-natural nucleic acid.
[00437] The antibody sequence based on or derived from at least a portion of the ultralong
CDR3 can contain 1 or more, 2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, 10 or more, 15 or more, 20 or more, 25 or more, 30 or more, 35 or more, 40 or more, 50 or more, or 60 or more amino acid modifications or alterations in the peptide sequence of the ultralong CDR3 from which it is based on or derived from. The modifications and/or alterations may comprise substitutions, deletions, and/or insertions. Substitutions may comprise replacing one amino acid with another amino acid. The amino acids to be substituted may contain one or more similar features to the amino acid by which it is replaced. The features may include, but are not limited to, size, polarity, hydrophobicity, acidity, side chain, and bond formations. The amino acid may be a natural amino acid or a non-natural amino acid. [00438] In certain embodiments, the half-life of an antibody described herein is greater than the half-life of the un-conjugated therapeutic peptide or un-conjugated non-antibody peptide that is incorporated in the antibody. In some embodiments, the half-life of an antibody provided herein is greater than 4 hours when administered to a subject. In certain embodiments, the half-life of an antibody provided herein is greater than 4 hours, greater than 6 hours, greater than 12 hours, greater than 24 hours, greater than 36 hours, greater than 2 days, greater than 3 days, greater than 4 days, greater than 5 days, greater than 6 days, greater than 7 days, greater than 8 days, greater than 9 days, greater than 10 days, greater than 11 days, greater than 12 days, greater than 13 days, or greater than 14 days when administered to a subject. In some instances, the subject is a mammal. In some embodiments, the subject is a mouse or a bovine. In other instances, the subject is a human. In certain embodiments, a pharmaceutical composition comprising the antibody is administered to the subject once a day, every two days, every three days, every 4 days, every 7 days, every 10 days, every 14 days, every 21 days, every 28 days, every 2 months, or every three months.
[00439] The antibodies may be modified or altered to reduce immunogenicity. For example, the sequence of a partially bovine or non-bovine antibody may be modified or altered to reduce immunogenicity to humans. A non-human antibody may be humanized to reduce imrnunogenicity to humans, while retaining the specificity and affinity of the parental non-human antibody.
Generally, a humanized antibody comprises one or more variable domains in which HVRs, e.g., 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. In some embodiments, some FR residues in a humanized antibody are substituted with corresponding residues from a non-human antibody (e.g., the antibody from which the HVR residues are derived), e.g., to restore or improve antibody specificity or affinity.
[00440] The antibodies comprising an ultralong CDR3 as disclosed herein are preferably monoclonal. Also encompassed within the scope of the disclosure are Fab, Fab', Fab'-SH and F(ab')2 fragments of the antibodies comprising an ultralong CDR3 as provided herein. These antibody fragments can be created by traditional means, such as enzymatic digestion, or may be generated by recombinant techniques. Such antibody fragments may be chimeric or humanized. These fragments are useful for the diagnostic and therapeutic purposes set forth below.
[00441] Monoclonal antibodies are obtained from a population of substantially homogeneous antibodies, e.g., the individual antibodies comprising the population are identical except for possible naturally occurring mutations that may be present in minor amounts. Thus, the modifier "monoclonal" indicates the character of the antibody as not being a mixture of discrete antibodies. [00442] The antibodies comprising an ultralong CDR3 as disclosed herein can be made using a hybridoma cell-based method first described by Kohler et ah, Nature, 256:495 (1975), or may be made by recombinant DNA methods.
[00443] Hybridoma cells can be generated by fusing B cells producing a desired antibody with an immortalized cell line, usually a myeloma cell line, so that the resulting fusion cells will be an immortalized cell line that secrets a particular antibody. By the same principle, myeloma cells can be first transfected with a nucleic acid encoding a germline antibody V region and can be screened for the expression of the germline V region. Those myeloma cells with highest level of proteolytic light chain expression can be subsequently fused with B cells that produce an antibody with desired target protein specificity. The fusion cells will produce two types of antibodies: one is a heterologous antibody containing an endogenous antibody chain (either heavy or light) operably joined to the recombinant germline V region (either heavy or light), and the other is the same antibody that the parental B cells would secrete (e.g. both endogenous heavy and light chains). The operably joined heterologous heavy and light chains can be isolated by conventional methods such as chromatography and identification can be confirmed by target protein binding assays, assays identifying a unique tag of the germline polypeptide, or endopeptidase activity assays described in other sections of this disclosure. In some cases, where the heterologous antibody is the predominant type in quantity among the two types of antibodies, such isolation may not be needed.
[00444] The hybridoma cells may be seeded and grown in a suitable culture medium that preferably contains one or more substances that inhibit the growth or survival of the unfused, parental myeloma cells. For example, if the parental myeloma cells lack the enzyme hypoxanthine guanine phosphoribosyl transferase (HGPRT or HPRT), the culture medium for the hybridomas typically will include hypoxanthine, aminopterin, and thymidine (HAT medium), which substances prevent the growth of HGPRT-deficient cells.
[00445] Preferred myeloma cells are those that fuse efficiently, support stable high-level production of antibody by the selected antibody-producing cells, and are sensitive to a medium such as HAT medium. Among these, myeloma cell lines may be murine myeloma lines, such as those derived from MOPC-21 and MPC-11 mouse tumors available from the Salk Institute Cell Distribution Center, San Diego, Calif. USA, and SP-2 or X63-Ag8-653 cells available from the American Type Culture Collection, Rockville, Md. USA. Human myeloma and mouse-human heteromyeloma cell lines also have been described for the production of human monoclonal antibodies (Kozbor, J. Immunol, 133:3001 (1984); Brodeur et al., Monoclonal Antibody
Production Techniques and Applications, pp. 51-63 (Marcel Dekker, Inc., New York, 1987)). [00446] Culture medium in which hybridoma cells are growing is assayed for production of antibodies comprising an ultralong CDR3. For example, the binding specificity of monoclonal antibodies produced by hybridoma cells may be determined by immunoprecipitation or by an in vitro binding assay, such as an enzyme- linked immuno adsorbent assay (ELISA).
[00447] The binding affinity of the monoclonal antibody can, for example, be determined by the Scatchard analysis of Munson et al., Anal. Biochem., 107:220 (1980).
[00448] After hybridoma cells are identified that produce antibodies of the desired specificity, affinity, and/or activity, the clones may be subcloned by limiting dilution procedures and grown by standard methods (Goding, Monoclonal Antibodies: Principles and Practice, pp. 59- 103 (Academic Press, 1986)). Suitable culture media for this purpose include, for example, D- MEM or RPMI-1640 medium. In addition, the hybridoma cells may be grown in vivo as ascites tumors in an animal.
[00449] The monoclonal antibodies secreted by the subclones are suitably separated from the culture medium, ascites fluid, or serum by conventional immunoglobulin purification procedures such as, for example, protein A-Sepharose, hydroxylapatite chromatography, gel electrophoresis, dialysis, or affinity chromatography.
[00450] The antibodies comprising an ultralong CDR3 as disclosed herein may be made by using combinatorial libraries to screen for synthetic antibody clones with the desired activity or activities. For example, synthetic antibody clones are selected by screening phage libraries containing phage that display various fragments of antibody variable regions {e.g., scFv or Fab) fused to phage coat protein. Such phage libraries may be panned, for example, by affinity chromatography against the desired antigen. Clones expressing antibody fragments capable of binding to the desired antigen may be adsorbed to the antigen and thus separated from the non- binding clones in the library. The binding clones may then be eluted from the antigen, and can be further enriched by additional cycles of antigen adsorption/elution. Any of the antibodies comprising an ultralong CDR3 as disclosed herein may be obtained by designing a suitable antigen screening procedure to select for the phage clone of interest followed by construction of a full length antibody comprising an ultralong CDR3 clone using the VH and VL {e.g., from scFv or Fab) sequences from the phage clone of interest and suitable constant region (Fc) sequences described in Kabat et al., Sequences of Proteins of Immunological Interest, Fifth Edition, NIH Publication 91- 3242, Bethesda Md. (1991), vols. 1-3.
[00451] The antigen-binding domain of an antibody is formed from two variable (V) regions, one each from the light (VL) and heavy (VH) chains, that both present three hypervariable loops or complementarity-determining regions (CDRs). Variable domains may be displayed functionally on phage, either as single-chain Fv (scFv, also referred to as single-chain antibody (SCA)) fragments, in which VH and VL are covalently linked through a short, flexible peptide, or as Fab fragments, in which they are each fused to a constant domain and interact non-covalently, as described in Winter et al., Ann. Rev. Immunol, 12: 433-455 (1994). scFv or SCA encoding phage clones and Fab encoding phage clones may be separately or collectively referred to as "Fv phage clones" or "Fv clones".
[00452] Repertoires of VH and VL genes may be separately cloned by polymerase chain reaction (PCR) and recombined randomly in phage libraries, which can then be searched for antigen-binding clones as described in Winter et al., Ann. Rev. Immunol, 12: 433-455 (1994). Libraries from immunized sources provide high-affinity antibodies to the immunogen without the requirement of constructing hybridomas. Alternatively, the naive repertoire may be cloned to provide a single source of human antibodies to a wide range of non-self and also self antigens without any immunization as described by Griffiths et al., EMBO J. 12: 725-734 (1993). Finally, naive libraries can also be made synthetically by cloning the unrearranged V-gene segments from stem cells, and using PCR primers containing random sequence to encode the highly variable CDR3 regions and to accomplish rearrangement in vitro as described by Hoogenboom and Winter, J. Mol. Biol, 227: 381-388 (1992).
[00453] Filamentous phage is used to display antibody fragments by fusion to the minor coat protein pill. Protein pill may include truncated forms of pill. The antibody fragments can be displayed as single chain Fv fragments, in which VH and VL domains are connected on the same polypeptide chain by a flexible polypeptide spacer, (e.g., as described by Marks et al., J. Mol. Biol, 222: 581-597 (1991)), or as Fab fragments, in which one chain is fused to pill (e.g., a truncated pill) and the other is secreted into the bacterial host cell periplasm where assembly of a Fab-coat protein structure which becomes displayed on the phage surface by displacing some of the wild type coat proteins, (e.g., as described in Hoogenboom et al., Nucl. Acids Res., 19: 4133-4137 (1991)).
[00454] Nucleic acid encoding antibody variable gene segments (including VH and VL segments) are recovered from the cells of interest and and may be amplified or copies made by recombinant DNA techniques (e.g., Kunkel mutagenesis). For example, in the case of rearranged VH and VL gene libraries, the desired DNA may be obtained by isolating genomic DNA or mRNA from lymphocytes followed by polymerase chain reaction (PCR) with primers matching the 5' and 3' ends of rearranged VH and VL genes as described in Orlandi et al., Proc. Natl. Acad. Sci. (USA), 86: 3833-3837 (1989), thereby making diverse V gene repertoires for expression. The V genes may be amplified from cDNA and genomic DNA, with back primers at the 5' end of the exon encoding the mature V-domain and forward primers based within the J-segment as described in Orlandi et al. (1989) and in Ward et al, Nature, 341 : 544-546 (1989). For amplifying from cDNA, back primers can also be based in the leader exon as described in Jones et al, Biotechnol, 9: 88-89 (1991), and forward primers within the constant region as described in Sastry et al, Proc. Natl. Acad. Sci. (USA), 86: 5728-5732 (1989). To enhance or maximize complementarity, degeneracy may be incorporated in the primers as described in Orlandi et al. (1989) or Sastry et al. (1989). Library diversity may be enhanced or maximized by using PCR primers targeted to each V-gene family in order to amplify available VH and VL arrangements present in the immune cell nucleic acid sample, for example, as described in the method of Marks et al, J. Mol. Biol, 222: 581-597 (1991) or as described in the method of Orum et al, Nucleic Acids Res., 21 : 4491-4498 (1993). For cloning of the amplified DNA into expression vectors, rare restriction may can be introduced within the PCR primer as a tag at one end as described in Orlandi et al. (1989), or by further PCR amplification with a tagged primer as described in Clackson et al, Nature, 352: 624-628 (1991).
[00455] Repertoires of synthetically rearranged V genes may be derived in vitro from V gene segments. Most of the human VH-gene segments have been cloned and sequenced (e.g., reported in Tomlinson et al, J. Mol. Biol, 227: 776-798 (1992)), and mapped (e.g., reported in Matsuda et al, Nature Genet., 3: 88-94 (1993); these cloned segments (including all the major conformations of the HI and H2 loop) may be used to generate diverse VH gene repertoires with PCR primers encoding H3 loops of diverse sequence and length as described in Hoogenboom and Winter, J. Mol. Biol, 227: 381-388 (1992). VH repertoires may also be made with all the sequence diversity focused in a long H3 loop of a single length as described in Barbas et al, Proc. Natl. Acad. Sci. USA, 89: 4457-4461 (1992). Human VK and νλ. segments have been cloned and sequenced (reported in Williams and Winter, Eur. J. Immunol, 23: 1456-1461 (1993)) and can be used to make synthetic light chain repertoires. Synthetic V gene repertoires, based on a range of VH and VL folds, and L3 and H3 lengths, will encode antibodies of considerable structural diversity.
Following amplification of V-gene encoding DNAs, germline V-gene segments can be rearranged in vitro according to the methods of Hoogenboom and Winter, J. Mol. Biol, 227: 381-388 (1992).
[00456] Repertoires of antibody fragments may be constructed by combining VH and VL gene repertoires together in several ways. Each repertoire may be created in different vectors, and the vectors recombined in vitro, for example, as described in Hogrefe et al, Gene, 128: 119-126 (1993), or in vivo by combinatorial infection, for example, the loxP system described in
Waterhouse et al, Nucl. Acids Res., 21 : 2265-2266 (1993). The in vivo recombination approach exploits the two-chain nature of Fab fragments to overcome the limit on library size imposed by E. coli transformation efficiency. Naive VH and VL repertoires are cloned separately, one into a phagemid and the other into a phage vector. The two libraries are then combined by phage infection of phagemid-containing bacteria so that each cell contains a different combination and the library size is limited only by the number of cells present (about 1012 clones). Both vectors contain in vivo recombination signals so that the VH and VL genes are recombined onto a single replicon and are co-packaged into phage virions. These large libraries may provide large numbers of diverse antibodies of good affinity (K 1 of about 10~8 M).
[00457] Alternatively, the repertoires may be cloned sequentially into the same vector, for example, as described in Barbas et al, Proc. Natl. Acad. Sci. USA, 88: 7978-7982 (1991), or assembled together by PCR and then cloned, for example, as described in Clackson et al, Nature, 352: 624-628 (1991). PCR assembly may also be used to join VH and VL DNAs with DNA encoding a flexible peptide spacer to form single chain Fv (scFv) repertoires. In yet another technique, "in cell PCR assembly" may be used to combine VH and VL genes within lymphocytes by PCR and then clone repertoires of linked genes as described in Embleton et al, Nucl. Acids Res., 20: 3831-3837 (1992).
[00458] The antibodies produced by naive libraries (either natural or synthetic) can be of moderate affinity (K 1 of about 106 to 107M_1), but affinity maturation may also be mimicked in vitro by constructing and reselecting from secondary libraries as described in Winter et al (1994), supra. For example, mutation can be introduced at random in vitro by using error-prone polymerase (reported in Leung et al, Technique, 1 : 11-15 (1989)) in the method of Hawkins et al, J. Mol. Biol, 226: 889-896 (1992) or in the method of Gram et al, Proc. Natl. Acad. Sci. USA, 89: 3576- 3580 (1992). Additionally, affinity maturation may be performed by randomly mutating one or more CDRs, for example, using PCR with primers carrying random sequence spanning the CDR of interest, in selected individual Fv clones and screening for higher affinity clones. WO 9607754 described a method for inducing mutagenesis in a complementarity determining region of an immunoglobulin light chain to create a library of light chain genes. Another effective approach is to recombine the VH or VL domains selected by phage display with repertoires of naturally occurring V domain variants obtained from unimmunized donors and screen for higher affinity in several rounds of chain reshuffling as described in Marks et al, BiotechnoL, 10: 779-783 (1992). This technique allows the production of antibodies and antibody fragments with affinities in the 10"9 M range.
[00459] The phage library samples are contacted with an immobilized protein under conditions suitable for binding of at least a portion of the phage particles with the adsorbent.
Normally, the conditions, including pH, ionic strength, temperature and the like are selected to mimic physiological conditions. The phages bound to the solid phase are washed and then eluted by acid, e.g., as described in Barbas et al, Proc. Natl. Acad. Sci. USA, 88: 7978-7982 (1991), or by alkali, {e.g., as described in Marks et al, J. Mol. Biol, 222: 581-597 (1991)), or by antigen competition, {e.g., in a procedure similar to the antigen competition method of Clackson et al, Nature, 352: 624-628 (1991)). Phages may be enriched 20-1,000-fold in a single round of selection. Moreover, the enriched phages may be grown in bacterial culture and subjected to further rounds of selection.
[00460] The efficiency of selection depends on many factors, including the kinetics of dissociation during washing, and whether multiple antibody fragments on a single phage can simultaneously engage with antigen. Antibodies with fast dissociation kinetics (and weak binding affinities) may be retained by use of short washes, multivalent phage display and high coating density of antigen in solid phase. The high density not only stabilizes the phage through multivalent interactions, but favors rebinding of phage that has dissociated. The selection of antibodies with slow dissociation kinetics (and good binding affinities) may be promoted by use of long washes and monovalent phage display as described in Bass et al, Proteins, 8: 309-314 (1990) and in WO 92/09690, and a low coating density of antigen as described in Marks et al, BiotechnoL, 10: 779- 783 (1992).
[00461] DNA encoding the hybridoma-derived monoclonal antibodies or phage display Fv clones disclosed herein is readily isolated and sequenced using conventional procedures {e.g., by using oligonucleotide primers designed to specifically amplify the heavy and light chain coding regions of interest from hybridoma or phage DNA template). Once isolated, the DNA can be placed into expression vectors, which are then transfected into host cells such as E. coli cells, simian COS cells, Chinese hamster ovary (CHO) cells, or myeloma cells that do not otherwise produce immunoglobulin protein, to obtain the synthesis of the desired monoclonal antibodies in the recombinant host cells. Recombinant expression in bacteria of antibody-encoding DNA has been described by Better et al, U.S. Patent No. 6,204,023 (see also, e.g., Skerra et al, Curr. Opinion in Immunol, 5: 256 (1993) and Pluckthun, Immunol. Revs, 130: 151 (1992)).
[00462] DNA encoding Fv clones as disclosed herein may be combined with known DNA sequences encoding heavy chain and/or light chain constant regions {e.g., the appropriate DNA sequences can be obtained from Kabat et al, supra) to form clones encoding full or partial length heavy and/or light chains. It will be appreciated that constant regions of any isotype can be used for this purpose, including IgG, IgM, IgA, IgD, and IgE constant regions, and that such constant regions may be obtained from any human or animal species. A Fv clone derived from the variable domain DNA of one animal (such as human) species and then fused to constant region DNA of another animal species to form coding sequence(s) for "hybrid", full length heavy chain and/or light chain is included in the definition of "chimeric" and "hybrid" antibody as used herein. In a preferred Fv clone embodiment, a Fv clone derived from human variable DNA is fused to human constant region DNA to form coding sequence(s) for all human, full or partial length heavy and/or light chains.
[00463] DNA encoding an antibody comprising an ultralong CDR3 derived from a hybridoma disclosed herein may also be modified, for example, by substituting the coding sequence for human heavy-and light-chain constant domains in place of homologous murine sequences derived from the hybridoma clone (e.g., as in the method of Morrison et al. , Proc. Natl. Acad. Sci. USA, 81 : 6851-6855 (1984)). DNA encoding a hybridoma or Fv clone-derived antibody or fragment can be further modified by covalently joining to the immunoglobulin coding sequence all or part of the coding sequence for a non-immunoglobulin polypeptide. In this manner, "chimeric" or "hybrid" antibodies are prepared that have the binding specificity of the Fv clone or hybridoma clone-derived antibodies disclosed herein.
Antibody Genes and Proteins
[00464] The present disclosure provides antibody genes and proteins including, for example, chimeric, recombinant, engineered, synthetic, hybrid, bovine, fully bovine, bovinized, human, fully human or humanized antibody genes or proteins that comprise an ultralong CDR3 sequence. The antibodies disclosed herein may selectively or specifically bind to an epitope of a target protein. In some embodiments, the antibody may be an antagonist (e.g., blocking) antibody or an agonist antibody.
[00465] The variable region of the heavy and light chains are encoded by multiple germline gene segments separated by non-coding regions, or introns, and often are present on different chromosomes. For example, the genes for the human immunoglobulin heavy chain region contains approximately 65 variable (VH;) genes, 27 Diversity (DH) genes, and 6 Joining (JH) genes. The human kappa (κ) and lambda (λ) light chains are also each encoded by a similar number of VL and JL gene segments, but do not include any D gene segments. Exemplary VH, DH, JH and VL (VK or νλ) and JL (JK or J ) germline gene segments are set forth in WO 2010/054007.
[00466] During B cell differentiation germline DNA is rearranged whereby one DH and one
JH gene segment of the heavy chain locus are recombined, which is followed by the joining of one VH gene segment forming a rearranged VDJ gene that encodes a VH chain. The rearrangement occurs only on a single heavy chain allele by the process of allelic exclusion. Allelic exclusion is regulated by in- frame or "productive" recombination of the VDJ segments, which occurs in only about one-third of VDJ recombinations of the variable heavy chain. When such productive recombination events first occur in a cell, this result in production of a μ heavy chain that gets expressed on the surface of a pre-B cell and transmits a signal to shut off further heavy chain recombination, thereby preventing expression of the allelic heavy chain locus. The surface- expressed μ heavy chain also acts to activate the kappa (κ) locus for rearrangement. The lambda (λ) locus is only activated for rearrangement if the κ recombination is unproductive on both loci. The light chain rearrangement events are similar to the heavy chain, except that only the VL and JL segments are recombined. Before primary transcription of each, the corresponding constant chain gene is added. Subsequent transcription and RNA splicing leads to mRNA that is translated into an intact light chain or heavy chain.
[00467] The variable regions of antibodies confer antigen binding and specificity due to recombination events of individual germline V, D and J segments, whereby the resulting recombined nucleic acid sequences encoding the variable region domains differ among antibodies and confer antigen-specificity to a particular antibody. The variation, however, is limited to three complementarity determining regions (CDR1, CDR2, and CDR3) found within the N-terminal domain of the heavy (H) and (L) chain variable regions. The CDRs are interspersed with regions that are more conserved, termed "framework regions" (FR). The extent of the framework region and CDRs has been precisely defined (see e.g., Kabat, E.A. et al. (1991) Sequences of Proteins of Immunological Interest, Fifth Edition, U.S. Department of Health and Human Services, NIH Publication No. 91-3242, and Chothia, C. et al. (1987) J. Mol. Biol. 196:901-917). Each VH and VL is typically composed of three CDRs and four FRs arranged from the amino terminus to carboxy terminus in the following order: FR1, CDR1, FR2, CDR2, FR3, CDR3 and FR4. Sequence variability among VL and VH domains is generally limited to the CDRs, which are the regions that form the antigen binding site. For example, for the heavy chain, generally, VH genes encode the N- terminal three framework regions, the first two complete CDRs and the first part of the third CDR), the DH gene encodes the central portion of the third CDR, and the JH gene encodes the last part of the third CDR and the fourth framework region. For the light chain, the VL genes encode the first CDR and second CDR. The third CDR (CDRL3) is formed by the joining of the VL and JL gene segments. Hence, CDRs 1 and 2 are exclusively encoded by germline V gene segment sequences. The VH and VL chain CDR3s form the center of the Ag-binding site, with CDRs 1 and 2 form the outside boundaries; the FRs support the scaffold by orienting the H and L CDRs. On average, an antigen binding site typically requires at least four of the CDRs make contact with the antigen's epitope, with CDR3 of both the heavy and light chain being the most variable and contributing the most specificity to antigen binding (see, e.g., Janis Kuby, Immunology, Third Edition, New York, W.H. Freeman and Company, 1998, pp. 115-118). CDRH3, which includes all of the D gene segment, is the most diverse component of the Ab-binding site, and typically plays a critical role in defining the specificity of the Ab. In addition to sequence variation, there is variation in the length of the CDRs between the heavy and light chains.
[00468] The constant regions, on the other hand, are encoded by sequences that are more conserved among antibodies. These domains confer functional properties to antibodies, for example, the ability to interact with cells of the immune system and serum proteins in order to cause clearance of infectious agents. Different classes of antibodies, for example IgM, IgD, IgG, IgE and IgA, have different constant regions, allowing them to serve distinct effector functions.
[00469] These natural recombination events of V, D, and J, can provide nearly 2x107 different antibodies with both high affinity and specificity. Additional diversity is introduced by nucleotide insertions and deletions in the joining segments and also by somatic hypermutation of V regions. The result is that there are approximately 1010 antibodies present in an individual with differing antigen specificities.
Antibody Fragments
[00470] The present disclosure encompasses antibody fragments. In certain circumstances there are advantages of using antibody fragments, rather than whole antibodies. The smaller size of the fragments allows for rapid clearance, and may lead to improved access to solid tumors.
Antibody fragments include, but are not limited to, Fab, Fab', Fab'-SH, F(ab')2, Fv, Fv', Fd, Fd', scFv, hsFv fragments, and diabodies, and other fragments described below. For a review of certain antibody fragments, see Hudson et al. Nat. Med. 9:129-134 (2003). For a review of scFv fragments, see, e.g., Pluckthun, in The Pharmacology of Monoclonal Antibodies, vol. 113, Rosenburg and Moore eds., (Springer- Verlag, New York), pp. 269-315 (1994); see also WO 93/16185; and U.S. Pat. Nos. 5,571,894 and 5,587,458. For discussion of Fab and F(ab')2 fragments comprising salvage receptor binding epitope residues and having increased in vivo half-life, see U.S. Pat. No.
5,869,046.
[00471] Diabodies are antibody fragments with two antigen binding sites that may be bivalent or bispecific. See, for example, EP 404,097; WO 1993/01161; Hudson et al, Nat. Med. 9: 129-134 (2003); and Hollinger et al, Proc. Natl. Acad. Sci. USA 90: 6444-6448 (1993).
Triabodies and tetrabodies are also described in Hudson et al, Nat. Med. 9: 129134 (2003).
[00472] Single-domain antibodies are antibody fragments comprising all or a portion of the heavy chain variable domain or all or a portion of the light chain variable domain of an antibody. In certain embodiments, a single-domain antibody is a human single-domain antibody (Domantis, Inc., Waltham, Mass.; see, e.g., U.S. Pat. No. 6,248,516). Antibody fragments can be made by various techniques, including but not limited to proteolytic digestion of an intact antibody as well as production by recombinant host cells (e.g. E. coli or phage), as described herein.
[00473] Various techniques have been developed for the production of antibody fragments.
Traditionally, these fragments were derived via proteolytic digestion of intact antibodies (see, e.g., Morimoto et al, Journal of Biochemical and Biophysical Methods 24: 107-117 (1992); and Brennan et al, Science, 229:81 (1985)). However, these fragments can now be produced directly by recombinant host cells. Fab, Fv and ScFv antibody fragments can all be expressed in and secreted from E. coli, thus allowing the facile production of large amounts of these fragments (see, e.g., U.S. Patent No. 6,204,023). Antibody fragments can be isolated from antibody phage libraries as discussed above. Alternatively, Fab'-SH fragments can be directly recovered from E. coli and chemically coupled to form F(ab')2 fragments (see, e.g., Carter et al, Bio/Technology 10: 163-167 (1992)). According to another approach, F(ab')2 fragments can be isolated directly from
recombinant host cell culture. Fab and F(ab')2 fragment with increased in vivo half-life comprising a salvage receptor binding epitope residues (see, e.g., in U.S. Patent No. 5,869,046). Other techniques for the production of antibody fragments will be apparent to the skilled practitioner. In other embodiments, the antibody of choice is a single chain Fv fragment (scFv or single chain antibody (SCA)). See WO 93/16185; U.S. Patent Nos. 5,571,894; and 5,587,458. Fv and sFv are the only species with intact combining sites that are devoid of constant regions; thus, they are suitable for reduced nonspecific binding during in vivo use. sFv fusion proteins may be constructed to yield fusion of an effector protein at either the amino or the carboxy terminus of an sFv. See Antibody Engineering, ed. Borrebaeck, Supra. The antibody fragment may also be a "linear antibody", for example, as described in U.S. Patent No. 5,641,870. Such linear antibody fragments may be monospecific or bispecific.
Humanized Antibodies
[00474] The present disclosure provides humanized antibodies comprising an ultralong
CDR3. Humanized antibodies may include human engineered antibodies (see, e.g., Studnicka et al. (1994) Protein Eng. 7(6) 805-814; and U.S. Patent No. 5,766,886). Various methods for
humanizing non-human antibodies are known in the art. For example, a humanized antibody can have one or more amino acid residues introduced into it from a source which is human or non- human. Humanization may be performed following the method of Studnicka (see, e.g., Studnicka et al. (1994) Protein Eng. 7(6) 805-814; and U.S. Patent No. 5,766,886), including the preparation of modified antibody variable domains. Humanization may alternatively be performed following the method of Winter and co-workers (Jones et al. (1986) Nature 321 :522-525; Riechmann et al. (1988) Nature 332:323-327; Verhoeyen et al. (1988) Science 239: 1534-1536), by substituting hypervariable region sequences for the corresponding sequences of a human antibody. Accordingly, such "humanized" or "human engineered" antibodies are chimeric antibodies, including wherein substantially less than an intact human variable domain has been substituted by or incorporated into the corresponding sequence from a non-human species. For example, humanized antibodies may be human antibodies in which some hypervariable region residues and possibly some FR residues are substituted by residues from analogous sites in rodent antibodies. Alternatively, humanized or human engineered antibodies may be non-human (e.g, rodent) antibodies in which some residues are substituted by residues from analogious sites in human antibodies (see, e.g., Studnicka et al. (1994) Protein Eng. 7(6) 805-814; and U.S. Patent No. 5,766,886).
[00475] The choice of human variable domains, both light and heavy, to be used in making the humanized antibodies is important to reduce antigenicity. For example, to the so-called "best- fit" method, the sequence of the variable domain of a rodent antibody is screened against the entire library of known human variable-domain sequences. The human sequence which is closest to that of the rodent is then accepted as the human framework for the humanized antibody (Sims et al. (1993) J. Immunol. 151 :2296; Chothia et al. (1987) J. Mol. Biol. 196:901). Another method uses a particular framework derived from the consensus sequence of all human antibodies of a particular subgroup of light or heavy chains. The same framework may be used for several different humanized antibodies (Carter et al. (1992) Proc. Natl. Acad. Sci. USA, 89:4285; Presta et al.
(1993) J. Immunol, 151 :2623).
[00476] It is further important that antibodies be humanized with retention of high affinity for the antigen and other favorable biological properties. To achieve this goal, according to one method, humanized antibodies are prepared by a process of analysis of the parental sequences and various conceptual humanized products using three-dimensional models of the parental and humanized sequences. Three-dimensional immunoglobulin models are commonly available and are familiar to those skilled in the art. Computer programs are available which illustrate and display probable three-dimensional conformational structures of selected candidate immunoglobulin sequences. Inspection of these displays permits analysis of the likely role of the residues in the functioning of the candidate immunoglobulin sequence, e.g., the analysis of residues that influence the ability of the candidate immunoglobulin to bind its antigen. In this way, FR residues can be selected and combined from the recipient and import sequences so that the desired antibody characteristic, such as increased affinity for the target antigen(s), is achieved. In general, the hypervariable region residues are directly and most substantially involved in influencing antigen binding. [00477] In some embodiments, the humanized antibodies comprising an ultralong CDR3 may be deimmunized. Methods of deimmunizing an antibody or protein are well known in the art. The immunogenicity of therapeutic proteins such as antibodies is thought to result from the presence of T-cell epitopes which can bind MHC class II molecules and generate a proliferative and cytokine response in CD4+ helper T-cells. These CD4+ helper cells then collaborate with B-cells to generate an antibody response against the therapeutic protein. Removal of the T-cell epitopes are thought to be key steps in deimmunizing a recombinant protein. T-cell epitopes can be predicted by in silico algorithms that identify residues required for binding MHC. Alternatively, epitopes can be identified directly by utilizing peripheral blood mononuclear cells from panels of human donors and measuring their response against the therapeutic protein when incubated with antigen presenting cells. Such in silico and in vitro systems are well known in the art [Jones TD, Crompton LJ, Carr FJ, Baker MP. Methods Mol Biol. 2009;525:405-23,Deimmunization of monoclonal antibodies; and Baker M, and Jones TD. The identification and removal of immunogenicity in therapeutic proteins. Curr. Opin. Drug Discovery Dev. 2007; (2007); 10(2): 219-227]. When peptides are identified that bind MHC II or otherwise stimulate CD4+ cell activation, the residues of the peptide can be mutated one by one and tested for T-cell activation until a mutation is found which disrupts MHC II binding and T-cell activation. Such mutations, when found in an individual peptide, can be encoded directly in the recombinant therapeutic protein. Incubation of the whole protein with antigen presenting cells will not induce a significant CD4+ response, indicating successful deimmunization.
Bovine Antibodies
[00478] The present disclosure provides for bovine antibodies comprising an ultralong
CDR3. The bovine antibodies may be recombinant antibodies, engineered antibodies, synthetic antibodies, bovinized antibodies, or fully bovine antibodies. Bovinized antibodies may include bovine engineered antibodies. Methods for producing a bovinized antibody may comprise introducing one or more amino acid residues into it from a source which is a bovine. In some instances, methods for producing a bovinized antibody may comprise introducing one or more amino acid residues into it from a source which is a non-bovine. Bovinization may be performed by preparing a modified antibody variable domains. Alternatively, bovinization may be performed by substituting hypervariable region sequences for the corresponding sequences of a bovine antibody. Accordingly, such "bovinized" or "bovine engineered" antibodies are chimeric antibodies.
Chimeric antibodies may include antibodies wherein substantially less than an intact bovine variable domain has been substituted by or incorporated into the corresponding sequence from a non-bovine species. Bovinized or bovine engineered antibodies may be bovine antibodies in which some hypervariable region residues and constant region residues are substituted by residues from analogous sites in non-bovine antibodies. Alternatively, bovinized, bovine engineered or fully bovine antibodies may be non-bovine (e.g, human) antibodies in which some residues are substituted by residues from analogious sites in bovine antibodies. For example, a bovine immunoglobuline region can be used to replace a non-bovine (e.g., human, rodent)
immunoglobulin region to produce a fully bovine, bovinized or bovine engineered antibody.
Bispecific Antibodies
[00479] Bispecific antibodies are monoclonal, preferably human or humanized, antibodies that have binding specificities for at least two different antigens. For example, one of the binding specificities may be for a first antigen and the other may be for any other antigen. Exemplary bispecific antibodies may bind to two different epitopes of the same protein. Bispecific antibodies may also be used to localize cytotoxic agents to cells which express a particular protein. These antibodies possess a binding arm specific for the particular protein and an arm which binds the cytotoxic agent (e.g., saporin, anti-interferon-a, vinca alkaloid, ricin A chain, methotrexate or radioactive isotope hapten). Bispecific antibodies may be prepared as full length antibodies or antibody fragments (e.g., F(ab')2 bispecific antibodies).
[00480] Methods for making bispecific antibodies are known in the art. Traditionally, the recombinant production of bispecific antibodies is based on the co-expression of two
immunoglobulin heavy chain-light chain pairs, where the two heavy chains have different specificities (Milstein and Cuello, Nature, 305: 537 (1983)). Because of the random assortment of immunoglobulin heavy and light chains, these hybridomas (quadromas) produce a potential mixture of 10 different antibody molecules, of which only one has the correct bispecific structure. The purification of the correct molecule, which is usually done by affinity chromatography steps, is rather cumbersome, and the product yields are low. Similar procedures are disclosed in WO
93/08829, and in Traunecker et al, EMBO J., 10: 3655 (1991).
[00481] According to a different approach, antibody variable domains with the desired binding specificities (antibody-antigen combining sites) are fused to immunoglobulin constant domain sequences. The fusion preferably is with an immunoglobulin heavy chain constant domain, comprising at least part of the hinge, CH2, and CH3 regions. It is preferred to have the first heavy- chain constant region (CHI), containing the site necessary for light chain binding, present in at least one of the fusions. DNAs encoding the immunoglobulin heavy chain fusions and, if desired, the immunoglobulin light chain, are inserted into separate expression vectors, and are co-transfected into a suitable host organism. This provides for flexibility in adjusting the mutual proportions of the three polypeptide fragments in embodiments when unequal ratios of the three polypeptide chains used in the construction provide the optimum yields. It is, however, possible to insert the coding sequences for two or all three polypeptide chains in one expression vector when the expression of at least two polypeptide chains in equal ratios results in high yields or when the ratios are not of particular significance.
[00482] In a preferred embodiment of this approach, the bispecific antibodies are composed of a hybrid immunoglobulin heavy chain with a first binding specificity in one arm, and a hybrid immunoglobulin heavy chain-light chain pair (providing a second binding specificity) in the other arm. This asymmetric structure may facilitate the separation of the desired bispecific compound from unwanted immunoglobulin chain combinations, as the presence of an immunoglobulin light chain in only one half of the bispecific molecule provides for a facile way of separation. This approach is disclosed in WO 94/04690. For further details of generating bispecific antibodies see, for example, Suresh et ah, Methods in Enzymology, 121 :210 (1986).
[00483] According to another approach, the interface between a pair of antibody molecules may can be engineered to maximize the percentage of heterodimers which are recovered from recombinant cell culture. The preferred interface comprises at least a part of the CH3 domain of an antibody constant domain. In this method, one or more small amino acid side chains from the interface of the first antibody molecule are replaced with larger side chains {e.g., tyrosine or tryptophan). Compensatory "cavities" of identical or similar size to the large side chain(s) are created on the interface of the second antibody molecule by replacing large amino acid side chains with smaller ones {e.g., alanine or threonine). This provides a mechanism for increasing the yield of the heterodimer over other unwanted end-products such as homodimers.
[00484] Bispecific antibodies include cross-linked or "heteroconjugate" antibodies. For example, one of the antibodies in the heteroconjugate may be coupled to avidin, the other to biotin. Such antibodies have, for example, been proposed to target immune system cells to unwanted cells (U.S. Patent No. 4,676,980), and for treatment of HIV infection (WO 91/00360, WO 92/00373, and EP 03089). Heteroconjugate antibodies may be made using any convenient cross-linking methods. Suitable cross-linking agents are well known in the art, and are disclosed in U.S. Patent No.
4,676,980, along with a number of cross-linking techniques.
[00485] Techniques for generating bispecific antibodies from antibody fragments have also been described in the literature. For example, bispecific antibodies may be prepared using chemical linkage. Brennan et al., Science, 229: 81 (1985) describe a procedure wherein intact antibodies are proteolytically cleaved to generate F(ab')2 fragments. These fragments are reduced in the presence of the dithiol complexing agent sodium arsenite to stabilize vicinal dithiols and prevent intermolecular disulfide formation. The Fab' fragments generated are then converted to
thionitrobenzoate (TNB) derivatives. One of the Fab'-TNB derivatives is then reconverted to the Fab'-thiol by reduction with mercaptoethylamine and is mixed with an equimolar amount of the other Fab'-TNB derivative to form the bispecific antibody. The bispecific antibodies produced may be used as agents for the selective immobilization of enzymes.
[00486] Recent progress has facilitated the direct recovery of Fab'-SH fragments from E. coli, which can be chemically coupled to form bispecific antibodies. Shalaby et al, J. Exp. Med., 175: 217-225 (1992) describe the production of a fully humanized bispecific antibody F(ab')2 molecule. Each Fab' fragment was separately secreted from E. coli and subjected to directed chemical coupling in vitro to form the bispecific antibody. The bispecific antibody thus formed was able to bind to cells overexpressing the HER2 receptor and normal human T cells, as well as trigger the lytic activity of human cytotoxic lymphocytes against human breast tumor targets.
[00487] Various techniques for making and isolating bispecific antibody fragments directly from recombinant cell culture have also been described. For example, bispecific antibodies have been produced using leucine zippers. See, e.g., Kostelny et al, J. Immunol, 148(5): 1547-1553 (1992). The leucine zipper peptides from the Fos and Jun proteins were linked to the Fab' portions of two different antibodies by gene fusion. The antibody homodimers were reduced at the hinge region to form monomers and then re-oxidized to form the antibody heterodimers. This method can also be utilized for the production of antibody homodimers. The "diabody" technology described by Hollinger et al, Proc. Natl. Acad. Sci. USA, 90:6444-6448 (1993) has provided an alternative mechanism for making bispecific antibody fragments. The fragments comprise a heavy-chain variable domain (VH) connected to a light-chain variable domain (VL) by a linker which is too short to allow pairing between the two domains on the same chain. Accordingly, the VH and VL domains of one fragment are forced to pair with the complementary VL and VH domains of another fragment, thereby forming two antigen-binding sites. Another strategy for making bispecific antibody fragments by the use of single-chain Fv (sFv) dimers has also been reported. See, Gruber et al, J. Immunol, 152:5368 (1994).
[00488] Antibodies with more than two valencies are contemplated. For example, trispecific antibodies can be prepared. See, e.g., Tutt et al. J. Immunol. 147: 60 (1991).
Multivalent Antibodies
[00489] A multivalent antibody may be internalized (and/or catabolized) faster than a bivalent antibody by a cell expressing an antigen to which the antibodies bind. The antibodies of the present disclosure may be multivalent antibodies (which are other than of the IgM class) with three or more antigen binding sites (e.g., tetravalent antibodies), which may be produced by recombinant expression of nucleic acid encoding the polypeptide chains of the antibody. The multivalent antibody may comprise a dimerization domain and three or more antigen binding sites. A preferred dimerization domain may comprise (or consist of) an Fc region or a hinge region. In this scenario, the antibody will comprise an Fc region and three or more antigen binding sites amino -terminal to the Fe region. A preferred multivalent antibody may comprise (or consist of) three to about eight, but preferably four, antigen binding sites. The multivalent antibody comprises at least one polypeptide chain (and preferably two polypeptide chains), wherein the polypeptide chain(s) comprise two or more variable domains. For instance, the polypeptide chain(s) may comprise VDl-(Xl)n-VD2-(X2)n-Fc, wherein VD 1 is a first variable domain, VD2 is a second variable domain, Fc is one polypeptide chain of an Fc region, XI and X2 represent an amino acid or polypeptide, and n is 0 or 1. For instance, the polypeptide chain(s) may comprise: VH-CH1- flexible linker-VH-CHl-Fc region chain; or VH-CHl-VH-CHl-Fc region chain. A multivalent antibody may preferably further comprises at least two (and preferably four) light chain variable domain polypeptides. A multivalent antibody may, for instance, comprise from about two to about eight light chain variable domain polypeptides. The light chain variable domain polypeptides may comprise a light chain variable domain and, optionally, further comprise a CL domain.
Antibody Variants
[00490] In some embodiments, amino acid sequence modification(s) of the antibodies comprising an ultralong CDR3 as described herein are contemplated. For example, it may be desirable to improve the binding affinity and/or other biological properties of the antibody. Amino acid sequence variants including, for example, conservatively modified variants, of the antibody are prepared by introducing appropriate nucleotide changes into the antibody nucleic acid, or by peptide synthesis. Such modifications include, for example, deletions from, and/or insertions into and/or substitutions of, residues within the amino acid sequences of the antibody. Any combination of deletion, insertion, and substitution is made to arrive at the final construct, provided that the final construct possesses the desired characteristics. The amino acid alterations may be introduced in the subject antibody amino acid sequence at the time that sequence is made.
[00491] A useful method for identification of certain residues or regions of the antibody that are preferred locations for mutagenesis is called "alanine scanning mutagenesis" as described by Cunningham and Wells (1989) Science, 244: 1081-1085. Here, a residue or group of target residues are identified (e.g., charged residues such as arg, asp, his, lys, and glu) and replaced by a neutral or negatively charged amino acid (most preferably alanine or polyalanine) to affect the interaction of the amino acids with antigen. Those amino acid locations demonstrating functional sensitivity to the substitutions then are refined by introducing further or other variants at, or for, the sites of substitution. Thus, while the site for introducing an amino acid sequence variation is
predetermined, the nature of the mutation per se need not be predetermined. For example, to analyze the performance of a mutation at a given site, ala scanning or random mutagenesis is conducted at the target codon or region and the expressed immunoglobulins are screened for the desired activity.
[00492] Amino acid sequence insertions include amino-and/or carboxyl-terminal fusions ranging in length from one residue to polypeptides containing a hundred or more residues, as well as intrasequence insertions of single or multiple amino acid residues. Examples of terminal insertions include an antibody with an N-terminal methionyl residue or the antibody fused to a cytotoxic polypeptide. Other insertional variants of the antibody molecule include the fusion to the N-or C-terminus of the antibody to an enzyme (e.g., for ADEPT) or a polypeptide which increases the serum half- life of the antibody.
[00493] Glycosylation of polypeptides is typically either N-linked or O-linked. N-linked refers to the attachment of the carbohydrate moiety to the side chain of an asparagine residue. The tripeptide sequences asparagine-X-serine and asparagine-X-threonine, where X is any amino acid except proline, are the recognition sequences for enzymatic attachment of the carbohydrate moiety to the asparagine side chain. Thus, the presence of either of these tripeptide sequences in a polypeptide creates a potential glycosylation site. O-linked glycosylation refers to the attachment of one of the sugars N-aceylgalactosamine, galactose, or xylose to a hydroxyamino acid, most commonly serine or threonine, although 5-hydroxyproline or 5-hydroxylysine may also be used.
[00494] Addition of glycosylation sites to the antibody is conveniently accomplished by altering the amino acid sequence such that it contains one or more of the above-described tripeptide sequences (for N-linked glycosylation sites). The alteration may also be made by the addition of, or substitution by, one or more serine or threonine residues to the sequence of the original antibody (for O-linked glycosylation sites).
[00495] Where the antibody comprises an Fc region, the carbohydrate attached thereto may be altered. For example, antibodies with a mature carbohydrate structure that lacks fucose attached to an Fc region of the antibody have been described (see, e.g., US 2003/0157108, US
2004/0093621. Antibodies with a bisecting N-acetylglucosamine (GlcNAc) in the carbohydrate attached to an Fc region of the antibody have been described (see, e.g., WO 2003/011878, and U.S. Patent No. 6,602,684). Antibodies with at least one galactose residue in the oligosaccharide attached to an Fc region of the antibody WO 1997/30087; see, also, WO 1998/58964 and WO 1999/22764 concerning antibodies with altered carbohydrate attached to the Fc region thereof). Antigen-binding molecules with modified glycosylation have been described (see, e.g., WO
99/54342, U.S. Patent Nos. 6,602,684 and 7,517,670, and US 2004/0072290; see also, e.g., U.S. Patent Nos. 7,214,775 and 7,682,610).
[00496] The preferred glycosylation variant herein comprises an Fc region, wherein a carbohydrate structure attached to the Fc region lacks fucose. Such variants have improved ADCC function. Optionally, the Fc region further comprises one or more amino acid substitutions therein which further improve ADCC, for example, substitutions at positions 298, 333, and/or 334 of the Fc region (Eu numbering of residues). Examples of publications related to "defucosylated" or "fucose-deficient" antibodies include: US 2003/0157108; WO 2000/61739; WO 2001/29246; US 2003/0115614 (now U.S. Patent No.6,946,292) US 2002/0164328 (now U.S. Patent No.
7,064,191); US 2004/0093621; US 2004/0132140; US 2004/0110704; US 2004/0110282 (now U.S. Patent No 7,749,753); US 2004/0109865; WO 2003/085119; WO 2003/084570; WO 2005/035586; WO 2005/035778; WO2005/053742; Okazaki et al. J. Mol. Biol. 336: 1239-1249 (2004); Yamane- Ohnuki et al. Biotech. Bioeng. 87: 614 (2004). Examples of cell lines producing defucosylated antibodies include Led 3 CHO cells deficient in protein fucosylation (Ripka et al. Arch. Biochem. Biophys. 249:533-545 (1986); US Pat Appl No US 2003/0157108 Al, Presta, L; and WO
2004/056312 Al, Adams et al., especially at Example 11), and knockout cell lines, such as alpha- 1,6-fucosyltransferase gene, FUT8, knockout CHO cells (Yamane-Ohnuki et al. Biotech. Bioeng. 87: 614 (2004)).
[00497] Another type of variant is an amino acid substitution variant. These variants have at least one amino acid residue in the antibody molecule replaced by a different residue. The sites of greatest interest for substitutional mutagenesis include the hypervariable regions, but FR alterations are also contemplated. Conservative substitutions are shown in Table 2 under the heading of "preferred substitutions". If such substitutions result in a change in biological activity, then more substantial changes, denominated "exemplary substitutions", or as further described below in reference to amino acid classes, may be introduced and the products screened.
Original Residue Exemplary Substitutions Preferred Substitutions
Ala (A) Val; Leu; He Val
Arg (R) Lys; Gin; Asn Lys
Asn (N) Gin; His; Asp, Lys; Arg Gin
Asp (D) Glu; Asn Glu
Cys (C) Ser; Ala Ser Gin (Q) Asn; Glu Asn
Glu (E) Asp; Gin Asp
Gly (G) Ala Ala
His (H) Asn; Gin; Lys; Arg Arg
He (I) Leu; Val; Met; Ala; Phe; Norleucine Leu
Leu (L) Norleucine; He; Val; Met; Ala; Phe He
Lys (K) Arg; Gin; Asn Arg
Met (M) Leu; Phe; He Leu
Phe (F) Trp; Leu; Val; He; Ala; Tyr Tyr
Pro (P) Ala Ala
Ser (S) Thr Thr
Thr (T) Val; Ser Ser
Trp (W) Tyr; Phe Tyr
Tyr (Y) Trp; Phe; Thr; Ser Phe
Val (V) He; Leu; Met; Phe; Ala; Norleucine Leu
[00498] Substantial modifications in the biological properties of the antibody are
accomplished by selecting substitutions that differ significantly in their effect on maintaining (a) the structure of the polypeptide backbone in the area of the substitution, for example, as a sheet or helical conformation, (b) the charge or hydrophobicity of the molecule at the target site, or (c) the bulk of the side chain. Naturally occurring amino acids are divided into groups based on common side-chain properties: (1) hydrophobic: norleucine, met, ala, val, leu, ile; (2) neutral hydrophilic: Cys, Ser, Thr, Asn, Gin; (3) acidic: asp, glu; (4) basic: his, lys, arg; (5) residues that influence chain orientation: gly, pro; and (6) aromatic: trp, tyr, phe.
[00499] Non-conservative substitutions will entail exchanging a member of one of these classes for another class.
[00500] One type of substitutional variant involves substituting one or more hypervariable region residues of a parent antibody (e.g., a humanized or human antibody). Generally, the resulting variant(s) selected for further development will have improved biological properties relative to the parent antibody from which they are generated. A convenient way for generating such
substitutional variants involves affinity maturation using phage display. Briefly, several hypervariable region sites (e.g., 6-7 sites) are mutated to generate all possible amino acid substitutions at each site. The antibodies thus generated are displayed from filamentous phage particles as fusions to the gene III product of Ml 3 packaged within each particle. The phage- displayed variants are then screened for their biological activity (e.g., binding affinity) as herein disclosed. In order to identify candidate hypervariable region sites for modification, alanine scanning mutagenesis can be performed to identify hypervariable region residues contributing significantly to antigen binding. Alternatively, or additionally, it may be beneficial to analyze a crystal structure of the antigen-antibody complex to identify contact points between the antibody and antigen. Such contact residues and neighboring residues are candidates for substitution according to the techniques elaborated herein. Once such variants are generated, the panel of variants is subjected to screening as described herein and antibodies with superior properties in one or more relevant assays may be selected for further development.
[00501] Nucleic acid molecules encoding amino acid sequence variants of the antibody are prepared by a variety of methods known in the art. These methods include, but are not limited to, isolation from a natural source (in the case of naturally occurring amino acid sequence variants) or preparation by oligonucleotide-mediated (or site-directed) mutagenesis, PCR mutagenesis, and cassette mutagenesis of an earlier prepared variant or a non-variant version of the antibody.
[00502] It may be desirable to introduce one or more amino acid modifications in an Fc region of the immunoglobulin polypeptides disclosed herein, thereby generating a Fc region variant. The Fc region variant may comprise a human Fc region sequence (e.g., a human IgGl, IgG2, IgG3 or IgG4 Fc region) comprising an amino acid modification (e.g., a substitution) at one or more amino acid positions including that of a hinge cysteine.
[00503] In accordance with this description and the teachings of the art, it is contemplated that in some embodiments, an antibody used in methods disclosed herein may comprise one or more alterations as compared to the wild type counterpart antibody, e.g,. in the Fc region. These antibodies would nonetheless retain substantially the same characteristics required for therapeutic utility as compared to their wild type counterpart. For example, it is thought that certain alterations can be made in the Fc region that would result in altered (e.g., either improved or diminished) Clq binding and/or Complement Dependent Cytotoxicity (CDC), e.g., as described in W099/51642. See also Duncan & Winter Nature 322:738-40 (1988); U.S. Patent No. 5,648,260; U.S. Patent No. 5,624,821; and W094/29351 concerning other examples of Fc region variants. WO00/42072 and WO 2004/056312 describe antibody variants with improved or diminished binding to FcRs. See, also, Shields et al. J. Biol. Chem. 9(2): 6591-6604 (2001). Antibodies with increased half lives and improved binding to the neonatal Fc receptor (FcRn), which is responsible for the transfer of maternal IgGs to the fetus (Guyer et al., J. Immunol. 117:587 (1976) and Kim et al., J. Immunol. 24:249 (1994)), are described in US2005/0014934 (Hinton et al.). These antibodies comprise an Fc reg on with one or more substitutions therein which improve binding of the Fc region to FcRn. Polypeptide variants with altered Fc region amino acid sequences and increased or decreased Clq binding capability are described in U.S. Patent No. 6, 194,551 , W099/51642. See, also, Idusogie et al. J. Immunol. 164:4178-4184 (2000).
[00504] In certain embodiments, the present disclosure contemplates an antibody variant that possesses some but not all effector functions, which make it a desirable candidate for applications in which the half life of the antibody in vivo is important yet certain effector functions (such as complement and ADCC) are unnecessary or deleterious. In vitro and/or in vivo cytotoxicity assays can be conducted to confirm the reduction/ depletion of CDC and/ or ADCC activities. For example, Fc receptor (FcR) binding assays can be conducted to ensure that the antibody lacks FcyR binding (hence likely lacking ADCC activity), but retains FcRn binding ability. The primary cells for mediating ADCC, NK cells, express FcyRIII only, whereas monocytes express FcyRI, FcyRII and FcyRIII. FcR expression on hematopoietic cells is summarized in Table 3 on page 464 of Ravetch and Kinet, Annu. Rev. Immunol. 9:457-492 (1991). Non-limiting examples of in vitro assays to assess ADCC activity of a molecule of interest is described in U.S. Pat. No. 5,500,362 (see, e.g. Hellstrom, I. et al. Proc. Nat' ! Acad. Sci. USA 83 :7059-7063 (1986)) and Hellstrom, I et al , Proc. Nat'l Acad. Sci. USA 82: 1499-1502 (1985); 5,821 ,337 (see, Bruggemann, M. et al, Exp. Med. 166: 1351-1361 (1987)). Alternatively, non-radioactive assays methods may be employed (see, for example, ACTITM non-radioactive cytotoxicity assay for flow cytometry
(CellTecllrlology, Inc. Mountain View, Calif ; and CytoTox 96® non-radioactive cytotoxicity assay (Promega, Madison, Wis.). Useful effector cells for such assays include peripheral blood mononuclear cells (PBMC) and Natural Killer (NK) cells. Alternatively, or additionally, ADCC activity of the molecule of interest may be assessed in vivo, e.g., in a animal model such as that disclosed in Clynes et al Proc. Nat'l Acad. Sci. USA 95 :652-656 (1998). Clqbinding assays may also be carried out to confirm that the antibody is unable to bind Clq and hence lacks CDC activity. See, e.g. , Clq and C3c binding ELISA in WO 2006/029879 and WO 2005/ 100402. To assess complement activation, a CDC assay may be performed (see, for example, Gazzano-Santoro et al , Immunol. Methods 202: 163 (1996); Cragg, M. S. et al, Blood 101 : 1045-1052 (2003); and Cragg, M. S, and M. J. Glennie, Blood 103 :27382743 (2004)). FcRn binding and in vivo clearance/half life determinations can also be performed using methods known in the art (see, e.g. , Petkova, S. B. et al , Int'l Immunol. 18(12): 1759-1769 (2006)).
[00505] Antibodies with reduced effector function include those with substitution of one or more of Fc region residues 238, 265, 269, 270, 297, 327 and 329 (U.S. Pat. No. 6,737, 056). Such Fc mutants include Fc mutants with substitutions at two or more of amino acid positions 265, 269, 270, 297 and 327, including the so-called "DANA" Fc mutant with substitution of residues 265 and 297 to alanine (U.S. Pat. No. 7,332,581).
[00506] Certain antibody variants with improved or diminished binding to FcRs are described. (See, e.g., U.S. Pat. No. 6,737,056; WO 2004/056312, and Shields et al., Biol. Chem. 9(2): 6591-6604 (2001).)
[00507] In certain embodiments, an antibody variant comprises an Fc region with one or more amino acid substitutions which improve ADCC, e.g., substitutions at positions 298, 333, and/or 334 of the Fc region (EU numbering of residues).
[00508] In some embodiments, alterations are made in the Fc region that result in altered
(i.e., either improved or diminished) Clq binding and/or Complement Dependent Cytotoxicity (CDC), e.g., as described in U.S. Pat. No. 6,194,551, WO 99/51642, and Idusogie et al. Immunol. 164: 41784184 (2000).
[00509] Antibodies with increased half lives and improved binding to the neonatal Fc receptor (FcRn), which is responsible for the transfer of maternal IgGs to the fetus (Guyer et al., Immunol. 117:587 (1976) and Kim et al., Immunol. 24:249 (1994)), are described in
US2005/0014934A1 (Hinton et al.). Those antibodies comprise an Fc region with one or more substitutions therein which improve binding of the Fc region to FcRn. Such Fc variants include those with substitutions at one or more of Fc region residues: 238, 256, 265, 272, 286,303,305, 307, 311,312, 317, 340,356, 360, 362, 376, 378, 380, 382, 413, 424 or 434, e.g., substitution of Fc region residue 434 (U.S. Pat. No. 7,371,826).
[00510] See also Duncan & Winter, Nature 322:738-40 (1988); U.S. Pat. No. 5,648,260;
U.S. Pat. No. 5,624,821; and WO 94/29351 concerning other examples of Fc region variants.
Antibody Derivatives
[00511] The antibodies comprising an ultralong CDR3 as disclosed herein may be further modified to contain additional nonproteinaceous moieties that are known in the art and readily available. Preferably, the moieties suitable for derivatization of the antibody are water soluble polymers. Non-limiting examples of water soluble polymers include, but are not limited to, polyethylene glycol (PEG), copolymers of ethylene glycol/propylene glycol,
carboxymethylcellulose, dextran, polyvinyl alcohol, polyvinyl pyrrolidone, poly- 1,3-dioxo lane, poly-l,3,6-trioxane, ethylene/maleic anhydride copolymer, polyamino acids (either homopolymers or random copolymers), and dextran or poly(n-vinyl pyrrolidone)poly ethylene glycol, propropylene glycol homopolymers, prolypropylene oxide/ethylene oxide co-polymers, polyoxyethylated polyols (e.g., glycerol), polyvinyl alcohol, and mixtures thereof. Polyethylene glycol propionaldehyde may have advantages in manufacturing due to its stability in water. The polymer may be of any molecular weight, and may be branched or unbranched. The number of polymers attached to the antibody may vary, and if more than one polymers are attached, they can be the same or different molecules. In general, the number and/or type of polymers used for derivatization can be determined based on considerations including, but not limited to, the particular properties or functions of the antibody to be improved, whether the antibody derivative will be used in a therapy under defined conditions, etc.
Vectors, Host Cells and Recombinant Methods
[00512] For recombinant production of an antibody or fragment thereof as disclosed herein, the nucleic acid encoding it is isolated and inserted into a replicable vector for further cloning (amplification of the DNA) or for expression. DNA encoding the antibody is readily isolated and sequenced using conventional procedures {e.g., by using oligonucleotide probes that are capable of binding specifically to genes encoding the heavy and light chains of the antibody). In an exemplary embodiment, nucleic acid encoding an antibody comprising an ultralong CDR3, a variable region comprising an ultralong CDR3, or an ultralong CDR3, is isolated and inserted into a replicable vector for further cloning (amplification of the DNA) or for expression. Many vectors are available. The choice of vector depends in part on the host cell to be used. Generally, preferred host cells are of either prokaryotic or eukaryotic (generally mammalian) origin. It will be appreciated that constant regions of any isotype can be used for this purpose, including IgG, IgM, IgA, IgD, and IgE constant regions, and that such constant regions can be obtained from any human or animal species.
[00513] Expression vectors containing regulatory elements from eukaryotic viruses are typically used in eukaryotic expression vectors, e.g., SV40 vectors, papilloma virus vectors, and vectors derived from Epstein-Barr virus. Other exemplary eukaryotic vectors include pMSG, pAV009/A+, pMTO10/A+, pMAMneo-5, baculo virus pDSVE, and any other vector allowing expression of proteins under the direction of the CMV promoter, SV40 early promoter, SV40 later promoter, metallothionein promoter, murine mammary tumor virus promoter, Rous sarcoma virus promoter, polyhedrin promoter, or other promoters shown effective for expression in eukaryotic cells.
[00514] Some expression systems have markers that provide gene amplification such as thymidine kinase and dihydrofolate reductase. Alternatively, high yield expression systems not involving gene amplification are also suitable, such as using a baculovirus vector in insect cells, with a nucleic acid sequence encoding a partially human ultralong CDR3 antibody chain under the direction of the polyhedrin promoter or other strong baculovirus promoters. [00515] a. Generating Antibodies Using Prokaryotic or Eukaryotic Host Cells:
[00516] i. Vector Construction
[00517] Polynucleotide sequences encoding polypeptide components of the antibodies disclosed herein can be obtained using standard recombinant techniques. Desired polynucleotide sequences may be isolated and sequenced from antibody producing cells such as hybridoma cells. Alternatively, polynucleotides can be synthesized using nucleotide synthesizer or PCR techniques. Once obtained, sequences encoding the polypeptides are inserted into a recombinant vector capable of replicating and expressing heterologous polynucleotides in prokaryotic hosts. Many vectors that are available and known in the art can be used for the purpose of the present disclosure. Selection of an appropriate vector will depend mainly on the size of the nucleic acids to be inserted into the vector and the particular host cell to be transformed with the vector. Each vector contains various components, depending on its function (amplification or expression of heterologous polynucleotide, or both) and its compatibility with the particular host cell in which it resides. The vector
components generally include, but are not limited to: an origin of replication, a selection marker gene, a promoter, a ribosome binding site (RBS), a signal sequence, the heterologous nucleic acid insert and a transcription termination sequence. Additionally, V regions comprising an ultralong CDR3 may optionally be fused to a C-region to produce an antibody comprising constant regions.
[00518] In general, plasmid vectors containing replicon and control sequences which are derived from species compatible with the host cell are used in connection with these hosts. The vector ordinarily carries a replication site, as well as marking sequences which are capable of providing phenotypic selection in transformed cells. For example, E. coli is typically transformed using pBR322, a plasmid derived from an E. coli species. pBR322 contains genes encoding ampicillin (Amp) and tetracycline (Tet) resistance and thus provides easy means for identifying transformed cells. pBR322, its derivatives, or other microbial plasmids or bacteriophage may also contain, or be modified to contain, promoters which can be used by the microbial organism for expression of endogenous proteins. Examples of pBR322 derivatives used for expression of particular antibodies have been described (see, e.g., U.S. Patent No. 5,648,237).
[00519] In addition, phage vectors containing replicon and control sequences that are compatible with the host microorganism can be used as transforming vectors in connection with these hosts. For example, bacteriophage such as λϋΕΜ™-11 may be utilized in making a recombinant vector which can be used to transform susceptible host cells such as E. coli LE392.
[00520] The expression vectors disclosed herein may comprise two or more promoter-cistron pairs, encoding each of the polypeptide components. A promoter is an untranslated regulatory sequence located upstream (5') to a cistron that modulates its expression. Prokaryotic promoters typically fall into two classes, inducible and constitutive. Inducible promoter is a promoter that initiates increased levels of transcription of the cistron under its control in response to changes in the culture condition, e.g., the presence or absence of a nutrient or a change in temperature.
[00521] A large number of promoters recognized by a variety of potential host cells are well known. The selected promoter can be operably linked to cistron DNA encoding the light or heavy chain by removing the promoter from the source DNA via restriction enzyme digestion and inserting the isolated promoter sequence into the vector disclosed herein. Both the native promoter sequence and many heterologous promoters may be used to direct amplification and/or expression of the target genes. In some embodiments, heterologous promoters are utilized, as they generally permit greater transcription and higher yields of expressed target gene as compared to the native target polypeptide promoter.
[00522] Promoters suitable for use with prokaryotic hosts include: an ara B promoter, a
PhoA promoter, β-galactamase and lactose promoter systems, a tryptophan (trp) promoter system and hybrid promoters such as the tac or the trc promoter. However, other promoters that are functional in bacteria (such as other known bacterial or phage promoters) are suitable as well. Their nucleotide sequences have been published, thereby enabling a skilled worker operably to ligate them to cistrons encoding the target light and heavy chains {e.g., Siebenlist et al (1980) Cell 20: 269) using linkers or adaptors to supply any required restriction sites.
[00523] Suitable bacterial promoters are well known in the art and fully described in scientific literature such as Sambrook and Russell, supra, and Ausubel et al, supra. Bacterial expression systems for expressing antibody chains of the recombinant catalytic polypeptide are available in, e.g., E. coli, Bacillus sp., and Salmonella (Palva et al, Gene, 22:229-235 (1983); Mosbach et al, Nature, 302:543-545 (1983)).
[00524] In one aspect disclosed herein, each cistron within the recombinant vector comprises a secretion signal sequence component that directs translocation of the expressed polypeptides across a membrane. In general, the signal sequence may be a component of the vector, or it may be a part of the target polypeptide DNA that is inserted into the vector. The signal sequence should be one that is recognized and processed {e.g., cleaved by a signal peptidase) by the host cell. For prokaryotic host cells that do not recognize and process the signal sequences native to the heterologous polypeptides, the signal sequence is substituted by a prokaryotic signal sequence selected, for example PelB, OmpA, alkaline phosphatase, penicillinase, Ipp, or heat-stable enterotoxin II (STII) leaders, LamB, PhoE, and MBP. In one embodiment disclosed herein, the signal sequences used in both cistrons of the expression system are STII signal sequences or variants thereof. [00525] In another aspect, the production of the immunoglobulins according to the disclosure can occur in the cytoplasm of the host cell, and therefore does not require the presence of secretion signal sequences within each cistron. In that regard, immunoglobulin light and heavy chains are expressed, folded and assembled to form functional immunoglobulins within the cytoplasm. Certain host strains (e.g., the E. coli trxB-strains) provide cytoplasm conditions that are favorable for disulfide bond formation, thereby permitting proper folding and assembly of expressed protein subunits (see e.g., Proba and Pluckthun Gene, 159:203 (1995)).
[00526] Suitable host cells for cloning or expression of antibody-encoding vectors include prokaryotic or eukaryotic cells described herein. In one embodiment, the host cell is eukaryotic, e.g. a Chinese Hamster Ovary (CHO) cell, Human Embryonic Kidney (HEK) cell or lymphoid cell {e.g., YO, NSO, Sp20 cell). For example, antibodies may be produced in bacteria, in particular when glycosylation and Fc effector function are not needed. For expression of antibody fragments and polypeptides in bacteria, see, e.g., U.S. Pat. Nos. 5,648,237, 5,789,199, and 5,840,523. (See also Charlton, Methods in Molecular Biology, Vol. 248 (B.K.C. Lo, ed., Humana Press, Totowa, N.J., 2003), pp. 245-254, describing expression of antibody fragments in E. coli.) After expression, the antibody may be isolated from the bacterial cell paste in a soluble fraction and can be further purified. In addition to prokaryotes, eukaryotic microbes such as filamentous fungi or yeast are suitable cloning or expression hosts for antibody-encoding vectors, including fungi and yeast strains whose glycosylation pathways have been "humanized," resulting in the production of an antibody with a partially or fully human glycosylation pattern. See Gemgross, Nat. Biotech. 22: 1409-1414 (2004), and Li et al, Nat. Biotech. 24:210-215 (2006). Suitable host cells for the expression of glycosylated antibody are also derived from multicellular organisms (invertebrates and vertebrates). Examples of invertebrate cells include plant and insect cells. Numerous baculo viral strains have been identified which may be used in conjunction with insect cells, particularly for transfection of Spodoptera frugiperda cells. These examples are illustrative rather than limiting. Methods for constructing derivatives of any of the above-mentioned bacteria having defined genotypes are known in the art and described in, for example, Bass et al, Proteins, 8:309- 314 (1990). It is generally necessary to select the appropriate bacteria taking into consideration replicability of the replicon in the cells of a bacterium. For example, E. coli, Serratia, or Salmonella species can be suitably used as the host when well known plasmids such as pBR322, pBR325, pACYC177, or pKN410 are used to supply the replicon. Typically the host cell should secrete minimal amounts of proteolytic enzymes, and additional protease inhibitors may desirably be incorporated in the cell culture. [00527] Plant cell cultures can also be utilized as hosts. See, e.g. U.S. Pat. Nos. 5,959,177,
6,040,498, 6,420,548, 7,125, 978, and 6,417,429 (describing PLA TIBODIESTM technology for producing antibodies in transgenic plants). Vertebrate cells may also be used as hosts. For example, mammalian cell lines that are adapted to grow in suspension may be useful. Other examples of useful mammalian host cell lines are monkey kidney CV1 line transformed by SV40 (COS-7); human embryonic kidney line (293 or 293 cells as described, e.g., in Graham et al, Gen VII '01. 36:59 (1977)); baby hamster kidney cells (BHK); mouse Sertoli cells (TM4 cells as described, e.g., in Mather, Biol. Reprod. 23:243-251 (1980)); monkey kidney cells (CV1); African green monkey kidney cells (V ERO-76); human cervical carcinoma cells (HELA); canine kidney cells (MDCK; buffalo rat liver cells (BRL 3 A); human lung cells (W138); human liver cells (Hep G2); mouse mammary tumor (MMT 060562); TR1 cells, as described, e.g., in Mather et al, Annals ΝΓ. Acad. Sci. 383:44-68 (1982); MRC 5 cells; and FS4 cells. Other useful mammalian host cell lines include Chinese hamster ovary (CHO) cells, including DHFR' CHO cells (Urlaub et al, Proc. Natl. Acad. Sci. USA 77:4216 (1980)); and myeloma cell lines such as YO, NSO and Sp2/0. For a review of certain mammalian host cell lines suitable for antibody production, see, e.g., Yazaki and Wu, Methods in Molecular Biology, Vol. 248 (B.K.C. Lo, ed., Humana Press, Totowa, N.].), pp. 255- 268 (2003).
[00528] In one such embodiment, a host cell comprises {e.g., has been transformed with): (1) a vector comprising a nucleic acid that encodes an amino acid sequence comprising the VL of the antibody and an amino acid sequence comprising the VH of the antibody, or (2) a first vector comprising a nucleic acid that encodes an amino acid sequence comprising the VL of the antibody and a second vector comprising a nucleic acid that encodes an amino acid sequence comprising the VH of the antibody.
[00529] ii. Antibody Production
[00530] For recombinant production of a partially human ultralong CDR3 antibody, nucleic acid encoding an antibody comprising an ultralong CDR3 is inserted into one or more expression vectors for further cloning and/or expression in a host cell. Such nucleic acid may be readily isolated and sequenced using conventional procedures {e.g., by using oligonucleotide probes that are capable of binding specifically to genes encoding the heavy and light chains of the antibody). Host cells are transformed with such expression vectors and cultured in conventional nutrient media modified as appropriate for inducing promoters, selecting transformants, or amplifying the genes encoding the desired sequences.
[00531] Transformation means introducing DNA into the prokaryotic host so that the DNA is replicable, either as an extrachromosomal element or by chromosomal integrant. Depending on the host cell used, transformation is done using standard techniques appropriate to such cells. The calcium treatment employing calcium chloride is generally used for bacterial cells that contain substantial cell-wall barriers. Another method for transformation employs polyethylene
glycol/DMSO. Yet another technique used is electroporation.
[00532] Prokaryotic cells used to produce the polypeptides disclosed herein are grown in media known in the art and suitable for culture of the selected host cells. Examples of suitable media include luria broth (LB) plus necessary nutrient supplements. In some embodiments, the media also contains a selection agent, chosen based on the construction of the expression vector, to selectively permit growth of prokaryotic cells containing the expression vector. For example, ampicillin is added to media for growth of cells expressing ampicillin resistant gene.
[00533] Any necessary supplements besides carbon, nitrogen, and inorganic phosphate sources may also be included at appropriate concentrations introduced alone or as a mixture with another supplement or medium such as a complex nitrogen source. Optionally the culture medium may contain one or more reducing agents selected from the group consisting of glutathione, cysteine, cystamine, thioglycollate, dithioerythritol and dithiothreitol.
[00534] The prokaryotic host cells are cultured at suitable temperatures. For E. coli growth, for example, the preferred temperature ranges from about 20° C. to about 39° C, more preferably from about 25° C. to about 37° C, even more preferably at about 30° C. The pH of the medium may be any pH ranging from about 5 to about 9, depending mainly on the host organism. For E. coli, the pH is preferably from about 6.8 to about 7.4, and more preferably about 7.0.
[00535] If an inducible promoter is used in the expression vector disclosed herein, protein expression is induced under conditions suitable for the activation of the promoter. For example, an ara B or phoA promoter may be used for controlling transcription of the polypeptides. A variety of inducers may be used, according to the vector construct employed, as is known in the art.
[00536] The expressed polypeptides of the present disclosure are secreted into and recovered from the periplasm of the host cells or transported into the culture media. Protein recovery from the periplasm typically involves disrupting the microorganism, generally by such means as osmotic shock, sonication or lysis. Once cells are disrupted, cell debris or whole cells may be removed by centrifugation or filtration. The proteins may be further purified, for example, by affinity resin chromatography. Alternatively, proteins that are transported into the culture media may be isolated therein. Cells may be removed from the culture and the culture supernatant being filtered and concentrated for further purification of the proteins produced. The expressed polypeptides can be further isolated and identified using commonly known methods such as polyacrylamide gel electrophoresis (PAGE) and Western blot assay. [00537] Antibody production may be conducted in large quantity by a fermentation process.
Various large-scale fed-batch fermentation procedures are available for production of recombinant proteins. Large-scale fermentations have at least 1000 liters of capacity, preferably about 1,000 to 100,000 liters of capacity. These fermentors use agitator impellers to distribute oxygen and nutrients, especially glucose (a preferred carbon/energy source). Small scale fermentation refers generally to fermentation in a fermentor that is no more than approximately 100 liters in volumetric capacity, and can range from about 1 liter to about 100 liters.
[00538] In a fermentation process, induction of protein expression is typically initiated after the cells have been grown under suitable conditions to a desired density, e.g., an OD550 of about 180-220, at which stage the cells are in the early stationary phase. A variety of inducers may be used, according to the vector construct employed, as is known in the art and described above. Cells may be grown for shorter periods prior to induction. Cells are usually induced for about 12-50 hours, although longer or shorter induction time may be used.
[00539] To improve the production yield and quality of the polypeptides disclosed herein, various fermentation conditions can be modified. For example, to improve the proper assembly and folding of the secreted antibody polypeptides, additional vectors overexpressing chaperone proteins, such as Dsb proteins (DsbA, DsbB, DsbC, DsbD and or DsbG) or FkpA (a peptidylprolyl cis,trans-isomerase with chaperone activity) may be used to co-transform the host prokaryotic cells. The chaperone proteins have been demonstrated to facilitate the proper folding and solubility of heterologous proteins produced in bacterial host cells, (see e.g., Chen et al. (1999) J Bio Chem 274: 19601-19605; U.S. Patent No. 6,083,715; U.S. Patent No. 6,027,888; Bothmann and Pluckthun (2000) J. Biol. Chem. 275: 17100-17105; Ramm and Pluckthun (2000) J. Biol. Chem. 275: 17106- 17113; Arie et al. (2001) Mol. Microbiol. 39: 199-210).
[00540] To minimize proteolysis of expressed heterologous proteins (especially those that are proteolytically sensitive), certain host strains deficient for proteolytic enzymes can be used for the present disclosure. For example, host cell strains may be modified to effect genetic mutation(s) in the genes encoding known bacterial proteases such as Protease III, OmpT, DegP, Tsp, Protease I, Protease Mi, Protease V, Protease VI and combinations thereof. Some E. coli protease-deficient strains are available (see, e.g., Joly et al. (1998), supra; U.S. Patent No. 5,264,365; U.S. Patent No. 5,508,192; Hara et al, Microbial Drug Resistance, 2:63-72 (1996)).
[00541] E. coli strains deficient for proteolytic enzymes and transformed with plasmids overexpressing one or more chaperone proteins may be used as host cells in the expression systems disclosed herein.
[00542] Hi. Antibody Purification [00543] Standard protein purification methods known in the art can be employed. The following procedures are exemplary of suitable purification procedures: fractionation on immuno affinity or ion-exchange columns, ethanol precipitation, reverse phase HPLC,
chromatography on silica or on a cation-exchange resin such as DEAE, chromatofocusing, SDS- PAGE, ammonium sulfate precipitation, and gel filtration using, for example, Sephadex G-75.
[00544] In one aspect, Protein A immobilized on a solid phase is used for immuno affinity purification of the full length antibody products disclosed herein. Protein A is a 41 kD cell wall protein from Staphylococcus aureas which binds with a high affinity to the Fc region of antibodies (see, e.g., Lindmark et al (1983) J. Immunol. Meth. 62: 1-13). The solid phase to which Protein A is immobilized is preferably a column comprising a glass or silica surface, more preferably a controlled pore glass column or a silicic acid column. In some applications, the column has been coated with a reagent, such as glycerol, in an attempt to prevent nonspecific adherence of contaminants.
[00545] As the first step of purification, the preparation derived from the cell culture as described above is applied onto the Protein A immobilized solid phase to allow specific binding of the antibody of interest to Protein A. The solid phase is then washed to remove contaminants non- specifically bound to the solid phase. Finally the antibody of interest is recovered from the solid phase by elution.
[00546] b. Generating Antibodies Using Eukaryotic Host Cells:
[00547] The vector components generally include, but are not limited to, one or more of the following: a signal sequence, an origin of replication, one or more marker genes, an enhancer element, a promoter, and a transcription termination sequence.
[00548] (i) Signal Sequence Component
[00549] A vector for use in a eukaryotic host cell may also contain a signal sequence or other polypeptide having a specific cleavage site at the N-terminus of the mature protein or polypeptide of interest. The heterologous signal sequence selected preferably is one that is recognized and processed {e.g., cleaved by a signal peptidase) by the host cell. In mammalian cell expression, mammalian signal sequences as well as viral secretory leaders, for example, the herpes simplex gD signal, are available.
[00550] The DNA for such precursor region is ligated in reading frame to DNA encoding the antibody.
[00551] (ii) Origin of Replication [00552] Generally, an origin of replication component is not needed for mammalian expression vectors. For example, the SV40 origin may be used only because it contains the early promoter.
[00553] (Hi) Selection Gene Component
[00554] Expression and cloning vectors may contain a selection gene, also termed a selectable marker. Typical selection genes encode proteins that (a) confer resistance to antibiotics or other toxins, e.g., ampicillin, neomycin, methotrexate, or tetracycline, (b) complement auxotrophic deficiencies, where relevant, or (c) supply critical nutrients not available from complex media.
[00555] One example of a selection scheme utilizes a drug to arrest growth of a host cell.
Those cells that are successfully transformed with a heterologous gene produce a protein conferring drug resistance and thus survive the selection regimen. Examples of such dominant selection use the drugs neomycin, mycophenolic acid and hygromycin.
[00556] Another example of suitable selectable markers for mammalian cells are those that enable the identification of cells competent to take up the antibody nucleic acid, such as DHFR, thymidine kinase, metallothionein-I and -II, preferably primate metallothionein genes, adenosine deaminase, ornithine decarboxylase, etc.
[00557] For example, cells transformed with the DHFR selection gene are first identified by culturing all of the transformants in a culture medium that contains methotrexate (Mtx), a competitive antagonist of DHFR. An appropriate host cell when wild-type DHFR is employed is the Chinese hamster ovary (CHO) cell line deficient in DHFR activity {e.g., ATCC CRL-9096).
[00558] Alternatively, host cells (particularly wild-type hosts that contain endogenous
DHFR) transformed or co-transformed with DNA sequences encoding an antibody, wild-type DHFR protein, and another selectable marker such as aminoglycoside 3 '-phosphotransferase (APH) can be selected by cell growth in medium containing a selection agent for the selectable marker such as an aminoglycosidic antibiotic, e.g., kanamycin, neomycin, or G418. See U.S. Patent No. 4,965,199.
[00559] (iv) Promoter Component
[00560] Expression and cloning vectors usually contain a promoter that is recognized by the host organism and is operably linked to the antibody polypeptide nucleic acid. Promoter sequences are known for eukaryotes. Virtually alleukaryotic genes have an AT -rich region located
approximately 25 to 30 bases upstream from the site where transcription is initiated. Another sequence found 70 to 80 bases upstream from the start of transcription of many genes is a
CNCAAT region where N may be any nucleotide. At the 3' end of most eukaryotic genes is an AATAAA sequence that may be the signal for addition of the poly A tail to the 3' end of the coding sequence. All of these sequences are suitably inserted into eukaryotic expression vectors.
[00561] Antibody polypeptide transcription from vectors in mammalian host cells is controlled, for example, by promoters obtained from the genomes of viruses such as polyoma virus, fowlpox virus, adenovirus (such as Adenovirus 2), bovine papilloma virus, avian sarcoma virus, cytomegalovirus, a retrovirus, hepatitis-B virus and Simian Virus 40 (SV40), from heterologous mammalian promoters, e.g., the actin promoter or an immunoglobulin promoter, from heat-shock promoters, provided such promoters are compatible with the host cell systems.
[00562] The early and late promoters of the SV40 virus are conveniently obtained as an
SV40 restriction fragment that also contains the SV40 viral origin of replication. The immediate early promoter of the human cytomegalovirus is conveniently obtained as a Hindlll E restriction fragment. A system for expressing DNA in mammalian hosts using the bovine papilloma virus as a vector is disclosed in U.S. Patent No. 4,419,446. A modification of this system is described in U.S. Patent No. 4,601,978. Alternatively, the Rous Sarcoma Virus long terminal repeat can be used as the promoter.
[00563] (v) Enhancer Element Component
[00564] Transcription of DNA encoding the antibody polypeptide of this disclosure by higher eukaryotes is often increased by inserting an enhancer sequence into the vector. Many enhancer sequences are now known from mammalian genes (globin, elastase, albumin, a- fetoprotein, and insulin). An enhancer from a eukaryotic cell virus may also be used. Examples include the SV40 enhancer on the late side of the replication origin (bp 100-270), the
cytomegalovirus early promoter enhancer, the polyoma enhancer on the late side of the replication origin, and adenovirus enhancers. See also Yaniv, Nature 297: 17-18 (1982) on enhancing elements for activation of eukaryotic promoters. The enhancer may be spliced into the vector at a position 5' or 3' to the antibody polypeptide-encoding sequence, but is preferably located at a site 5' from the promoter.
[00565] (vi) Transcription Termination Component
[00566] Expression vectors used in eukaryotic host cells will typically also contain sequences necessary for the termination of transcription and for stabilizing the mRNA. Such sequences are commonly available from the 5' and, occasionally 3', untranslated regions of eukaryotic or viral DNAs or cDNAs. These regions contain nucleotide segments transcribed as polyadenylated fragments in the untranslated portion of the mRNA encoding an antibody. One useful transcription termination component is the bovine growth hormone polyadenylation region. See W094/11026 and the expression vector disclosed therein. [00567] (νίί) Selection and Transformation of Host Cells
[00568] Suitable host cells for cloning or expressing the DNA in the vectors herein include higher eukaryote cells described herein, including vertebrate host cells. Propagation of vertebrate cells in culture (tissue culture) has become a routine procedure. Examples of useful mammalian host cell lines are monkey kidney CVl line transformed by SV40 (COS-7, ATCC CRL 1651); human embryonic kidney line (293 or 293 cells subcloned for growth in suspension culture, Graham et al, J. Gen Virol. 36:59 (1977)); baby hamster kidney cells (BHK, ATCC CCL 10); Chinese hamster ovary cells/-DHFR (CHO, Urlaub et al, Proc. Natl. Acad. Sci. USA 77:4216 (1980)); mouse Sertoli cells (TM4, Mather, Biol. Reprod. 23:243-251 (1980); monkey kidney cells (CVl ATCC CCL 70); African green monkey kidney cells (VERO-76, ATCC CRL-1587); human cervical carcinoma cells (HELA, ATCC CCL 2); canine kidney cells (MDCK, ATCC CCL 34); buffalo rat liver cells (BRL 3A, ATCC CRL 1442); human lung cells (W138, ATCC CCL 75); human liver cells (Hep G2, HB 8065); mouse mammary tumor (MMT 060562, ATCC CCL51); TRI cells (Mather et al, Annals N.Y. Acad. Sci. 383:44-68 (1982)); MRC 5 cells; FS4 cells; and a human hepatoma line (Hep G2).
[00569] Any of the well-known procedures for introducing foreign nucleotide sequences into host cells may be used. These include the use of calcium phosphate transfection, polybrene, protoplast fusion, electroporation, biolistics, liposomes, microinjection, plasma vectors, viral vectors and any of the other well known methods for introducing cloned genomic DNA, cDNA, synthetic DNA, or other foreign genetic material into a host cell (see, e.g., Sambrook and Russell, supra). It is only necessary that the particular genetic engineering procedure used be capable of successfully introducing at least both genes into the host cell capable of expressing germline antibody polypeptide.
[00570] Host cells are transformed with the above-described expression or cloning vectors for antibody production and cultured in conventional nutrient media modified as appropriate for inducing promoters, selecting transformants, or amplifying the genes encoding the desired sequences.
[00571] (viii) Culturing the Host Cells
[00572] The host cells used to produce an antibody of this disclosure may be cultured in a variety of media. Commercially available media such as Ham's F10 (Sigma), Minimal Essential Medium ((MEM), (Sigma), RPMI-1640 (Sigma), and Dulbecco's Modified Eagle's Medium ((DMEM), Sigma) are suitable for culturing the host cells. In addition, any of the media described in Ham et al, Meth. Enz. 58:44 (1979), Barnes et al, Anal. Biochem. 102:255 (1980), U.S. Patent Nos. 4,767,704; 4,657,866; 4,927,762; 4,560,655; or 5,122,469; WO 90/03430; WO 87/00195; or U.S. Patent Reissue 30,985 may be used as culture media for the host cells. Any of these media may be supplemented as necessary with hormones and/or other growth factors (such as insulin, transferrin, or epidermal growth factor), salts (such as sodium chloride, calcium, magnesium, and phosphate), buffers (such as HEPES), nucleotides (such as adenosine and thymidine), antibiotics (such as GENTAMYCIN™ drug), trace elements (defined as inorganic compounds usually present at final concentrations in the micromolar range), and glucose or an equivalent energy source. Any other necessary supplements may also be included at appropriate concentrations that would be known to those skilled in the art. The culture conditions, such as temperature, pH, and the like, are those previously used with the host cell selected for expression, and will be apparent to the ordinarily skilled artisan.
[00573] (ix) Purification of Antibody
[00574] When using recombinant techniques, the antibody can be produced intracellularly, or directly secreted into the medium. If the antibody is produced intracellularly, as a first step, the particulate debris, either host cells or lysed fragments, are removed, for example, by centrifugation or ultrafiltration. Where the antibody is secreted into the medium, supernatants from such expression systems are generally first concentrated using a commercially available protein concentration filter, for example, an Amicon or Millipore Pellicon® ultrafiltration unit. A protease inhibitor such as PMSF may be included in any of the foregoing steps to inhibit proteolysis and antibiotics may be included to prevent the growth of adventitious contaminants.
[00575] The antibody composition prepared from the cells can be purified using, for example, hydroxylapatite chromatography, gel electrophoresis, dialysis, and affinity
chromatography, with affinity chromatography being the preferred purification technique. The suitability of protein A as an affinity ligand depends on the species and isotype of any
immunoglobulin Fc domain that is present in the antibody. Protein A can be used to purify antibodies that are based on human γΐ, γ2, or γ4 heavy chains (Lindmark et al., J. Immunol. Meth. 62: 1-13 (1983)). Protein G is recommended for all mouse isotypes and for human γ3 (Guss et al, EMBO J. 5: 15671575 (1986)). The matrix to which the affinity ligand is attached is most often agarose, but other matrices are available. Mechanically stable matrices such as controlled pore glass or poly(styrenedivinyl)benzene allow for faster flow rates and shorter processing times than can be achieved with agarose. Where the antibody comprises a CH3 domain, the Bakerbond ABX™ resin (J. T. Baker, Phillipsburg, N.J.) is useful for purification. Other techniques for protein purification such as fractionation on an ion-exchange column, ethanol precipitation, Reverse Phase HPLC, chromatography on silica, chromatography on heparin SEPHAROSE™ chromatography on an anion or cation exchange resin (such as a polyaspartic acid column), chromatofocusing, SDS- PAGE, and ammonium sulfate precipitation are also available depending on the antibody to be recovered.
[00576] Soluble forms of antibody or fragment present either in the cytoplasm or released from the periplasmic space may be further purified using methods known in the art, for example Fab fragments are released from the bacterial periplasmic space by osmotic shock techniques.
[00577] If inclusion bodies comprising an antibody or fragment have formed, they can often bind to the inner and/or outer cellular membranes and thus will be found primarily in the pellet material after centrifugation. The pellet material can then be treated at pH extremes or with chaotropic agent such as a detergent, guanidine, guanidine derivatives, urea, or urea derivatives in the presence of a reducing agent such as dithiothreitol at alkaline pH or tris carboxyethyl phosphine at acid pH to release, break apart, and solubilize the inclusion bodies. The soluble antibody or fragment can then be analyzed using gel electrophoresis, immunoprecipitation or the like. If it is desired to isolate a solublized antibody or antigen binding fragment isolation may be accomplished using standard methods such as those set forth below and in Marston et al. (Meth. Enz., 182:264- 275 (1990)).
[00578] Following any preliminary purification step(s), the mixture comprising the antibody of interest and contaminants may be subjected to low pH hydrophobic interaction chromatography using an elution buffer at a pH between about 2.5-4.5, preferably performed at low salt
concentrations (e.g., from about 0-0.25 M salt).
[00579] In some cases, an antibody or fragment may not be biologically active upon isolation. Various methods for "refolding" or converting a polypeptide to its tertiary structure and generating disulfide linkages, can be used to restore biological activity. Such methods include exposing the solubilized polypeptide to a pH usually above 7 and in the presence of a particular concentration of a chaotrope. The selection of chaotrope is very similar to the choices used for inclusion body solubilization, but usually the chaotrope is used at a lower concentration and is not necessarily the same as chaotropes used for the solubilization. In most cases the refolding/oxidation solution will also contain a reducing agent or the reducing agent plus its oxidized form in a specific ratio to generate a particular redox potential allowing for disulfide shuffling to occur in the formation of the protein's cysteine bridge(s). Some of the commonly used redox couples include cysteine/cystamine, glutathione (GSH)/dithiobis GSH, cupric chloride, dithiothreitol(DTT)/dithiane DTT, and 2-mercaptoethanol(bME)/di-thio-b(ME). In many instances, a cosolvent may be used to increase the efficiency of the refolding, and common reagents used for this purpose include glycerol, polyethylene glycol of various molecular weights, arginine and the like. Immunoconj ugates
[00580] The disclosure also provides immuno conjugates (interchangeably termed "antibody- drug conjugates" or "ADC"), comprising any of the antibodies comprising an ultralong CDR3 as described herein conjugated to a cytotoxic agent such as a chemotherapeutic agent, a drug, a growth inhibitory agent, a toxin (e.g., an enzymatically active toxin of bacterial, fungal, plant, or animal origin, or fragments thereof), or a radioactive isotope (e.g., a radio conjugate). Alternatively, the immuno conjugate comprises any of the antibodies comprising an ultralong CDR3 as described herein conjugated to a peptide. The peptide may be a non-antibody peptide, therapeutic
polypeptide, cytokine, hormone or growth factor. The peptide may be encoded by a non-antibody sequence.
[00581] The antibody-drug conjugates may be used for the local delivery of cytotoxic or cytostatic agents. For example, drugs to kill or inhibit tumor cells in the treatment of cancer (Syrigos and Epenetos (1999) Anticancer Research 19:605-614; Niculescu-Duvaz and Springer (1997) Adv. Drg Del. Rev. 26: 151-172; U.S. Patent No. 4,975,278) allows targeted delivery of the drug moiety to tumors, and intracellular accumulation therein, where systemic administration of these unconjugated drug agents may result in unacceptable levels of toxicity to normal cells as well as the tumor cells sought to be eliminated (Baldwin et al., (1986) Lancet pp. (Mar. 15, 1986):603- 05; Thorpe, (1985) "Antibody Carriers Of Cytotoxic Agents In Cancer Therapy: A Review," in Monoclonal Antibodies '84: Biological And Clinical Applications, A. Pinchera et al. (ed.s), pp. 475-506). Maximal efficacy with minimal toxicity is sought thereby. Both polyclonal antibodies and monoclonal antibodies have been reported as useful in these strategies (Rowland et al., (1986) Cancer Immunol. Immunother., 21 : 183-87). Drugs used in these methods include daunomycin, doxorubicin, methotrexate, and vindesine (Rowland et al, (1986) Supra). Toxins used in antibody- toxin conjugates include bacterial toxins such as diphtheria toxin, plant toxins such as ricin, small molecule toxins such as geldanamycin (Mandler et al (2000) Jour, of the Nat. Cancer Inst.
92(19): 1573-1581; Mandler et al (2000) Bioorganic & Med. Chem. Letters 10: 1025-1028;
Mandler et al (2002) Bioconjugate Chem. 13:786-791), maytansinoids (EP 1391213; Liu et al., (1996) Proc. Natl. Acad. Sci. USA 93:8618-8623), and calicheamicin (Lode et al (1998) Cancer Res. 58:2928; Hinman et al (1993) Cancer Res. 53:3336-3342). The toxins may effect their cytotoxic and cytostatic effects by mechanisms including tubulin binding, DNA binding, or topoisomerase inhibition. Some cytotoxic drugs tend to be inactive or less active when conjugated to large antibodies or protein receptor ligands.
[00582] ZEVALIN® (ibritumomab tiuxetan, Biogen/Idec) is an antibody-radioisotope conjugate composed of a murine IgGl kappa monoclonal antibody directed against the CD20 antigen found on the surface of normal and malignant B lymphocytes and mIn or 90Y radioisotope bound by a thiourea linker-chelator (Wiseman et al (2000) Eur. Jour. Nucl. Med. 27(7):766-77; Wiseman et al (2002) Blood 99(12):4336-42; Witzig et al (2002) J. Clin. Oncol. 20(10):2453-63; Witzig et al (2002) J. Clin. Oncol. 20(15):3262-69). Although ZEVALIN has activity against B-cell non-Hodgkin's Lymphoma (NHL), administration results in severe and prolonged cytopenias in most patients. MYLOTARG™ (gemtuzumab ozogamicin, Wyeth Pharmaceuticals), an antibody drug conjugate composed of a hu CD33 antibody linked to calicheamicin, was approved in 2000 for the treatment of acute myeloid leukemia by injection (Drugs of the Future (2000) 25(7):686; U.S. Patent Nos. 4,970,198; 5,079,233; 5,585,089; 5,606,040; 5,693,762; 5,739,116; 5,767,285;
5,773,001). Cantuzumab mertansine (Immunogen, Inc.), an antibody drug conjugate composed of the huC242 antibody linked via the disulfide linker SPP to the maytansinoid drug moiety, DM1, is advancing into Phase II trials for the treatment of cancers that express CanAg, such as colon, pancreatic, gastric, and others. MLN-2704 (Millennium Pharm., BZL Biologies, Immunogen Inc.), an antibody drug conjugate composed of the anti-prostate specific membrane antigen (PSMA) monoclonal antibody linked to the maytansinoid drug moiety, DM1, is under development for the potential treatment of prostate tumors. The auristatin peptides, auristatin E (AE) and
monomethylauristatin (MMAE), synthetic analogs of dolastatin, were conjugated to chimeric monoclonal antibodies cBR96 (specific to Lewis Y on carcinomas) and cACIO (specific to CD30 on hematological malignancies) (Doronina et al (2003) Nature Biotechnology 21(7):778-784) and are under therapeutic development.
[00583] Chemotherapeutic agents useful in the generation of immuno conjugates are described herein. Enzymatically active toxins and fragments thereof that can be used include diphtheria A chain, nonbinding active fragments of diphtheria toxin, exotoxin A chain (from Pseudomonas aeruginosa), ricin A chain, abrin A chain, modeccin A chain, alpha-sarcin, Aleurites fordii proteins, dianthin proteins, Phytolaca americana proteins (PAPI, PAPII, and PAP-S), momordica charantia inhibitor, curcin, crotin, sapaonaria officinalis inhibitor, gelonin, mitogellin, restrictocin, phenomycin, enomycin, and the tricothecenes. See, e.g., WO 93/21232 published Oct. 28, 1993. A variety of radionuclides are available for the production of radio conjugated antibodies. Examples include 212Bi, 131I, 131In, 90Y, and 186Re. Conjugates of the antibody and cytotoxic agent are made using a variety of biiunctional protein-coupling agents such as N-succinimidyl-3-(2- pyridyldithiol) propionate (SPDP), iminothiolane (IT), biiunctional derivatives of imidoesters (such as dimethyl adipimidate HC1), active esters (such as disuccinimidyl suberate), aldehydes (such as glutaraldehyde), bis-azido compounds (such as bis (p-azidobenzoyl) hexanediamine), bis- diazonium derivatives (such as bis-(p-diazoniumbenzoyl)-ethylenediamine), diisocyanates (such as toluene 2,6-diisocyanate), and bis-active fluorine compounds (such as l,5-difluoro-2,4- dinitrobenzene). For example, a ricin immunotoxin may be prepared as described in Vitetta et al., Science, 238: 1098 (1987). Carbon- 14-labeled l-isothiocyanatobenzyl-3-methyldiethylene triaminepentaacetic acid (MX-DTPA) is an exemplary chelating agent for conjugation of radionucleotide to the antibody. See W094/11026.
[00584] Conjugates of an antibody and one or more small molecule toxins, such as a calicheamicin, maytansinoids, dolastatins, aurostatins, a trichothecene, and CC1065, and the derivatives of these toxins that have toxin activity, are also contemplated herein.
[00585] a. Maytansine and Maytansinoids
[00586] In some embodiments, the immuno conjugate comprises an antibody (full length or fragments) comprising an ultralong CDR3 as disclosed herein conjugated to one or more maytansinoid molecules.
[00587] Maytansinoids are mitototic inhibitors which act by inhibiting tubulin
polymerization. Maytansine was first isolated from the east African shrub Maytenus serrata (U.S. Patent No. 3,896,111). Subsequently, it was discovered that certain microbes also produce maytansinoids, such as maytansinol and C-3 maytansinol esters (U.S. Patent No. 4,151,042).
Synthetic maytansinol and derivatives and analogues thereof are disclosed, for example, in U.S. Patent Nos. 4,137,230; 4,248,870; 4,256,746; 4,260,608; 4,265,814; 4,294,757; 4,307,016;
4,308,268; 4,308,269; 4,309,428; 4,313,946; 4,315,929; 4,317,821; 4,322,348; 4,331,598;
4,361,650; 4,364,866; 4,424,219; 4,450,254; 4,362,663; and 4,371,533.
[00588] Maytansinoid drug moieties are attractive drug moieties in antibody drug conjugates because they are: (i) relatively accessible to prepare by fermentation or chemical modification, derivatization of fermentation products, (ii) amenable to derivatization with functional groups suitable for conjugation through the non-disulfide linkers to antibodies, (iii) stable in plasma, and (iv) effective against a variety of tumor cell lines.
[00589] Immunoconjugates containing maytansinoids, methods of making same, and their therapeutic use are disclosed, for example, in U.S. Patent Nos. 5,208,020, 5,416,064 and EP 0 425 235. Liu et al, Proc. Natl. Acad. Sci. USA 93:8618-8623 (1996) described immunoconjugates comprising a maytansinoid designated DM1 linked to the monoclonal antibody C242 directed against human colorectal cancer. The conjugate was found to be highly cytotoxic towards cultured colon cancer cells, and showed antitumor activity in an in vivo tumor growth assay. Chari et al., Cancer Research 52: 127-131 (1992) describe immunoconjugates in which a maytansinoid was conjugated via a disulfide linker to the murine antibody A7 binding to an antigen on human colon cancer cell lines, or to another murine monoclonal antibody TA.1 that binds the HER-2/neu oncogene. The cytotoxicity of the TA.1-maytansinoid conjugate was tested in vitro on the human breast cancer cell line SK-BR-3, which expresses 3xl05 HER-2 surface antigens per cell. The drug conjugate achieved a degree of cytotoxicity similar to the free maytansinoid drug, which could be increased by increasing the number of maytansinoid molecules per antibody molecule. The A7- maytansinoid conjugate showed low systemic cytotoxicity in mice.
[00590] Antibody-maytansinoid conjugates are prepared by chemically linking an antibody to a maytansinoid molecule without significantly diminishing the biological activity of either the antibody or the maytansinoid molecule. See, e.g., U.S. Patent No. 5,208,020. An average of 3-4 maytansinoid molecules conjugated per antibody molecule has shown efficacy in enhancing cytotoxicity of target cells without negatively affecting the function or solubility of the antibody, although even one molecule of toxin/antibody would be expected to enhance cytotoxicity over the use of naked antibody. Maytansinoids are well known in the art and can be synthesized by known techniques or isolated from natural sources. Suitable maytansinoids are disclosed, for example, in U.S. Patent No. 5,208,020 and in the other patents and nonpatent publications referred to hereinabove. Preferred maytansinoids are maytansinol and maytansinol analogues modified in the aromatic ring or at other positions of the maytansinol molecule, such as various maytansinol esters.
[00591] There are many linking groups known in the art for making antibody-maytansinoid conjugates, including, for example, those disclosed in U.S. Patent Nos. 5,208,020, 6,441,163, or EP Patent 0 425 235, Chari et al., Cancer Research 52: 127-131 (1992). Antibody-maytansinoid conjugates comprising the linker component SMCC may be prepared. The linking groups include disulfide groups, thioether groups, acid labile groups, photolabile groups, peptidase labile groups, or esterase labile groups, as disclosed in the above-identified patents, disulfide and thioether groups being preferred. Additional linking groups are described and exemplified herein.
[00592] Conjugates of the antibody and maytansinoid may be made using a variety of bifunctional protein coupling agents such as N-succinimidyl-3-(2-pyridyldithio) propionate (SPDP), succinimidyl-4-(N-maleimidomethyl)cyclohexane-l-carboxylate (SMCC), iminothiolane (IT), bifunctional derivatives of imidoesters (such as dimethyl adipimidate HC1), active esters (such as disuccinimidyl suberate), aldehydes (such as glutaraldehyde), bis-azido compounds (such as bis (p-azidobenzoyl) hexanediamine), bis-diazonium derivatives (such as bis-(p-diazoniumbenzoyl)- ethylenediamine), diisocyanates (such as toluene 2,6-diisocyanate), and bis-active fluorine compounds (such as l,5-difluoro-2,4-dinitrobenzene). Particularly preferred coupling agents include N-succinimidyl-3-(2-pyridyldithio) propionate (SPDP) (Carlsson et al, Biochem. J.
173:723-737 (1978)) and N-succinimidyl-4-(2-pyridylthio)pentanoate (SPP) to provide for a disulfide linkage. [00593] The linker may be attached to the maytansinoid molecule at various positions, depending on the type of the link. For example, an ester linkage may be formed by reaction with a hydroxyl group using conventional coupling techniques. The reaction may occur at the C-3 position having a hydroxyl group, the C-14 position modified with hydro xymethyl, the C-15 position modified with a hydroxyl group, and the C-20 position having a hydroxyl group. In a preferred embodiment, the linkage is formed at the C-3 position of maytansinol or a maytansinol analogue.
[00594] b. Auristatins and Dolastatins
[00595] In some embodiments, the immuno conjugate comprises an antibody disclosed herein conjugated to dolastatins or dolostatin peptidic analogs and derivatives, the auristatins (U.S. Patent Nos. 5,635,483; 5,780,588). Dolastatins and auristatins have been shown to interfere with microtubule dynamics, GTP hydrolysis, and nuclear and cellular division (Woyke et al (2001) Antimicrob. Agents and Chemother. 45(12):3580-3584) and have anticancer (U.S. Patent No. 5,663,149) and antifungal activity (Pettit et al (1998) Antimicrob. Agents Chemother. 42:2961- 2965). The dolastatin or auristatin drug moiety may be attached to the antibody through the N (amino) terminus or the C (carboxyl) terminus of the peptidic drug moiety (WO 02/088172).
[00596] Exemplary auristatin embodiments include the N-terminus linked
monomethylauristatin drug moieties DE and DF, (see, e.g., U.S. Patent No. 7,498,298).
[00597] Typically, peptide-based drug moieties can be prepared by forming a peptide bond between two or more amino acids and/or peptide fragments. Such peptide bonds can be prepared, for example, according to the liquid phase synthesis method (see, e.g., E. Schroder and K. Lubke, "The Peptides", volume 1, pp 76-136, 1965, Academic Press) that is well known in the field of peptide chemistry. The auristatin dolastatin drug moieties may be prepared according to the methods of: U.S. Patent No. 5,635,483; U.S. Patent No. 5,780,588; Pettit et al (1989) J. Am. Chem. Soc. 111 :5463-5465; Pettit et al. (1998) Anti-Cancer Drug Design 13:243-277; Pettit, G. R., et al. Synthesis, 1996, 719-725; and Pettit et al. (1996) J. Chem. Soc. Perkin Trans. 1 5:859-863. See also Doronina (2003) Nat Biotechnol 21(7):778-784; U.S. Patent No. 7,498,289, (disclosing, linkers and methods of preparing monomethylvaline compounds such as MMAE and MMAF conjugated to linkers).
[00598] c. Calicheamicin
[00599] In other embodiments, the immuno conjugate comprises an antibody disclosed herein conjugated to one or more calicheamicin molecules. The calicheamicin family of antibiotics are capable of producing double-stranded DNA breaks at sub-picomolar concentrations. For the preparation of conjugates of the calicheamicin family, see U.S. Patent Nos. 5,712,374, 5,714,586, 5,739,116, 5,767,285, 5,770,701, 5,770,710, 5,773,001, 5,877,296. Structural analogues of calicheamicin which may be used include, but are not limited to, γ , α2 7, a , N-acetyl-y , PSAG and θ\ (see, e.g., Hinman et al, Cancer Research 53:3336-3342 (1993), Lode et ah, Cancer Research 58:2925-2928 (1998) and the aforementioned U.S. patents). Another anti-tumor drug that the antibody can be conjugated is QFA which is an antifolate. Both calicheamicin and QFA have intracellular sites of action and do not readily cross the plasma membrane. Therefore, cellular uptake of these agents through antibody mediated internalization greatly enhances their cytotoxic effects.
[00600] d. Other Cytotoxic Agents
[00601] Other antitumor agents that can be conjugated to the antibodies disclosed herein include BCNU, streptozoicin, vincristine and 5-fluorouracil, the family of agents known
collectively LL-E33288 complex described in U.S. Patent Nos. 5,053,394, 5,770,710, as well as esperamicins (U.S. Patent No. 5,877,296).
[00602] Enzymatically active toxins and fragments thereof which can be used include diphtheria A chain, nonbinding active fragments of diphtheria toxin, exotoxin A chain (from Pseudomonas aeruginosa), ricin A chain, abrin A chain, modeccin A chain, alpha-sarcin, Aleurites fordii proteins, dianthin proteins, Phytolaca americana proteins (PAPI, PAPII, and PAP-S), momordica charantia inhibitor, curcin, crotin, sapaonaria officinalis inhibitor, gelonin, mitogellin, restrictocin, phenomycin, enomycin and the tricothecenes. See, for example, WO 93/21232 published Oct. 28, 1993.
[00603] The present disclosure further contemplates an immuno conjugate formed between an antibody and a compound with nucleo lytic activity {e.g., a ribonuclease or a DNA endonuclease such as a deoxyribonuclease; DNase).
[00604] For selective destruction of the tumor, the antibody may comprise a highly radioactive atom. A variety of radioactive isotopes are available for the production of
radioconjugated antibodies. Examples include At 2U, I131, 1125, Y90, Re186, Re188, Sm153, Bi212, P32, Pb212 and radioactive isotopes of Lu. When the conjugate is used for detection, it may comprise a radioactive atom for scintigraphic studies, for example tc99m or I123, or a spin label for nuclear magnetic resonance (NMR) imaging (also known as magnetic resonance imaging, mri), such as iodine- 123 again, iodine-131, indium-I l l, fluorine- 19, carbon- 13, nitrogen- 15, oxygen- 17, gadolinium, manganese or iron.
[00605] The radio labels or other labels may be incorporated in the conjugate in known ways.
For example, the peptide may be biosynthesized or may be synthesized by chemical amino acid synthesis using suitable amino acid precursors involving, for example, fluorine- 19 in place of hydrogen. Labels such as tc99m or I123, Re186, Re188 and In111 can be attached via a cysteine residue in the peptide. Yttrium-90 can be attached via a lysine residue. The IODOGEN method (Fraker et al (1978) Biochem. Biophys. Res. Commun. 80: 49-57) can be used to incorporate iodine-123. "Monoclonal Antibodies in Immunoscintigraphy" (Chatal, CRC Press 1989) describes other methods.
[00606] Conjugates of the antibody and cytotoxic agent may be made using a variety of bifunctional protein coupling agents such as N-succinimidyl-3-(2-pyridyldithio) propionate (SPDP), succinimidyl-4-(N-maleimidomethyl)cyclohexane-l-carboxylate (SMCC), iminothiolane (IT), bifunctional derivatives of imidoesters (such as dimethyl adipimidate HC1), active esters (such as disuccinimidyl suberate), aldehydes (such as glutaraldehyde), bis-azido compounds (such as bis (p-azidobenzoyl) hexanediamine), bis-diazonium derivatives (such as bis-(p-diazoniumbenzoyl)- ethylenediamine), diisocyanates (such as toluene 2,6-diisocyanate), and bis-active fluorine compounds (such as l,5-difluoro-2,4-dinitrobenzene). For example, a ricin immunotoxin can be prepared as described in Vitetta et al., Science 238: 1098 (1987). Carbon- 14-labeled 1- isothiocyanatobenzyl-3-methyldiethylene triaminepentaacetic acid (MX-DTPA) is an exemplary chelating agent for conjugation of radionucleotide to the antibody. See W094/11026. The linker may be a "cleavable linker" facilitating release of the cytotoxic drug in the cell. For example, an acid-labile linker, peptidase-sensitive linker, photolabile linker, dimethyl linker or disulfide- containing linker (Chari et al, Cancer Research 52: 127-131 (1992); U.S. Patent No. 5,208,020) may be used.
[00607] The compounds disclosed herein expressly contemplate, but are not limited to, ADC prepared with cross-linker reagents: BMPS, EMCS, GMBS, HBVS, LC-SMCC, MBS, MPBH, SBAP, SIA, SIAB, SMCC, SMPB, SMPH, sulfo-EMCS, sulfo-GMBS, sulfo-KMUS, sulfo-MBS, sulfo-SIAB, sulfo-SMCC, and sulfo-SMPB, and SVSB (succinimidyl-(4-vinylsulfone)benzoate) which are commercially available (e.g., from Pierce Biotechnology, Inc., Rockford, III, U.S.A). See pages 467-498, 2003-2004 Applications Handbook and Catalog.
[00608] e. Preparation of Antibody Drug Conjugates
[00609] In the antibody drug conjugates (ADC) disclosed herein, an antibody (Ab) is conjugated to one or more drug moieties (D), e.g,. about 1 to about 20 drug moieties per antibody, through a linker (L). An ADC of Formula I [Ab-(L-D)^] may be prepared by several routes, employing organic chemistry reactions, conditions, and reagents known to those skilled in the art, including: (1) reaction of a nucleophilic group of an antibody with a bivalent linker reagent, to form Ab-L, via a covalent bond, followed by reaction with a drug moiety D; and (2) reaction of a nucleophilic group of a drug moiety with a bivalent linker reagent, to form D-L, via a covalent bond, followed by reaction with the nucleophilic group of an antibody. Additional methods for preparing ADC are described herein.
[00610] The linker may be composed of one or more linker components. Exemplary linker components include 6-maleimidocaproyl ("MC"), maleimidopropanoyl ("MP"), valine-citrulline ("val-cit"), alanine-phenylalanine ("ala-phe"), p-aminobenzyloxycarbonyl ("PAB"), N- Succinimidyl 4-(2-pyridylthio) pentanoate ("SPP"), N-Succinimidyl 4-(N- maleimidomethyl)cyclohexane-l carboxylate ("SMCC"), and N-Succinimidyl (4-iodo- acetyl)aminobenzoate ("SIAB"). Additional linker components are known in the art and some are disclosed herein (see, e.g., U.S. Patent No. 7,498,298).
[00611] In some embodiments, the linker may comprise amino acid residues. Exemplary amino acid linker components include a dipeptide, a tripeptide, a tetrapeptide or a pentapeptide. Exemplary dipeptides include: valine-citrulline (vc or val-cit), alanine-phenylalanine (af or ala- phe). Exemplary tripeptides include: glycine-valine-citrulline (gly-val-cit) and glycine-glycine- glycine (gly-gly-gly). Amino acid residues which comprise an amino acid linker component include those occurring naturally, as well as minor amino acids and non-naturally occurring amino acids including analogs, such as citrulline. Amino acid linker components can be designed and optimized in their selectivity for enzymatic cleavage by a particular enzymes, for example, a tumor-associated protease, cathepsin B, C and D, or a plasmin protease.
[00612] Nucleophilic groups on antibodies include, but are not limited to: (i) N-terminal amine groups, (ii) side chain amine groups, e.g., lysine, (iii) side chain thiol groups, e.g., cysteine, and (iv) sugar hydroxyl or amino groups where the antibody is glycosylated. Amine, thiol, and hydroxyl groups are nucleophilic and capable of reacting to form covalent bonds with electrophilic groups on linker moieties and linker reagents including: (i) active esters such as NHS esters, HOBt esters, halo formates, and acid halides; (ii) alkyl and benzyl halides such as haloacetamides; (iii) aldehydes, ketones, carboxyl, and maleimide groups. Certain antibodies have reducible interchain disulfides, e.g., cysteine bridges. Antibodies may be made reactive for conjugation with linker reagents by treatment with a reducing agent such as DTT (dithiothreitol). Each cysteine bridge will thus form, theoretically, two reactive thiol nucleophiles. Additional nucleophilic groups can be introduced into antibodies through the reaction of lysines with 2-iminothiolane (Traut's reagent) resulting in conversion of an amine into a thiol. Reactive thiol groups may be introduced into the antibody (or fragment thereof) by introducing one, two, three, four, or more cysteine residues (e.g., preparing mutant antibodies comprising one or more non-native cysteine amino acid residues).
[00613] Antibody drug conjugates disclosed herein may also be produced by modification of the antibody to introduce electrophilic moieties, which can react with nucleophilic substituents on the linker reagent or drug. The sugars of glycosylated antibodies may be oxidized, e.g., with periodate oxidizing reagents, to form aldehyde or ketone groups which may react with the amine group of linker reagents or drug moieties. The resulting imine Schiff base groups may form a stable linkage, or may be reduced, e.g., by borohydride reagents to form stable amine linkages. In one embodiment, reaction of the carbohydrate portion of a glycosylated antibody with either glactose oxidase or sodium meta-periodate may yield carbonyl (aldehyde and ketone) groups in the protein that can react with appropriate groups on the drug (Hermanson, Bioconjugate Techniques). In another embodiment, proteins containing N-terminal serine or threonine residues can react with sodium meta-periodate, resulting in production of an aldehyde in place of the first amino acid (Geoghegan & Stroh, (1992) Bioconjugate Chem. 3: 138-146; U.S. Patent No. 5,362,852). Such aldehyde can be reacted with a drug moiety or linker nucleophile.
[00614] Likewise, nucleophilic groups on a drug moiety include, but are not limited to:
amine, thiol, hydroxyl, hydrazide, oxime, hydrazine, thiosemicarbazone, hydrazine carboxylate, and arylhydrazide groups capable of reacting to form covalent bonds with electrophilic groups on linker moieties and linker reagents including: (i) active esters such as NHS esters, HOBt esters, halo formates, and acid halides; (ii) alkyl and benzyl halides such as haloacetamides; (iii) aldehydes, ketones, carboxyl, and maleimide groups.
[00615] Alternatively, a fusion protein comprising the antibody and cytotoxic agent may be made, e.g., by recombinant techniques or peptide synthesis. The length of DNA may comprise respective regions encoding the two portions of the conjugate either adjacent one another or separated by a region encoding a linker peptide which does not destroy the desired properties of the conjugate.
[00616] In yet another embodiment, the antibody may be conjugated to a "receptor" (such streptavidin) for utilization in tumor pre-targeting wherein the antibody-receptor conjugate is administered to the patient, followed by removal of unbound conjugate from the circulation using a clearing agent and then administration of a "ligand" {e.g., avidin) which is conjugated to a cytotoxic agent {e.g., a radionucleotide).
Engineered Hybridomas
[00617] Hybridoma cells can be generated by fusing B cells producing a desired antibody with an immortalized cell line, usually a myeloma cell line, so that the resulting fusion cells will be an immortalized cell line that secrets a particular antibody. By the same principle, myeloma cells can be first transfected with a nucleic acid encoding a germline antibody V region and can be screened for the expression of the germline V region. Those myeloma cells with highest level of proteolytic light chain expression can be subsequently fused with B cells that produce an antibody with desired target protein specificity. The fusion cells will produce two types of antibodies: one is a heterologous antibody containing an endogenous antibody chain (either heavy or light) operably joined to the recombinant germline V region (either heavy or light), and the other is the same antibody that the parental B cells would secrete (e.g. both endogenous heavy and light chains). The operably joined heterologous heavy and light chains can be isolated by conventional methods such as chromatography and identification can be confirmed by target protein binding assays, assays identifying a unique tag of the germline polypeptide, or endopeptidase activity assays described in other sections of this disclosure. In some cases, where the heterologous antibody is the predominant type in quantity among the two types of antibodies, such isolation may not be needed. Hybridomas. Including bovine hybridomas, may be a source of bovine antibody gene sequences, including ultralong CDR3 sequences.
Transgenic Mammals
[00618] A nucleic acid sequence encoding a germline antibody polypeptide of the present disclosure can be introduced into a non-human mammal to generate a transgenic animal that expresses the germline antibody polypeptide. Unlike the transgenic animal models more commonly seen, the transgene expressed by the transgenic mammals of the present disclosure need not replace at least one allele of the endogenous coding sequence responsible for the variable regions of antibody chains following somatic recombination. Due to allelic exclusion, the presence of an exogenous, post-somatic rearrangement version of the germline V region DNA will inhibit the endogenous alleles of pre-somatic rearrangement V minigenes from undergoing somatic rearrangement and contributing to the makeup of antibody chains this mammal may produce. Thus, when exposed to a particular antigen, the mammal will generate heterologous antibodies comprising one endogenously rearranged antibody chain, and one transgenic gene which was rearranged a priori. Such heterologous antibodies are invaluable in research and in treating certain conditions in live subjects. On the other hand, a method that directs the integration of the transgene to the locus of an endogenous allele will fully serve the purpose of practicing the present disclosure as well.
[00619] The general methods of generating transgenic animals have been well established and frequently practiced. For reviews and protocols for generating transgenic animals and related methods for genetic manipulations, see, e.g., Mansour et al, Nature 336:348-352 (1988); Capecchi et al, Trends Genet. 5:70-76 (1989); Capecchi, Science 244: 1288-1292 (1989); Capecchi et al, Current Communications in Molecular Biology, pp45-52, Capecchi, M.R. (ed.), Cold Spring Harbor Press, Cold Spring Harbor, N.Y. (1989); Frohman et al, Cell 56: 145-147 (1989); Brinster et al, Proc. Natl. Acad. Sci. USA 82:4438-4442 (1985); Evans et. al, Nature 292: 154-156 (1981); Bradley et al, Nature 309:255-258 (1984); Gossler et al, Proc. Natl. Acad. Sci. USA 83:9065- 9069 (1986); Robertson et al, Nature 322:445-448 (1986); Jaenisch Science 240: 1468-1474 (1988); and Siedel, G. E., Jr., "Critical review of embryo transfer procedures with cattle" in
Fertilization and Embryonic Development in Vitro, page 323, L. Mastroianni, Jr. and J. D. Biggers, ed., Plenum Press, New York, N.Y. (1981).
[00620] An exemplary transgenic animal of the present disclosure is mouse, whereas a number of other transgenic animals can also be produced using the same general method. These animals include, but are not limited to: rabbits, sheep, cattle, and pigs (Jaenisch Science 240: 1468- 1474 (1988); Hammer et al, J. Animal. Sci. 63:269 (1986); Hammer et al Nature 315:680 (1985); Wagner et al, Theriogenology 21 :29 (1984)).
Pharmaceutical Compositions
[00621] Antibodies comprising an ultralong CDR3, antibody fragments, nucleic acids, or vectors disclosed herein can be formulated in compositions, especially pharmaceutical
compositions. Such compositions with antibodies comprising an ultralong CDR3 comprise a therapeutically or prophylactically effective amount of antibodies comprising an ultralong CDR3, antibody fragment, nucleic acid, or vector disclosed herein in admixture with a suitable carrier, e.g., a pharmaceutically acceptable agent. Typically, antibodies comprising an ultralong CDR3, antibody fragments, nucleic acids, or vectors disclosed herein are sufficiently purified for administration before formulation in a pharmaceutical composition.
[00622] Pharmaceutically acceptable salts, excipients, or vehicles for use in the present pharmaceutical compositions include carriers, excipients, diluents, antioxidants, preservatives, coloring, flavoring and diluting agents, emulsifying agents, suspending agents, solvents, fillers, bulking agents, buffers, delivery vehicles, tonicity agents, cosolvents, wetting agents, complexing agents, buffering agents, antimicrobials, and surfactants.
[00623] Neutral buffered saline or saline mixed with serum albumin are exemplary appropriate carriers. The pharmaceutical compositions may include antioxidants such as ascorbic acid; low molecular weight polypeptides; proteins, such as serum albumin, gelatin, or
immunoglobulins; hydrophilic polymers such as polyvinylpyrrolidone; amino acids such as glycine, glutamine, asparagine, arginine or lysine; monosaccharides, disaccharides, and other carbohydrates including glucose, mannose, or dextrins; chelating agents such as EDTA; sugar alcohols such as mannitol or sorbitol; salt-forming counterions such as sodium; and/or nonionic surfactants such as Tween, pluronics, or polyethylene glycol (PEG). Also by way of example, suitable tonicity enhancing agents include alkali metal halides (preferably sodium or potassium chloride), mannitol, sorbitol, and the like. Suitable preservatives include benzalkonium chloride, thimerosal, phenethyl alcohol, methylparaben, propylparaben, chlorhexidine, sorbic acid and the like. Hydrogen peroxide also may be used as preservative. Suitable cosolvents include glycerin, propylene glycol, and PEG. Suitable complexing agents include caffeine, polyvinylpyrrolidone, beta-cyclodextrin or hydroxy-propyl-beta-cyclodextrin. Suitable surfactants or wetting agents include sorbitan esters, polysorbates such as polysorbate 80, tromethamine, lecithin, cholesterol, tyloxapal, and the like. The buffers may be conventional buffers such as acetate, borate, citrate, phosphate, bicarbonate, or Tris-HCl. Acetate buffer may be about pH 4-5.5, and Tris buffer can be about pH 7-8.5. Additional pharmaceutical agents are set forth in Remington's Pharmaceutical Sciences, 18th Edition, A. R. Gennaro, ed., Mack Publishing Company, 1990.
[00624] The composition may be in liquid form or in a lyophilized or freeze-dried form and may include one or more lyoprotectants, excipients, surfactants, high molecular weight structural additives and/or bulking agents (see, for example, U.S. Patent Nos. 6,685,940, 6,566,329, and 6,372,716). In one embodiment, a lyoprotectant is included, which is a non-reducing sugar such as sucrose, lactose or trehalose. The amount of lyoprotectant generally included is such that, upon reconstitution, the resulting formulation will be isotonic, although hypertonic or slightly hypotonic formulations also may be suitable. In addition, the amount of lyoprotectant should be sufficient to prevent an unacceptable amount of degradation and/or aggregation of the protein upon
lyophilization. Exemplary lyoprotectant concentrations for sugars (e.g., sucrose, lactose, trehalose) in the pre-lyophilized formulation are from about 10 mM to about 400 mM. In another
embodiment, a surfactant is included, such as for example, nonionic surfactants and ionic surfactants such as polysorbates (e.g., polysorbate 20, polysorbate 80); poloxamers (e.g., poloxamer 188); poly(ethylene glycol) phenyl ethers (e.g., Triton); sodium dodecyl sulfate (SDS); sodium laurel sulfate; sodium octyl glycoside; lauryl-, myristyl-, linoleyl-, or stearyl-sulfobetaine; lauryl-, myristyl-, linoleyl-or stearyl-sarcosine; linoleyl, myristyl-, or cetyl-betaine; lauroamidopropyl-, cocamidopropyl-, linoleamidopropyl-, myristamidopropyl-, palmidopropyl-, or
isostearamidopropyl-betaine (e.g., lauroamidopropyl); myristamidopropyl-, palmidopropyl-, or isostearamidopropyl-dimethylamine; sodium methyl cocoyl-, or disodium methyl ofeyl-taurate; and the MONAQUAT™. series (Mona Industries, Inc., Paterson, N.J.), polyethyl glycol, polypropyl glycol, and copolymers of ethylene and propylene glycol (e.g., Pluronics, PF68 etc). Exemplary amounts of surfactant that may be present in the pre-lyophilized formulation are from about 0.001- 0.5%. High molecular weight structural additives (e.g., fillers, binders) may include for example, acacia, albumin, alginic acid, calcium phosphate (dibasic), cellulose, carboxymethylcellulose, carboxymethylcellulose sodium, hydroxyethylcellulose, hydroxypropylcellulose,
hydroxypropylmethylcellulose, micro crystalline cellulose, dextran, dextrin, dextrates, sucrose, tylose, pregelatinized starch, calcium sulfate, amylose, glycine, bentonite, maltose, sorbitol, ethylcellulose, disodium hydrogen phosphate, disodium phosphate, disodium pyrosulfite, polyvinyl alcohol, gelatin, glucose, guar gum, liquid glucose, compressible sugar, magnesium aluminum silicate, maltodextrin, polyethylene oxide, polymethacrylates, povidone, sodium alginate, tragacanth micro crystalline cellulose, starch, and zein. Exemplary concentrations of high molecular weight structural additives are from 0.1% to 10% by weight. In other embodiments, a bulking agent (e.g., mannitol, glycine) may be included.
[00625] Compositions may be suitable for parenteral administration. Exemplary
compositions are suitable for injection or infusion into an animal by any route available to the skilled worker, such as intraarticular, subcutaneous, intravenous, intramuscular, intraperitoneal, intracerebral (intraparenchymal), intracerebroventricular, intramuscular, intraocular, intraarterial, or intralesional routes. A parenteral formulation typically will be a sterile, pyrogen- free, isotonic aqueous solution, optionally containing pharmaceutically acceptable preservatives.
[00626] Examples of non-aqueous solvents are propylene glycol, polyethylene glycol, vegetable oils such as olive oil, and injectable organic esters such as ethyl oleate. Aqueous carriers include water, alcoholic/aqueous solutions, emulsions or suspensions, including saline and buffered media. Parenteral vehicles include sodium chloride solution, Ringers' dextrose, dextrose and sodium chloride, lactated Ringer's, or fixed oils. Intravenous vehicles include fluid and nutrient replenishers, electrolyte replenishers, such as those based on Ringer's dextrose, and the like.
Preservatives and other additives may also be present, such as, for example, anti-microbials, antioxidants, chelating agents, inert gases and the like. See generally, Remington's Pharmaceutical Science, 16th Ed., Mack Eds., 1980.
[00627] Pharmaceutical compositions described herein may be formulated for controlled or sustained delivery in a manner that provides local concentration of the product (e.g., bolus, depot effect) and/or increased stability or half-life in a particular local environment. The compositions can include the formulation of antibodies comprising an ultralong CDR3, antibody fragments, nucleic acids, or vectors disclosed herein with particulate preparations of polymeric compounds such as polylactic acid, polyglycolic acid, etc., as well as agents such as a biodegradable matrix, injectable microspheres, microcapsular particles, microcapsules, bioerodible particles beads, liposomes, and implantable delivery devices that provide for the controlled or sustained release of the active agent which then can be delivered as a depot injection. Techniques for formulating such sustained-or controlled-delivery means are known and a variety of polymers have been developed and used for the controlled release and delivery of drugs. Such polymers are typically
biodegradable and biocompatible. Polymer hydrogels, including those formed by complexation of enantiomeric polymer or polypeptide segments, and hydrogels with temperature or pH sensitive properties, may be desirable for providing drug depot effect because of the mild and aqueous conditions involved in trapping bioactive protein agents (e.g., antibodies comprising an ultralong CDR3). See, for example, the description of controlled release porous polymeric microparticles for the delivery of pharmaceutical compositions in WO 93/15722.
[00628] Suitable materials for this purpose include polylactides (see, e.g., U.S. Patent No.
3,773,919), polymers of poly-(a-hydroxycarboxylic acids), such as poly-D-(-)-3-hydroxybutyric acid (EP 133,988A), copolymers of L-glutamic acid and gamma ethyl-L-glutamate (Sidman et al, Biopolymers, 22: 547-556 (1983)), poly(2-hydroxyethyl-methacrylate) (Langer et al, J. Biomed. Mater. Res., 15: 167-277 (1981), and Langer, Chem. Tech., 12: 98-105 (1982)), ethylene vinyl acetate, or poly-D(-)-3-hydroxybutyric acid. Other biodegradable polymers include poly(lactones), poly(acetals), poly(orthoesters), and poly(ortho carbonates). Sustained-release compositions also may include liposomes, which can be prepared by any of several methods known in the art (see, e.g., Eppstein et al, Proc. Natl. Acad. Sci. USA, 82: 3688-92 (1985)). The carrier itself, or its degradation products, should be nontoxic in the target tissue and should not further aggravate the condition. This can be determined by routine screening in animal models of the target disorder or, if such models are unavailable, in normal animals.
[00629] Microencapsulation of recombinant proteins for sustained release has been performed successfully with human growth hormone (rhGH), interferon-(rhlFN-), inter leukin-2, and MN rgpl20. Johnson et al, Nat. Med., 2:795-799 (1996); Yasuda, Biomed. Ther., 27: 1221- 1223 (1993); Hora et al, Bio/Technology. 8:755-758 (1990); Cleland, "Design and Production of Single Immunization Vaccines Using Polylactide Polyglycolide Microsphere Systems," in Vaccine Design: The Subunit and Adjuvant Approach, Powell and Newman, eds, (Plenum Press: New York, 1995), pp. 439-462; WO 97/03692, WO 96/40072, WO 96/07399; and U.S. Patent No.
5,654,010. The sustained-release formulations of these proteins were developed using poly-lactic- coglycolic acid (PLGA) polymer due to its biocompatibility and wide range of biodegradable properties. The degradation products of PLGA, lactic and glycolic acids can be cleared quickly within the human body. Moreover, the degradability of this polymer can be depending on its molecular weight and composition. Lewis, "Controlled release of bioactive agents from
lactide/glycolide polymer," in: M. Chasin and R. Langer (Eds.), Biodegradable Polymers as Drug Delivery Systems (Marcel Dekker: New York, 1990), pp. 1-41. Additional examples of sustained release compositions include, for example, EP 58,481A, U.S. Patent No. 3,887,699, EP 158,277A, Canadian Patent No. 1176565, U. Sidman et al, Biopolymers 22, 547 [1983], R. Langer et al, Chem. Tech. 12, 98 [1982], Sinha et al, J. Control. Release 90, 261 [2003], Zhu et al, Nat.
Biotechnol. 18, 24 [2000], and Dai et al, Colloids Surf B Biointerfaces 41, 117 [2005].
[00630] Bioadhesive polymers are also contemplated for use in or with compositions of the present disclosure. Bioadhesives are synthetic and naturally occurring materials able to adhere to biological substrates for extended time periods. For example, Carbopol and polycarbophil are both synthetic cross-linked derivatives of poly( acrylic acid). Bioadhesive delivery systems based on naturally occurring substances include for example hyaluronic acid, also known as hyaluronan. Hyaluronic acid is a naturally occurring mucopolysaccharide consisting of residues of D-glucuronic and N-acetyl-D-glucosamine. Hyaluronic acid is found in the extracellular tissue matrix of vertebrates, including in connective tissues, as well as in synovial fluid and in the vitreous and aqueous humor of the eye. Esterified derivatives of hyaluronic acid have been used to produce microspheres for use in delivery that are biocompatible and biodegradable (see, for example, Cortivo et al, Biomaterials (1991) 12:727-730; EP 517,565; WO 96/29998; Ilium et al, J.
Controlled Rel. (1994) 29: 133-141). Exemplary hyaluronic acid containing compositions of the present disclosure comprise a hyaluronic acid ester polymer in an amount of approximately 0.1% to about 40% (w/w) of an antibody comprising an ultralong CDR3 to hyaluronic acid polymer.
[00631] Both biodegradable and non-biodegradable polymeric matrices may be used to deliver compositions of the present disclosure, and such polymeric matrices may comprise natural or synthetic polymers. Biodegradable matrices are preferred. The period of time over which release occurs is based on selection of the polymer. Typically, release over a period ranging from between a few hours and three to twelve months is most desirable. Exemplary synthetic polymers which may be used to form the biodegradable delivery system include: polymers of lactic acid and glycolic acid, polyamides, polycarbonates, polyalkylenes, polyalkylene glycols, polyalkylene oxides, polyalkylene terepthalates, polyvinyl alcohols, polyvinyl ethers, polyvinyl esters, poly-vinyl halides, polyvinylpyrrolidone, polyglycolides, polysiloxanes, polyanhydrides, polyurethanes and co-polymers thereof, poly(butic acid), poly( valeric acid), alkyl cellulose, hydroxyalkyl celluloses, cellulose ethers, cellulose esters, nitro celluloses, polymers of acrylic and methacrylic esters, methyl cellulose, ethyl cellulose, hydroxypropyl cellulose, hydroxypropyl methyl cellulose, hydroxybutyl methyl cellulose, cellulose acetate, cellulose propionate, cellulose acetate butyrate, cellulose acetate phthalate, carboxylethyl cellulose, cellulose triacetate, cellulose sulphate sodium salt, poly(methyl methacrylate), poly(ethyl methacrylate), poly(butylmethacrylate), poly(isobutyl methacrylate), poly(hexylmethacrylate), poly(isodecyl methacrylate), poly(lauryl methacrylate), poly(phenyl methacrylate), poly(methyl acrylate), poly(isopropyl acrylate), poly(isobutyl acrylate), poly(octadecyl acrylate), polyethylene, polypropylene, poly(ethylene glycol), poly(ethylene oxide), poly(ethylene terephthalate), poly( vinyl alcohols), polyvinyl acetate, poly vinyl chloride, polystyrene and polyvinylpyrrolidone. Exemplary natural polymers include alginate and other polysaccharides including dextran and cellulose, collagen, chemical derivatives thereof
(substitutions, additions of chemical groups, for example, alkyl, alkylene, hydroxylations, oxidations, and other modifications routinely made by those skilled in the art), albumin and other hydrophilic proteins, zein and other prolamines and hydrophobic proteins, copolymers and mixtures thereof. In general, these materials degrade either by enzymatic hydrolysis or exposure to water in vivo, by surface or bulk erosion. The polymer optionally is in the form of a hydrogel (see, for example, WO 04/009664, WO 05/087201, Sawhney, et al, Macromolecules, 1993, 26, 581-587) that can absorb up to about 90% of its weight in water and further, optionally is cross-linked with multi-valent ions or other polymers.
[00632] Delivery systems also include non-polymer systems that are lipids including sterols such as cholesterol, cholesterol esters and fatty acids or neutral fats such as mono-di-and triglycerides; hydrogel release systems; silastic systems; peptide based systems; wax coatings;
compressed tablets using conventional binders and excipients; partially fused implants; and the like. Specific examples include, but are not limited to: (a) erosional systems in which the product is contained in a form within a matrix such as those described in U.S. Patent Nos. 4,452,775,
4,675,189 and 5,736,152 and (b) diffusional systems in which a product permeates at a controlled rate from a polymer such as described in U.S. Patent Nos. 3,854,480, 5,133,974 and 5,407,686. Liposomes containing the product may be prepared by methods known methods, such as for example (DE 3,218,121; Epstein et al, Proc. Natl. Acad. Sci. USA, 82: 3688-3692 (1985); Hwang et al, Proc. Natl. Acad. Sci. USA, 77: 4030-4034 (1980); EP 52,322; EP 36,676; EP 88,046; EP 143,949; EP 142,641; JP 83-118008; U.S. Patent Nos. 4,485,045 and 4,544,545; and EP 102,324).
[00633] Alternatively or additionally, the compositions may be administered locally via implantation into the affected area of a membrane, sponge, or other appropriate material on to which an antibody comprising an ultralong CDR3, antibody fragment, nucleic acid, or vector disclosed herein has been absorbed or encapsulated. Where an implantation device is used, the device may be implanted into any suitable tissue or organ, and delivery of an antibody comprising an ultralong CDR3 antibody fragment, nucleic acid, or vector disclosed herein can be directly through the device via bolus, or via continuous administration, or via catheter using continuous infusion. [00634] A pharmaceutical composition comprising an antibody comprising an ultralong
CDR3, antibody fragment, nucleic acid, or vector disclosed herein may be formulated for inhalation, such as for example, as a dry powder. Inhalation solutions also may be formulated in a liquefied propellant for aerosol delivery. In yet another formulation, solutions may be nebulized. Additional pharmaceutical composition for pulmonary administration include, those described, for example, in WO 94/20069, which discloses pulmonary delivery of chemically modified proteins. For pulmonary delivery, the particle size should be suitable for delivery to the distal lung. For example, the particle size may be from 1 μιη to 5 um; however, larger particles may be used, for example, if each particle is fairly porous.
[00635] Certain formulations containing antibodies comprising an ultralong CDR3, antibody fragments, nucleic acids, or vectors disclosed herein may be administered orally. Formulations administered in this fashion may be formulated with or without those carriers customarily used in the compounding of solid dosage forms such as tablets and capsules. For example, a capsule can be designed to release the active portion of the formulation at the point in the gastrointestinal tract when bioavailability is maximized and pre-systemic degradation is minimized. Additional agents may be included to facilitate absorption of a selective binding agent. Diluents, flavorings, low melting point waxes, vegetable oils, lubricants, suspending agents, tablet disintegrating agents, and binders also can be employed.
[00636] Another preparation may involve an effective quantity of an antibody comprising an ultralong CDR3, antibody fragment, nucleic acid, or vector disclosed herein in a mixture with nontoxic excipients which are suitable for the manufacture of tablets. By dissolving the tablets in sterile water, or another appropriate vehicle, solutions may be prepared in unit dose form. Suitable excipients include, but are not limited to, inert diluents, such as calcium carbonate, sodium carbonate or bicarbonate, lactose, or calcium phosphate; or binding agents, such as starch, gelatin, or acacia; or lubricating agents such as magnesium stearate, stearic acid, or talc.
[00637] Suitable and/or preferred pharmaceutical formulations may be determined in view of the present disclosure and general knowledge of formulation technology, depending upon the intended route of administration, delivery format, and desired dosage. Regardless of the manner of administration, an effective dose may be calculated according to patient body weight, body surface area, or organ size. Further refinement of the calculations for determining the appropriate dosage for treatment involving each of the formulations described herein are routinely made in the art and is within the ambit of tasks routinely performed in the art. Appropriate dosages may be ascertained through use of appropriate dose-response data. [00638] In some embodiments, antibodies comprising an ultralong CDR3 or fragments thereof are provided with a modified Fc region where a naturally-occurring Fc region is modified to increase the half-life of the antibody or fragment in a biological environment, for example, the serum half- life or a half- life measured by an in vitro assay. Methods for altering the original form of a Fc region of an IgG also are described in U.S. Patent No. 6,998,253.
[00639] In certain embodiments, it may be desirable to modify the antibody or fragment in order to increase its serum half-life, for example, adding molecules such as PEG or other water soluble polymers, including polysaccharide polymers, to antibody fragments to increase the half- life. This may also be achieved, for example, by incorporation of a salvage receptor binding epitope into the antibody fragment {e.g., by mutation of the appropriate region in the antibody fragment or by incorporating the epitope into a peptide tag that is then fused to the antibody fragment at either end or in the middle, e.g., by DNA or peptide synthesis) (see, International Publication No.
W096/32478). Salvage receptor binding epitope refers to an epitope of the Fc region of an IgG molecule {e.g., IgGl, IgG2, IgG3, or IgG4) that is responsible for increasing the in vivo serum half- life of the IgG molecule.
[00640] A salvage receptor binding epitope may include a region wherein any one or more amino acid residues from one or two loops of a Fc domain are transferred to an analogous position of the antibody fragment. Even more preferably, three or more residues from one or two loops of the Fc domain are transferred. Still more preferred, the epitope is taken from the CH2 domain of the Fc region {e.g., of an IgG) and transferred to the CHI, CH3, or VH region, or more than one such region, of the antibody. Alternatively, the epitope is taken from the CH2 domain of the Fc region and transferred to the CL region or VL region, or both, of the antibody fragment. See also WO 97/34631 and WO 96/32478 which describe Fc variants and their interaction with the salvage receptor.
[00641] Mutation of residues within Fc receptor binding sites may result in altered effector function, such as altered ADCC or CDC activity, or altered half-life. Potential mutations include insertion, deletion or substitution of one or more residues, including substitution with alanine, a conservative substitution, a non-conservative substitution, or replacement with a corresponding amino acid residue at the same position from a different IgG subclass {e.g., replacing an IgGl residue with a corresponding IgG2 residue at that position). For example, it has been reported that mutating the serine at amino acid position 241 in IgG4 to proline (found at that position in IgGl and IgG2) led to the production of a homogeneous antibody, as well as extending serum half-life and improving tissue distribution compared to the original chimeric IgG4. (Angal et al., Mol.
Immunol. 30: 105-8, 1993). [00642] In some embodiments is a pharmaceutical composition comprising an antibody comprising an ultralong CDR3; and a pharmaceutically acceptable carrier. The antibody may comprise a therapeutic polypeptide, or derivative or variant thereof. The therapeutic polypeptide may be a non-antibody sequence. The therapeutic polypeptide, or derivative or variant thereof can be within the ultralong CDR3. In some instances, the therapeutic polypeptide is Mokal, Vm24, GLP-1, Exendin-4, human EPO, human FGF21, human GMCSF, human interferon-beta, human GCSF, bovine GCSF or derivative or variant thereof. Alternatively, the antibody is an
immuno conjugate as described herein. The antibody can comprise one or more immunoglobulin domains. In some embodiments, the immunoglobulin domain is an immunoglobulin A, an immunoglobulin D, an immunoglobulin E, an immunoglobulin G, or an immunoglobulin M. The immunoglobulin domain can be an immunoglobulin heavy chain region or fragment thereof. In some instances, the immunoglobulin domain is from a mammalian antibody. Alternatively, the immunoglobulin domain is from a chimeric antibody. In some instances, the immunoglobulin domain is from an engineered antibody or recombinant antibody. In other instances, the
immunoglobulin domain is from a humanized, human engineered or fully human antibody. The mammalian antibody may be a bovine antibody. The mammalin antibody may be a human antibody. In other instances, the mammalian antibody is a murine antibody. The ultralong CDR3 can comprise at least a portion of a knob domain in the CDR3. The therapeutic polypeptide can be attached to the knob domain. Alternatively, or additionally, the ultralong CDR3 comprises at least a portion of a stalk domain in the CDR3. The therapeutic polypeptide may be attached to the stalk domain. In some instances, the antibody further comprises a linker. The linker can be within the ultralong CDR3. The linker can attach the therapeutic polypeptide to the immunoglobulin domain or fragment thereof. In other instances, the linker attaches the therapeutic polypeptide to the knob domain or stalk domain. In certain embodiments is a method of preventing or treating a disease in a subject in need thereof comprising administering this pharmaceutical composition to the subject. In some embodiments, the pharmaceutical composition comprising an immunoglobulin construct comprising a heavy chain polypeptide comprising a sequence based on or derived from a sequence selected from any one of SEQ ID NOS: 24-44and the polypeptide sequence encoded by the DNA any one of SEQ ID NOS: 2-22; and a light chain polypeptide comprising a sequence selected from SEQ ID NO: 23 and a polypeptide sequence encoded by the DNA of SEQ ID NO: I; and a pharmaceutically acceptable carrier. In certain embodiments is a method of preventing or treating a disease in a mammal in need thereof comprising administering this phartmaceutical composition to the mammal. In some embodiments, the disease is an infectious disease such as mastitis. In certain embodiments, the mammal in need is a dairy animal selected from a list comprising cow, camel, donkey, goat, horse, reindeer, sheep, water buffalo, moose and yak. In some embodiments, the mammal in need is bovine.
[00643] In some embodiments, the pharmaceutical compositions disclosed herein may be useful for providing prognostic or providing diagnostic information.
Kits/ Articles of Manufacture
[00644] As an additional aspect, the present disclosure includes kits which comprise one or more compounds or compositions packaged in a manner which facilitates their use to practice methods of the present disclosure. In one embodiment, such a kit includes a compound or composition described herein (e.g., a composition comprising an antibody comprising an ultralong CDR3 alone or in combination with a second agent), packaged in a container with a label affixed to the container or a package insert that describes use of the compound or composition in practicing the method. Suitable containers include, for example, bottles, vials, syringes, etc. The containers may be formed from a variety of materials such as glass or plastic. The container may have a sterile access port (for example the container may be an intravenous solution bag or a vial having a stopper pierceable by a hypodermic injection needle). The article of manufacture may comprise (a) a first container with a composition contained therein, wherein the composition comprises an antibody comprising an ultralong CDR3 as disclosed herein; and (b) a second container with a composition contained therein, wherein the composition comprises a further therapeutic agent. The article of manufacture in this embodiment disclosed herein may further comprise a package insert indicating that the first and second compositions can be used to treat a particular condition.
Alternatively, or additionally, the article of manufacture may further comprise a second (or third) container comprising a pharmaceutically-acceptable buffer, such as bacteriostatic water for injection (BWFI), phosphate-buffered saline, Ringer's solution and dextrose solution. It may further include other materials desirable from a commercial and user standpoint, including other buffers, diluents, filters, needles, and syringes. Preferably, the compound or composition is packaged in a unit dosage form. The kit may further include a device suitable for administering the composition according to a specific route of administration or for practicing a screening assay. Preferably, the kit contains a label that describes use of the antibody comprising an ultralong CDR3 composition.
[00645] In certain embodiments, the composition comprising the antibody is formulated in accordance with routine procedures as a pharmaceutical composition adapted for intravenous administration to mammals, such as humans, bovines, felines, canines, and murines. Typically, compositions for intravenous administration are solutions in sterile isotonic aqueous buffer. Where necessary, the composition may also include a solubilizing agent and a local anesthetic such as lignocaine to ease pain at the site of the injection. Generally, the ingredients are supplied either separately or mixed together in unit dosage form, for example, as a dry lyophilized powder or water free concentrate in a hermetically sealed container such as an ampoule or sachette indicating the quantity of active agent. Where the composition is to be administered by infusion, it can be dispensed with an infusion bottle containing sterile pharmaceutical grade water or saline. Where the composition is administered by injection, an ampoule of sterile water for injection or saline can be provided so that the ingredients may be mixed prior to administration.
[00646] The amount of the composition described herein which will be effective in the treatment, inhibition and prevention of a disease or disorder associated with aberrant expression and/or activity of a Therapeutic protein can be determined by standard clinical techniques. In addition, in vitro assays may optionally be employed to help identify optimal dosage ranges. The precise dose to be employed in the formulation will also depend on the route of administration, and the seriousness of the disease or disorder, and should be decided according to the judgment of the practitioner and each patient's circumstances. Effective doses are extrapolated from dose-response curves derived from in vitro or animal model test systems.
[00647] The following are examples of the methods and compositions of the disclosure. It is understood that various other embodiments may be practiced, given the general description provided above.
Methods of Treatment
[00648] Further disclosed herein are methods of preventing or treating a disease or condition in a subject in need thereof comprising administering a composition comprising one or more antibodies comprising an ultralong CDR3 as disclosed herein to said subject. The composition can further comprise a pharmaceutically acceptable carrier. The subject may be a mammal. The mammal may be a human. Alternatively, the mammal is a bovine. The antibody may comprise a therapeutic polypeptide, or derivative or variant thereof. The therapeutic polypeptide can be encoded by a non-antibody sequence. The therapeutic polypeptide, or derivative or variant thereof can be attached to the immunoglobulin domain. The therapeutic polypeptide, or derivative or variant thereof may be within the ultralong CDR3. Alternatively, the therapeutic polypeptide, or derivative or variant thereof is conjugated to the ultralong CDR3. In some instances, the therapeutic polypeptide is Mokal, Vm24, human GLP-1, Exendin-4, human EPO, human FGF21, human GMCSF, human interferon-beta, or derivative or variant thereof. The antibody may be an immuno conjugate as described herein. The antibody can comprise one or more immunoglobulin domains. The immunoglobulin domain may be an immunoglobulin A, an immunoglobulin D, an immunoglobulin E, an immunoglobulin G, or an immunoglobulin M. The immunoglobulin domain can be an immunoglobulin heavy chain region or fragment thereof. In some instances, the immunoglobulin domain is from a mammalian antibody. Alternatively, the immunoglobulin domain is from a chimeric antibody. The immunoglobulin domain may be from an engineered antibody or recombinant antibody. The immunoglobulin domain may be from a humanized, human engineered or fully human antibody. The mammalian antibody can be a bovine antibody. The mammalin antibody may be a human antibody. In other instances, the mammalian antibody is a murine antibody. The ultralong CDR3 may be 35 amino acids in length or more. The ultralong CDR3 may comprise at least 3 cysteine residues or more. The ultralong CDR3 may comprise one or more cysteine motifs. The one or more cysteine motifs may be based on or derived from SEQ ID NOS: 45-156. The one or more cysteine motifs may be based on or derived from SEQ ID NOS: 45- 99. The one or more cysteine motifs may be based on or derived from SEQ ID NOS: 100-135. The one or more cysteine motifs may be based on or derived from SEQ ID NOS: 136-156. The ultralong CDR3 can comprise at least a portion of a knob domain. The knob domain may comprise a conserved motif within the knob domain of an ultralong CDR3. For example, the knob domain may comprise a cysteine motif disclosed herein. The therapeutic polypeptide can be attached to the knob domain. Alternatively, or additionally, the ultralong CDR3 comprises at least a portion of a stalk domain. The stalk domain may comprise a conserved motif within the stalk domain of an ultralong CDR3. The conserved motif within the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 157-307 and SEQ ID NOS: 333- 336. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 157-224. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 157-161. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 223-234. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 235-239. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 296-299. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 300-303. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from a first sequence selected from the derived from SEQ ID NOS: 300-303. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence basegroup comprising SEQ ID NOS: 157-234 and a second sequence selected from the group comprising SEQ ID NOS: 235-307 and SEQ ID NOS: 333-336. The antibodies disclosed herein may comprise 2 or more, 3 or more, 4 or more, 5 or more sequences based on or derived from SEQ ID NOS: 157-307 and SEQ ID NOS: 333-336. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 304-307 AND SEQ ID NOS: 333- 336. For example, the stalk domain may comprise a T(S/T)VHQ motif. The therapeutic polypeptide can be attached to the stalk domain. In some instances, the antibody, antibody fragment or immunoglobulin construct further comprises a linker. The linker can attach the therapeutic polypeptide to the immunoglobulin domain or fragment thereof. In other instances, the linker attaches the therapeutic polypeptide to the knob domain or stalk domain. In some instances, the disease or condition is an autoimmune disease, heteroimmune disease or condition, inflammatory disease, pathogenic infection, thromboembolic disorder, respiratory disease or condition, metabolic disease, central nervous system (CNS) disorder, bone disease or cancer. In other instances, the disease or condition is a blood disorder. In some instances, the disease or condition is obesity, diabetes, osteoporosis, anemia, or pain.
[00649] In some embodiments is a method of preventing or treating a disease or condition in a subject in need thereof comprising administering to the subject a composition comprising: an immunoglobulin construct comprising a heavy chain polypeptide comprising a sequence that is substantially similar to a sequence selected from SEQ ID NOS: 24-44; and a light chain
polypeptide comprising the sequence that is substantially similar to a sequence of SEQ ID NO: 23. The heavy chain polypeptide sequence may share 50%, 60%, 70%, 80%, 85%, 90%, 95%, 97%, 99%), or more amino acid sequence identity to a heavy chain sequence provided by any one of SEQ ID NOS: 24-44. The light chain polypeptide sequence may share 50%, 60%, 70%, 80%, 85%, 90%, 95%), 97%), 99%), or more amino acid sequence identity to a light chain sequence provided by SEQ ID NO: 23. In some instances, the disease or condition is an autoimmune disease, heteroimmune disease or condition, inflammatory disease, pathogenic infection, thromboembolic disorder, respiratory disease or condition, metabolic disease, central nervous system (CNS) disorder, bone disease or cancer. In other instances, the disease or condition is a blood disorder. In some instances, the disease or condition is obesity, diabetes, osteoporosis, anemia, or pain.
[00650] In an embodiment is provided a method of preventing or treating a disease or condition in a subject in need thereof comprising administering to the subject a composition comprising: an immunoglobulin construct comprising a heavy chain polypeptide comprising a polypeptide sequence encoded by a DNA sequence that is substantially similar to a sequence selected from SEQ ID NOS: 2-22; and a light chain polypeptide comprising a polypeptide sequence encoded by a DNA sequence that is substantially similar to a sequence of SEQ ID NO: 1. The heavy chain nucleotide sequence may share 50%, 60%, 70%, 80%, 85%, 90%, 95%, 97%, 99%, or more homology to a heavy chain sequence provided by any one of SEQ ID NOS: 2-22. The light chain nucleotide sequence may share 50%, 60%, 70%, 80%, 85%, 90%, 95%, 97%, 99%, or more homology to a light chain sequence provided by SEQ ID NO: 1. In some instances, the disease or condition is an autoimmune disease, heteroimmune disease or condition, inflammatory disease, pathogenic infection, thromboembolic disorder, respiratory disease or condition, metabolic disease, central nervous system (CNS) disorder, bone disease or cancer. In other instances, the disease or condition is a blood disorder. In some instances, the disease or condition is obesity, diabetes, osteoporosis, anemia, or pain.
[00651] Disclosed herein in some embodiments is a method of preventing or treating an autoimmune disease in a subject in need thereof comprising administering a composition comprising one or more antibodies comprising an ultralong CDR3 as disclosed herein to said subject. The composition can further comprise a pharmaceutically acceptable carrier. The subject may be a mammal. The mammal may be a human. Alternatively, the mammal is a bovine. The antibody may comprise a therapeutic polypeptide, or derivative or variant thereof. The therapeutic polypeptide can be encoded by a non-antibody sequence. The therapeutic polypeptide, or derivative or variant thereof can be attached to the immunoglobulin domain. The therapeutic polypeptide, or derivative or variant thereof may be within the ultralong CDR3. Alternatively, the therapeutic polypeptide, or derivative or variant thereof is conjugated to the ultralong CDR3. In some instances, the therapeutic polypeptide is Mokal, VM-24 or beta-interferon or derivative or variant thereof. The antibody may be an immuno conjugate as described herein. The antibody can comprise one or more immunoglobulin domains. The immunoglobulin domain may be an immunoglobulin A, an immunoglobulin D, an immunoglobulin E, an immunoglobulin G, or an immunoglobulin M. The immunoglobulin domain can be an immunoglobulin heavy chain region or fragment thereof. In some instances, the immunoglobulin domain is from a mammalian antibody. Alternatively, the immunoglobulin domain is from a chimeric antibody. The immunoglobulin domain may be from an engineered antibody or recombinant antibody. The immunoglobulin domain may be from a humanized, human engineered or fully human antibody. The mammalian antibody can be a bovine antibody. The mammalin antibody may be a human antibody. In other instances, the mammalian antibody is a murine antibody. The ultralong CDR3 may be 35 amino acids in length or more. The ultralong CDR3 may comprise at least 3 cysteine residues or more. The ultralong CDR3 may comprise one or more cysteine motifs. The one or more cysteine motifs may be based on or derived from SEQ ID NOS: 45-156. The one or more cysteine motifs may be based on or derived from SEQ ID NOS: 45-99. The one or more cysteine motifs may be based on or derived from SEQ ID NOS: 100-135. The one or more cysteine motifs may be based on or derived from SEQ ID NOS: 136-156. The ultralong CDR3 comprises at least a portion of a knob domain. The knob domain may comprise a conserved motif within the knob domain of an ultralong CDR3. For example, the knob domain may comprise a cysteine motif disclosed herein. The Mokal, VM-24, beta-interferon, or a derivative or variant thereof can be attached to the knob domain. Alternatively, or additionally, the ultralong CDR3 comprises at least a portion of a stalk domain. The stalk domain may comprise a conserved motif within the stalk domain of an ultralong CDR3. The conserved motif within the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 157-307 and SEQ ID NOS: 333-336. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 157-224. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 157-161. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 223-234. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 235-239. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 296-299. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 300-303. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from a first sequence selected from the derived from SEQ ID NOS: 300-303. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence basegroup comprising SEQ ID NOS: 157-234 and a second sequence selected from the group comprising SEQ ID NOS: 235-307 and SEQ ID NOS: 333-336. The antibodies disclosed herein may comprise 2 or more, 3 or more, 4 or more, 5 or more sequences based on or derived from SEQ ID NOS: 157-307 and SEQ ID NOS: 333-336. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 304-307 AND SEQ ID NOS: 333-336. For example, the stalk domain may comprise a T(S/T)VHQ motif. The Mokal, VM-24, beta-interferon, or a derivative or variant thereof can be attached to the stalk domain. In some instances, the antibody, antibody fragment or immunoglobulin construct further comprises a linker. The linker can attach Mokal, VM-24, beta-interferon, or a derivative or variant thereof to the immunoglobulin domain or fragment thereof. In other instances, the linker attaches Mokal, VM-24, beta-interferon, or a derivative or variant thereof to the knob domain or stalk domain. In some instances, the autoimmune disease is a T-cell mediated autoimmune disease. T-cell mediated autoimmune diseases include, but are not limited to, multiple sclerosis, type-1 diabetes, and psoriasis. In other instances, the autoimmune disease lupus, Sjogren's syndrome, scleroderma, rheumatoid arthritis, dermatomyositis, Hasmimoto's thyroiditis, Addison's disease, celiac disease, Crohn's disease, pernicious anemia, pemphigus vulgaris, vitiligo, autoimmune hemolytic anemia, idiopathic thrombocytopenic purpura, myasthenia gravis, Ord's thyroiditis, Graves' disease, Guillain-Barre syndrome, acute disseminated encephalomyelitis, opsoclonus-myoclonus syndrome, ankylosing spondylitisis, antiphospho lipid antibody syndrome, aplastic anemia, autoimmune hepatitis,
Goodpasture's syndrome, Reiter's syndrome, Takayasu's arteritis, temporal arteritis, Wegener's granulomatosis, alopecia universalis, Behcet's disease, chronic fatigue, dysautonomia,
endometriosis, interstitial cystitis, neuromyotonia, scleroderma, and vulvodynia. Lupus can include, but is not limited to, acute cutaneous lupus erythematosus, subacute cutaneous lupus
erythematosus, chronic cutaneous lupus erythematosus, discoid lupus erythematosus, childhood discoid lupus erythematosus, generalized discoid lupus erythematosus, localized discoid lupus erythematosus, chilblain lupus erythematosus (hutchinson), lupus erythematosus-lichen planus overlap syndrome, lupus erythematosus panniculitis (lupus erythematosus profundus), tumid lupus erythematosus, verrucous lupus erythematosus (hypertrophic lupus erythematosus), complement deficiency syndromes, drug-induced lupus erythematosus, neonatal lupus erythematosus, and systemic lupus erythematosus.
[00652] Further disclosed herein is a method of preventing or treating a disease or condition which would benefit from the modulation of a potassium voltage-gated channel in a subject in need thereof comprising administering a composition comprising one or more antibodies comprising an ultralong CDR3 as disclosed herein to said subject. The composition can further comprise a pharmaceutically acceptable carrier. In some instances, the potassium voltage-gated channel is a KCNA3 or Kv1.3 channel. The subject may be a mammal. The mammal may be a human.
Alternatively, the mammal is a bovine. The antibody may comprise a therapeutic polypeptide, or derivative or variant thereof. The therapeutic polypeptide can be encoded by a non-antibody sequence. The therapeutic polypeptide, or derivative or variant thereof can be attached to the immunoglobulin domain. The therapeutic polypeptide, or derivative or variant thereof may be within the ultralong CDR3. Alternatively, the therapeutic polypeptide, or derivative or variant thereof is conjugated to the ultralong CDR3. In some instances, the therapeutic polypeptide is Mokal, VM-24, or derivative or variant thereof. The antibody may be an immuno conjugate as described herein. The antibody can comprise one or more immunoglobulin domains. The immunoglobulin domain may be an immunoglobulin A, an immunoglobulin D, an immunoglobulin E, an immunoglobulin G, or an immunoglobulin M. The immunoglobulin domain can be an immunoglobulin heavy chain region or fragment thereof. In some instances, the immunoglobulin domain is from a mammalian antibody. Alternatively, the immunoglobulin domain is from a chimeric antibody. The immunoglobulin domain may be from an engineered antibody or recombinant antibody. The immunoglobulin domain may be from a humanized, human engineered or fully human antibody. The mammalian antibody can be a bovine antibody. The mammalin antibody may be a human antibody. In other instances, the mammalian antibody is a murine antibody. The ultralong CDR3 may be 35 amino acids in length or more. The ultralong CDR3 may comprise at least 3 cysteine residues or more. The ultralong CDR3 may comprise one or more cysteine motifs. The one or more cysteine motifs may be based on or derived from SEQ ID NOS: 45-156. The one or more cysteine motifs may be based on or derived from SEQ ID NOS: 45-99. The one or more cysteine motifs may be based on or derived from SEQ ID NOS: 100-135. The one or more cysteine motifs may be based on or derived from SEQ ID NOS: 136-156. The ultralong CDR3 comprises at least a portion of a knob domain. The knob domain may comprise a conserved motif within the knob domain of an ultralong CDR3. For example, the knob domain may comprise a cysteine motif disclosed herein. The Mokal, VM-24, or a derivative or variant thereof can be attached to the knob domain. Alternatively, or additionally, the ultralong CDR3 comprises at least a portion of a stalk domain. The stalk domain may comprise a conserved motif within the stalk domain of an ultralong CDR3. The conserved motif within the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 157-307 and SEQ ID NOS: 333-336. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 157-224. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 157-161. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 223-234. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 235-239. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 296-299. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 300-303. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from a first sequence selected from the derived from SEQ ID NOS: 300-303. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence basegroup comprising SEQ ID NOS: 157-234 and a second sequence selected from the group comprising SEQ ID NOS: 235-307 and SEQ ID NOS: 333-336. The antibodies disclosed herein may comprise 2 or more, 3 or more, 4 or more, 5 or more sequences based on or derived from SEQ ID NOS: 157-307 and SEQ ID NOS: 333-336. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 304-307 AND SEQ ID NOS: 333-336. For example, the stalk domain may comprise a T(S/T)VHQ motif. The Mokal, VM-24, or a derivative or variant thereof can be attached to the stalk domain. In some instances, the antibody, antibody fragment or immunoglobulin construct further comprises a linker. The linker can attach Mokal, VM-24, or a derivative or variant thereof to the immunoglobulin domain or fragment thereof. In other instances, the linker attaches Mokal, VM-24, beta-interferon, or a derivative or variant thereof to the knob domain or stalk domain. In some instances, the disease or condition is an autoimmune disease. The autoimmune disease can be a T-cell mediated autoimmune disease. In some instances, modulating a potassium voltage-gated channel comprises inhibiting or blocking a potassium voltage-gated channel. In some instances, the disease or condition is episodic ataxia, seizure, or neuromyotonia.
[00653] Provided herein is a method of preventing or treating a metabolic disease or condition in a subject in need thereof comprising administering a composition comprising one or more antibodies comprising an ultralong CDR3 as disclosed herein to said subject. The
composition can further comprise a pharmaceutically acceptable carrier. The subject may be a mammal. The mammal may be a human. Alternatively, the mammal is a bovine. The antibody may comprise a therapeutic polypeptide, or derivative or variant thereof. The therapeutic polypeptide can be encoded by a non-antibody sequence. The therapeutic polypeptide, or derivative or variant thereof can be attached to the immunoglobulin domain. The therapeutic polypeptide, or derivative or variant thereof may be within the ultralong CDR3. Alternatively, the therapeutic polypeptide, or derivative or variant thereof is conjugated to the ultralong CDR3. In some instances, the therapeutic polypeptide is GLP-1, Exendin-4, FGF21, or derivative or variant thereof. The GLP-1 may be a human GLP-1. In some instances, the FGF21 is a human FGF21. The antibody may be an immuno conjugate as described herein. The antibody can comprise one or more immunoglobulin domains. The immunoglobulin domain may be an immunoglobulin A, an immunoglobulin D, an immunoglobulin E, an immunoglobulin G, or an immunoglobulin M. The immunoglobulin domain can be an immunoglobulin heavy chain region or fragment thereof. In some instances, the immunoglobulin domain is from a mammalian antibody. Alternatively, the immunoglobulin domain is from a chimeric antibody. The immunoglobulin domain may be from an engineered antibody or recombinant antibody. The immunoglobulin domain may be from a humanized, human engineered or fully human antibody. The mammalian antibody can be a bovine antibody. The mammalin antibody may be a human antibody. In other instances, the mammalian antibody is a murine antibody. The ultralong CDR3 may be 35 amino acids in length or more. The ultralong CDR3 may comprise at least 3 cysteine residues or more. The ultralong CDR3 may comprise one or more cysteine motifs. The one or more cysteine motifs may be based on or derived from SEQ ID NOS: 45-156. The one or more cysteine motifs may be based on or derived from SEQ ID NOS: 45- 99. The one or more cysteine motifs may be based on or derived from SEQ ID NOS: 100-135. The one or more cysteine motifs may be based on or derived from SEQ ID NOS: 136-156. The ultralong CDR3 comprises at least a portion of a knob domain. The knob domain may comprise a conserved motif within the knob domain of an ultralong CDR3. For example, the knob domain may comprise a cysteine motif disclosed herein. The GLP-1, Exendin-4, FGF21, or a derivative or variant thereof can be attached to the knob domain. Alternatively, or additionally, the ultralong CDR3 comprises at least a portion of a stalk domain. The stalk domain may comprise a conserved motif within the stalk domain of an ultralong CDR3. The conserved motif within the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 157-307 and SEQ ID NOS: 333-336. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 157-224. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 157-161. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 223-234. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 235-239. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 296-299. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 300-303. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from a first sequence selected from the derived from SEQ ID NOS: 300-303. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence basegroup comprising SEQ ID NOS: 157-234 and a second sequence selected from the group comprising SEQ ID NOS: 235-307 and SEQ ID NOS: 333-336. The antibodies disclosed herein may comprise 2 or more, 3 or more, 4 or more, 5 or more sequences based on or derived from SEQ ID NOS: 157-307 and SEQ ID NOS: 333-336. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 304-307 AND SEQ ID NOS: 333-336. For example, the stalk domain may comprise a T(S/T)VHQ motif. The GLP-1, Exendin-4, FGF21, or a derivative or variant thereof can be attached to the stalk domain. In some instances, the antibody, antibody fragment or immunoglobulin construct further comprises a linker. The linker can attach GLP-1, Exendin-4, FGF21, or a derivative or variant thereof to the immunoglobulin domain or fragment thereof. In other instances, the linker attaches GLP-1, Exendin-4, FGF21, or a derivative or variant thereof to the knob domain or stalk domain. Metabolic diseases and/or conditions can include disorders of carbohydrate metabolism, amino acid metabolism, organic acid metabolism (organic acidurias), fatty acid oxidation and mitochondrial metabolism, porphyrin metabolism, purine or pyrimidine metabolism, steroid metabolism, mitochondrial function, peroxisomal function, urea cycle disorder, urea cycle defects or lysosomal storage disorders. In some instances, the metabolic disease or condition is diabetes. In other instances, the metabolic disese or condition is glycogen storage disease, phenylketonuria, maple syrup urine disease, glutaric acidemia type 1, Carbamoyl phosphate synthetase I deficiency, alcaptonuria, Medium-chain acyl-coenzyme A dehydrogenase deficiency (MCADD), acute intermittent porphyria, Lesch-Nyhan syndrome, lipoid congenital adrenal hyperplasia, congenital adrenal hyperplasia, Kearns-Sayre syndrome, Zellweger syndrome, Gaucher's disease, or Niemann Pick disease.
[00654] Provided herein is a method of preventing or treating a central nervous system
(CNS) disorder in a subject in need thereof comprising administering a composition comprising one or more antibodies comprising an ultralong CDR3 as disclosed herein to said subject. The composition can further comprise a pharmaceutically acceptable carrier. The subject may be a mammal. The mammal may be a human. Alternatively, the mammal is a bovine. The antibody may comprise a therapeutic polypeptide, or derivative or variant thereof. The therapeutic polypeptide can be encoded by a non-antibody sequence. The therapeutic polypeptide, or derivative or variant thereof can be attached to the immunoglobulin domain. The therapeutic polypeptide, or derivative or variant thereof may be within the ultralong CDR3. Alternatively, the therapeutic polypeptide, or derivative or variant thereof is conjugated to the ultralong CDR3. In some instances, the therapeutic polypeptide is GLP-1, Exendin-4, or derivative or variant thereof. The GLP-1 may be a human GLP-1. The antibody may be an immunoconjugate as described herein. The antibody can comprise one or more immunoglobulin domains. The immunoglobulin domain may be an immunoglobulin A, an immunoglobulin D, an immunoglobulin E, an immunoglobulin G, or an immunoglobulin M. The immunoglobulin domain can be an immunoglobulin heavy chain region or fragment thereof. In some instances, the immunoglobulin domain is from a mammalian antibody. Alternatively, the immunoglobulin domain is from a chimeric antibody. The immunoglobulin domain may be from an engineered antibody or recombinant antibody. The immunoglobulin domain may be from a humanized, human engineered or fully human antibody. The mammalian antibody can be a bovine antibody. The mammalin antibody may be a human antibody. In other instances, the mammalian antibody is a murine antibody. The ultralong CDR3 may be 35 amino acids in length or more. The ultralong CDR3 may comprise at least 3 cysteine residues or more. The ultralong CDR3 may comprise one or more cysteine motifs. The one or more cysteine motifs may be based on or derived from SEQ ID NOS: 45-156. The one or more cysteine motifs may be based on or derived from SEQ ID NOS: 45-99. The one or more cysteine motifs may be based on or derived from SEQ ID NOS: 100-135. The one or more cysteine motifs may be based on or derived from SEQ ID NOS: 136-156. The ultralong CDR3 comprises at least a portion of a knob domain. The knob domain may comprise a conserved motif within the knob domain of an ultralong CDR3. For example, the knob domain may comprise a cysteine motif disclosed herein. The GLP-1, Exendin-4, or a derivative or variant thereof can be attached to the knob domain. Alternatively, or additionally, the ultralong CDR3 comprises at least a portion of a stalk domain. The stalk domain may comprise a conserved motif within the stalk domain of an ultralong CDR3. The conserved motif within the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 157-307 and SEQ ID NOS: 333-336. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 157-224. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 157-161. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 223-234. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 235-239. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 296-299. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 300-303. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from a first sequence selected from the derived from SEQ ID NOS: 300-303. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence basegroup comprising SEQ ID NOS: 157-234 and a second sequence selected from the group comprising SEQ ID NOS: 235-307 and SEQ ID NOS: 333-336. The antibodies disclosed herein may comprise 2 or more, 3 or more, 4 or more, 5 or more sequences based on or derived from SEQ ID NOS: 157-307 and SEQ ID NOS: 333-336. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 304-307 AND SEQ ID NOS: 333-336. For example, the stalk domain may comprise a T(S/T)VHQ motif. The GLP-1, Exendin-4, or a derivative or variant thereof can be attached to the stalk domain. In some instances, the antibody, antibody fragment or immunoglobulin construct further comprises a linker. The linker can attach GLP-1, Exendin-4, or a derivative or variant thereof to the immunoglobulin domain or fragment thereof. In other instances, the linker attaches GLP-1, Exendin-4, or a derivative or variant thereof to the knob domain or stalk domain. In some instances, the CNS disorder is Alzheimer's disease (AD). Additional CNS disorders include, but are not limited to, encephalitis, meningitis, tropical spastic paraparesis, arachnoid cysts, Huntington's disease, locked-in syndrome, Parkinson's disease, Tourette's, and multiple sclerosis.
[00655] Provided herein is a method of preventing or treating a disease or condition which benefits from a GLP-1R and/or glucagon receptor (GCGR) agonist in a subject in need thereof comprising administering a composition comprising one or more antibodies comprising an ultralong CDR3 as disclosed herein to said subject. The composition can further comprise a pharmaceutically acceptable carrier. The subject may be a mammal. The mammal may be a human. Alternatively, the mammal is a bovine. The antibody may comprise a therapeutic polypeptide, or derivative or variant thereof. The therapeutic polypeptide can be encoded by a non-antibody sequence. The therapeutic polypeptide, or derivative or variant thereof can be attached to the immunoglobulin domain. The therapeutic polypeptide, or derivative or variant thereof may be within the ultralong CDR3. Alternatively, the therapeutic polypeptide, or derivative or variant thereof is conjugated to the ultralong CDR3. In some instances, the therapeutic polypeptide is GLP- 1, Exendin-4, or derivative or variant thereof. The GLP-1 may be a human GLP-1. The antibody may be an immuno conjugate as described herein. The antibody can comprise one or more immunoglobulin domains. The immunoglobulin domain may be an immunoglobulin A, an immunoglobulin D, an immunoglobulin E, an immunoglobulin G, or an immunoglobulin M. The immunoglobulin domain can be an immunoglobulin heavy chain region or fragment thereof. In some instances, the immunoglobulin domain is from a mammalian antibody. Alternatively, the immunoglobulin domain is from a chimeric antibody. The immunoglobulin domain may be from an engineered antibody or recombinant antibody. The immunoglobulin domain may be from a humanized, human engineered or fully human antibody. The mammalian antibody can be a bovine antibody. The mammalin antibody may be a human antibody. In other instances, the mammalian antibody is a murine antibody. The ultralong CDR3 may be 35 amino acids in length or more. The ultralong CDR3 may comprise at least 3 cysteine residues or more. The ultralong CDR3 may comprise one or more cysteine motifs. The one or more cysteine motifs may be based on or derived from SEQ ID NOS: 45-156. The one or more cysteine motifs may be based on or derived from SEQ ID NOS: 45-99. The one or more cysteine motifs may be based on or derived from SEQ ID NOS: 100-135. The one or more cysteine motifs may be based on or derived from SEQ ID NOS: 136-156. The ultralong CDR3 comprises at least a portion of a knob domain. The knob domain may comprise a conserved motif within the knob domain of an ultralong CDR3. For example, the knob domain may comprise a cysteine motif disclosed herein. The GLP-1, Exendin-4, or a derivative or variant thereof can be attached to the knob domain. Alternatively, or additionally, the ultralong CDR3 comprises at least a portion of a stalk domain. The stalk domain may comprise a conserved motif within the stalk domain of an ultralong CDR3. The conserved motif within the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 157-307 and SEQ ID NOS: 333-336. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 157-224. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 157-161. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 223-234. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 235-239. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 296-299. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 300-303. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from a first sequence selected from the derived from SEQ ID NOS: 300-303. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence basegroup comprising SEQ ID NOS: 157-234 and a second sequence selected from the group comprising SEQ ID NOS: 235-307 and SEQ ID NOS: 333-336. The antibodies disclosed herein may comprise 2 or more, 3 or more, 4 or more, 5 or more sequences based on or derived from SEQ ID NOS: 157-307 and SEQ ID NOS: 333-336. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 304-307 AND SEQ ID NOS: 333-336. For example, the stalk domain may comprise a T(S/T)VHQ motif. The GLP-1, Exendin-4, or a derivative or variant thereof can be attached to the stalk domain. In some instances, the antibody, antibody fragment or immunoglobulin construct further comprises a linker. The linker can attach GLP-1, Exendin-4, or a derivative or variant thereof to the immunoglobulin domain or fragment thereof. In other instances, the linker attaches GLP-1, Exendin-4, or a derivative or variant thereof to the knob domain or stalk domain. The disease or condition can be a metabolic disease or disorder. In some instances, the disease or condition is diabetes. In other instances, the disease or condition is obesity. Additional diseases and/or conditions which benefit from a GLP-1R and/or GCGR agonist include, but are not limited to, dyslipidemia, cardiovascular and fatty liver diseases.
[00656] Provided herein is a method of preventing or treating a blood disorder in a subject in need thereof comprising administering a composition comprising one or more antibodies comprising an ultralong CDR3 as disclosed herein to said subject. The composition can further comprise a pharmaceutically acceptable carrier. The subject may be a mammal. The mammal may be a human. Alternatively, the mammal is a bovine. The antibody may comprise a therapeutic polypeptide, or derivative or variant thereof. The therapeutic polypeptide can be encoded by a non- antibody sequence. The therapeutic polypeptide, or derivative or variant thereof can be attached to the immunoglobulin domain. The therapeutic polypeptide, or derivative or variant thereof may be within the ultralong CDR3. Alternatively, the therapeutic polypeptide, or derivative or variant thereof is conjugated to the ultralong CDR3. In some instances, the therapeutic polypeptide is erythropoietin, GMCSF, or derivative or variant thereof. The erythropoietin may be a human erythropoietin. The GMCSF may be a human GMCSF. The antibody may be an immuno conjugate as described herein. The antibody can comprise one or more immunoglobulin domains. The immunoglobulin domain may be an immunoglobulin A, an immunoglobulin D, an immunoglobulin E, an immunoglobulin G, or an immunoglobulin M. The immunoglobulin domain can be an immunoglobulin heavy chain region or fragment thereof. In some instances, the immunoglobulin domain is from a mammalian antibody. Alternatively, the immunoglobulin domain is from a chimeric antibody. The immunoglobulin domain may be from an engineered antibody or recombinant antibody. The immunoglobulin domain may be from a humanized, human engineered or fully human antibody. The mammalian antibody can be a bovine antibody. The mammalin antibody may be a human antibody. In other instances, the mammalian antibody is a murine antibody. The ultralong CDR3 may be 35 amino acids in length or more. The ultralong CDR3 may comprise at least 3 cysteine residues or more. The ultralong CDR3 may comprise one or more cysteine motifs. The one or more cysteine motifs may be based on or derived from SEQ ID NOS: 45-156. The one or more cysteine motifs may be based on or derived from SEQ ID NOS: 45-99. The one or more cysteine motifs may be based on or derived from SEQ ID NOS: 100-135. The one or more cysteine motifs may be based on or derived from SEQ ID NOS: 136-156. The ultralong CDR3 comprises at least a portion of a knob domain. The knob domain may comprise a conserved motif within the knob domain of an ultralong CDR3. For example, the knob domain may comprise a cysteine motif disclosed herein. The erythropoietin, GMCSF, or a derivative or variant thereof can be attached to the knob domain. Alternatively, or additionally, the ultralong CDR3 comprises at least a portion of a stalk domain. The stalk domain may comprise a conserved motif within the stalk domain of an ultralong CDR3. The conserved motif within the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 157-307 and SEQ ID NOS: 333-336. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 157-224. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 157-161. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 223-234. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 235-239. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 296-299. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 300-303. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from a first sequence selected from the derived from SEQ ID NOS: 300-303. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence basegroup comprising SEQ ID NOS: 157-234 and a second sequence selected from the group comprising SEQ ID NOS: 235-307 and SEQ ID NOS: 333-336. The antibodies disclosed herein may comprise 2 or more, 3 or more, 4 or more, 5 or more sequences based on or derived from SEQ ID NOS: 157-307 and SEQ ID NOS: 333-336. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 304-307 AND SEQ ID NOS: 333-336. For example, the stalk domain may comprise a T(S/T)VHQ motif. The erythropoietin, GMCSF, or a derivative or variant thereof can be attached to the stalk domain. In some instances, the antibody, antibody fragment or immunoglobulin construct further comprises a linker. The linker can attach erythropoietin, GMCSF, or a derivative or variant thereof to the immunoglobulin domain or fragment thereof. In other instances, the linker attaches erythropoietin, GMCSF, or a derivative or variant thereof to the knob domain or stalk domain. In some instances, the blood disorder is anemia. Examples of anemia include, but are not limited to, herditary xerocytosis, congenital dyserythropoietic anemia, Rh null disease, infectious mononucleosis related anemia, drugs-related anemia, aplastic anemia, microcytic anemia, macrocytic anemia, normocytic anemia, hemolytic anemia, poikilocytic anemia, spherocytic anemia, drepanocytic anemia, normochromic anemia, hyperchromic anemia, hypochromic anemia, macrocytic-normochromic anemia, microcytic-hypochromic anemia, normocytic-normo chromic anemia, iron-deficiency anemia, pernicious anemia, fo late-deficiency anemia, thalassemia, sideroblastic anemia, posthemorrhagic anemia, sickle cell anemia, chronic anemia, achrestic anemia, autoimmune haemolytic anemia, Cooley's anemia, drug-induced immune haemolytic anemia, erythroblastic anemia, hypoplastic anemia, Diamond-Blackfan anemia, Pearson's anemia, transient anemia, Fanconi's anemia, Lederer's anemia, myelpathic anemia, nutritional anemia, spur- cell anemia, Von Jaksh's anemia, sideroblatic anemia, sideropenic anemia, alpha thalassemia, beta thalassemia, hemoglobin h disease, acute acquired hemolytic anemia, warm autoimmune hemolytic anemia, cold autoimmune hemolytic anemia, primary cold autoimmune hemolytic anemia, secondary cold autoimmune hemolytic anemia, secondary autoimmune hemolytic anemia, primary autoimmune hemolytic anemia, x-linked sideroblastic anemia, pyridoxine-responsive anemia, nutritional sideroblastic anemia, pyridoxine deficiency-induced sideroblastic anemia, copper deficiency- induced sideroblastic anemia, cycloserine-induced sideroblastic anemia,
chloramphenicol- induced sideroblastic anemia, ethanol- induced sideroblastic anemia, isoniazid- induced sideroblastic anemia, drug-induced sideroblastic anemia, toxin-induced sideroblastic anemia, microcytic hyperchromic anemia, macrocytic hyperchromic anemia, megalocytic- normochromic anemia, drug-induced immune hemolytic anemia, non-hereditary spherocytic anemia, inherited spherocytic anemia, and congenital spherocytic anemia. In other instances, the blood disorder is malaria. Alternatively, the blood disorder is lymphoma, leukemia, multiple myeloma, or myelodysplastic syndrome. In some instances, the blood disorder is neutropenia, Shwachmann-Daimond syndrome, Kostmann syndrome, chronic granulomatous disease, leukocyte adhesion deficiency, meyloperoxidase deficiency, or Chediak Higashi syndrome.
[00657] Provided herein is a method of preventing or treating a disease or disorder which benefitis from stimulating or increasing white blood cell production in a subject in need thereof comprising administering a composition comprising one or more antibodies comprising an ultralong CDR3 as disclosed herein to said subject. The composition can further comprise a pharmaceutically acceptable carrier. The subject may be a mammal. The mammal may be a human. Alternatively, the mammal is a bovine. The antibody may comprise a therapeutic polypeptide, or derivative or variant thereof. The therapeutic polypeptide can be encoded by a non-antibody sequence. The therapeutic polypeptide, or derivative or variant thereof can be attached to the immunoglobulin domain. The therapeutic polypeptide, or derivative or variant thereof may be within the ultralong CDR3. Alternatively, the therapeutic polypeptide, or derivative or variant thereof is conjugated to the ultralong CDR3. In some instances, the therapeutic polypeptide is GMCSF, or derivative or variant thereof. The GMCSF may be a human GMCSF. The antibody may be an immuno conjugate as described herein. The antibody can comprise one or more immunoglobulin domains. The immunoglobulin domain may be an immunoglobulin A, an immunoglobulin D, an immunoglobulin E, an immunoglobulin G, or an immunoglobulin M. The immunoglobulin domain can be an immunoglobulin heavy chain region or fragment thereof. In some instances, the immunoglobulin domain is from a mammalian antibody. Alternatively, the immunoglobulin domain is from a chimeric antibody. The immunoglobulin domain may be from an engineered antibody or recombinant antibody. The immunoglobulin domain may be from a humanized, human engineered or fully human antibody. The mammalian antibody can be a bovine antibody. The mammalin antibody may be a human antibody. In other instances, the mammalian antibody is a murine antibody. The ultralong CDR3 may be 35 amino acids in length or more. The ultralong CDR3 may comprise at least 3 cysteine residues or more. The ultralong CDR3 may comprise one or more cysteine motifs. The one or more cysteine motifs may be based on or derived from SEQ ID NOS: 45-156. The one or more cysteine motifs may be based on or derived from SEQ ID NOS: 45-99. The one or more cysteine motifs may be based on or derived from SEQ ID NOS: 100-135. The one or more cysteine motifs may be based on or derived from SEQ ID NOS: 136-156. The ultralong CDR3 comprises at least a portion of a knob domain. The knob domain may comprise a conserved motif within the knob domain of an ultralong CDR3. For example, the knob domain may comprise a cysteine motif disclosed herein. The GMCSF, or a derivative or variant thereof can be attached to the knob domain. Alternatively, or additionally, the ultralong CDR3 comprises at least a portion of a stalk domain. The stalk domain may comprise a conserved motif within the stalk domain of an ultralong CDR3. The conserved motif within the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 157-307 and SEQ ID NOS: 333-336. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 157-224. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 157-161. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 223-234. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 235-239. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 296-299. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 300-303. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from a first sequence selected from the derived from SEQ ID NOS: 300-303. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence basegroup comprising SEQ ID NOS: 157-234 and a second sequence selected from the group comprising SEQ ID NOS: 235-307 and SEQ ID NOS: 333-336. The antibodies disclosed herein may comprise 2 or more, 3 or more, 4 or more, 5 or more sequences based on or derived from SEQ ID NOS: 157-307 and SEQ ID NOS: 333-336. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 304-307 AND SEQ ID NOS: 333-336. For example, the stalk domain may comprise a T(S/T)VHQ motif. The GMCSF, or a derivative or variant thereof can be attached to the stalk domain. In some instances, the antibody, antibody fragment or immunoglobulin construct further comprises a linker. The linker can attach GMCSF, or a derivative or variant thereof to the immunoglobulin domain or fragment thereof. In other instances, the linker attaches GMCSF, or a derivative or variant thereof to the knob domain or stalk domain. In some instances, the disese or disorder is neutropenia, Shwachmann-Daimond syndrome, Kostmann syndrome, chronic granulomatous disease, leukocyte adhesion deficiency,
meyloperoxidase deficiency, or Chediak Higashi syndrome.
[00658] Provided herein is a method of preventing or treating a disease or disorder which benefitis from stimulating or increasing red blood cell production in a subject in need thereof comprising administering a composition comprising one or more antibodies comprising an ultralong CDR3 as disclosed herein to said subject. The composition can further comprise a pharmaceutically acceptable carrier. The subject may be a mammal. The mammal may be a human. Alternatively, the mammal is a bovine. The antibody may comprise a therapeutic polypeptide, or derivative or variant thereof. The therapeutic polypeptide can be encoded by a non-antibody sequence. The therapeutic polypeptide, or derivative or variant thereof can be attached to the immunoglobulin domain. The therapeutic polypeptide, or derivative or variant thereof may be within the ultralong CDR3. Alternatively, the therapeutic polypeptide, or derivative or variant thereof is conjugated to the ultralong CDR3. In some instances, the therapeutic polypeptide is erythropoietin, or derivative or variant thereof. The erythropoietin may be a human erythropoietin. The antibody may be an immunoconjugate as described herein. The antibody can comprise one or more immunoglobulin domains. The immunoglobulin domain may be an immunoglobulin A, an immunoglobulin D, an immunoglobulin E, an immunoglobulin G, or an immunoglobulin M. The immunoglobulin domain can be an immunoglobulin heavy chain region or fragment thereof. In some instances, the immunoglobulin domain is from a mammalian antibody. Alternatively, the immunoglobulin domain is from a chimeric antibody. The immunoglobulin domain may be from an engineered antibody or recombinant antibody. The immunoglobulin domain may be from a humanized, human engineered or fully human antibody. The mammalian antibody can be a bovine antibody. The mammalin antibody may be a human antibody. In other instances, the mammalian antibody is a murine antibody. The ultralong CDR3 may be 35 amino acids in length or more. The ultralong CDR3 may comprise at least 3 cysteine residues or more. The ultralong CDR3 may comprise one or more cysteine motifs. The one or more cysteine motifs may be based on or derived from SEQ ID NOS: 45-156. The one or more cysteine motifs may be based on or derived from SEQ ID NOS: 45-99. The one or more cysteine motifs may be based on or derived from SEQ ID NOS: 100-135. The one or more cysteine motifs may be based on or derived from SEQ ID NOS: 136-156. The ultralong CDR3 comprises at least a portion of a knob domain. The knob domain may comprise a conserved motif within the knob domain of an ultralong CDR3. For example, the knob domain may comprise a cysteine motif disclosed herein. The erythropoietin, or a derivative or variant thereof can be attached to the knob domain. Alternatively, or additionally, the ultralong CDR3 comprises at least a portion of a stalk domain. The stalk domain may comprise a conserved motif within the stalk domain of an ultralong CDR3. The conserved motif within the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 157-307 and SEQ ID NOS: 333-336. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 157-224. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 157-161. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 223-234. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 235-239. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 296-299. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 300-303. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from a first sequence selected from the derived from SEQ ID NOS: 300-303. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence basegroup comprising SEQ ID NOS: 157-234 and a second sequence selected from the group comprising SEQ ID NOS: 235-307 and SEQ ID NOS: 333-336. The antibodies disclosed herein may comprise 2 or more, 3 or more, 4 or more, 5 or more sequences based on or derived from SEQ ID NOS: 157-307 and SEQ ID NOS: 333-336. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 304-307 AND SEQ ID NOS: 333-336. For example, the stalk domain may comprise a T(S/T)VHQ motif. The erythropoietin, or a derivative or variant thereof can be attached to the stalk domain. In some instances, the antibody, antibody fragment or immunoglobulin construct further comprises a linker. The linker can attach erythropoietin, or a derivative or variant thereof to the immunoglobulin domain or fragment thereof. In other instances, the linker attaches erythropoietin, or a derivative or variant thereof to the knob domain or stalk domain. In some instances, the disease or disorder is anemia.
[00659] Provided herein is a method of preventing or treating obesity in a subject in need thereof comprising administering a composition comprising one or more antibodies comprising an ultralong CDR3 as disclosed herein to said subject. The composition can further comprise a pharmaceutically acceptable carrier. The subject may be a mammal. The mammal may be a human. Alternatively, the mammal is a bovine. The antibody may comprise a therapeutic polypeptide, or derivative or variant thereof. The therapeutic polypeptide can be encoded by a non-antibody sequence. The therapeutic polypeptide, or derivative or variant thereof can be attached to the immunoglobulin domain. The therapeutic polypeptide, or derivative or variant thereof may be within the ultralong CDR3. Alternatively, the therapeutic polypeptide, or derivative or variant thereof is conjugated to the ultralong CDR3. In some instances, the therapeutic polypeptide is GLP- 1, Exendin-4, FGF21, or derivative or variant thereof. The GLP-1 may be a human GLP-1. In some instances, the FGF21 is a human FGF21. The antibody may be an immuno conjugate as described herein. The antibody can comprise one or more immunoglobulin domains. The immunoglobulin domain may be an immunoglobulin A, an immunoglobulin D, an immunoglobulin E, an
immunoglobulin G, or an immunoglobulin M. The immunoglobulin domain can be an
immunoglobulin heavy chain region or fragment thereof. In some instances, the immunoglobulin domain is from a mammalian antibody. Alternatively, the immunoglobulin domain is from a chimeric antibody. The immunoglobulin domain may be from an engineered antibody or recombinant antibody. The immunoglobulin domain may be from a humanized, human engineered or fully human antibody. The mammalian antibody can be a bovine antibody. The mammalin antibody may be a human antibody. In other instances, the mammalian antibody is a murine antibody. The ultralong CDR3 may be 35 amino acids in length or more. The ultralong CDR3 may comprise at least 3 cysteine residues or more. The ultralong CDR3 may comprise one or more cysteine motifs. The one or more cysteine motifs may be based on or derived from SEQ ID NOS: 45-156. The one or more cysteine motifs may be based on or derived from SEQ ID NOS: 45-99. The one or more cysteine motifs may be based on or derived from SEQ ID NOS: 100-135. The one or more cysteine motifs may be based on or derived from SEQ ID NOS: 136-156. The ultralong CDR3 comprises at least a portion of a knob domain. The knob domain may comprise a conserved motif within the knob domain of an ultralong CDR3. For example, the knob domain may comprise a cysteine motif disclosed herein. The GLP-1, Exendin-4, FGF21, or a derivative or variant thereof can be attached to the knob domain. Alternatively, or additionally, the ultralong CDR3 comprises at least a portion of a stalk domain. The stalk domain may comprise a conserved motif within the stalk domain of an ultralong CDR3. The conserved motif within the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 157-307 and SEQ ID NOS: 333-336. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 157-224. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 157-161. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 223-234. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 235-239. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 296-299. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 300-303. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from a first sequence selected from the derived from SEQ ID NOS: 300-303. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence basegroup comprising SEQ ID NOS: 157-234 and a second sequence selected from the group comprising SEQ ID NOS: 235-307 and SEQ ID NOS: 333-336. The antibodies disclosed herein may comprise 2 or more, 3 or more, 4 or more, 5 or more sequences based on or derived from SEQ ID NOS: 157-307 and SEQ ID NOS: 333-336. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 304-307 AND SEQ ID NOS: 333-336. For example, the stalk domain may comprise a T(S/T)VHQ motif. The GLP-1, Exendin-4, FGF21, or a derivative or variant thereof can be attached to the stalk domain. In some instances, the antibody, antibody fragment or
immunoglobulin construct further comprises a linker. The linker can attach GLP-1, Exendin-4, FGF21, or a derivative or variant thereof to the immunoglobulin domain or fragment thereof. In other instances, the linker attaches GLP-1, Exendin-4, FGF21, or a derivative or variant thereof to the knob domain or stalk domain.
[00660] Provided herein is a method of preventing or treating a pain in a subject in need thereof comprising administering a composition comprising one or more antibodies, antibody fragments, or immunoglobulin constructs described herein to said subject. In some instances, the subject is a mammal. In certain instances, the mammal is a human. Alternatively, the mammal is a bovine. In some instances, the one or more antibodies, antibody fragments, or immunoglobulin constructs comprise a protoxin2 or a derivative or variant thereof. Alternatively, or additionally, the one or more antibodies, antibody fragments, or immunoglobulin constructs comprise at least a portion of a CDR3H. The portion of the CDR3H can be a stalk domain or knob domain in the CDR3H. In some instances, the one or more antibodies, antibody fragments, or immunoglobulin constructs further comprise a linker. The linker can attach the protoxin2 or a derivative or variant thereof to the portion of the CDR3H.
[00661] Provided herein is a method of preventing or treating a disease or condition which benefits from modulating a sodium ion channel in a subject in need thereof comprising
administering a composition comprising one or more antibodies, antibody fragments, or
immunoglobulin constructs described herein to said subject. In some instances, the subject is a mammal. In certain instances, the mammal is a human. Alternatively, the mammal is a bovine. In some instances, the one or more antibodies, antibody fragments, or immunoglobulin constructs comprise a protoxin2 or a derivative or variant thereof. Alternatively, or additionally, the one or more antibodies, antibody fragments, or immunoglobulin constructs comprise at least a portion of a CDR3H. The portion of the CDR3H can be a stalk domain or knob domain in the CDR3H. In some instances, the one or more antibodies, antibody fragments, or immunoglobulin constructs further comprise a linker. The linker can attach the protoxin2 or a derivative or variant thereof to the portion of the CDR3H. In some instances, the sodium ion channel is a Nav channel. In some instances, the Nav channel is a Nav1.7 channel. In some instances, modulating a sodium ion channel comprises inhibiting or blocking a sodium ion channel. In some instances, the disease or condition is Dravet Syndrome, generalized epilepsy with febrile seizures plus (GEFS+), paramyotonia congenital or erythromelalgia. In some instances, the disease or condition is pain.
[00662] Provided herein is a method of preventing or treating a disease or condition which benefits from modulating an acid sensing ion channel (ASIC) in a subject in need thereof comprising administering a composition comprising one or more antibodies, antibody fragments, or immunoglobulin constructs described herein to said subject. In some instances, the subject is a mammal. In certain instances, the mammal is a human. Alternatively, the mammal is a bovine. In some instances, the one or more antibodies, antibody fragments, or immunoglobulin constructs comprise a protoxin2 or a derivative or variant thereof. Alternatively, or additionally, the one or more antibodies, antibody fragments, or immunoglobulin constructs comprise at least a portion of a CDR3H. The portion of the CDR3H can be a stalk domain or knob domain in the CDR3H. In some instances, the one or more antibodies, antibody fragments, or immunoglobulin constructs further comprise a linker. The linker can attach the protoxin2 or a derivative or variant thereof to the portion of the CDR3H. In some instances, modulating an ASIC comprises inhibiting or blocking the ASIC. In some instances, the disease or condition is a central nervous system disorder. In other instances, the disease or condition is pain.
[00663] Provided herein is a method of preventing or treating a pathogenic infection in a subject in need thereof comprising administering a composition comprising one or more antibodies comprising an ultralong CDR3 as disclosed herein to said subject. The composition can further comprise a pharmaceutically acceptable carrier. The subject may be a mammal. The mammal may be a human. Alternatively, the mammal is a bovine. The antibody may comprise a therapeutic polypeptide, or derivative or variant thereof. The therapeutic polypeptide can be encoded by a non- antibody sequence. The therapeutic polypeptide, or derivative or variant thereof can be attached to the immunoglobulin domain. The therapeutic polypeptide, or derivative or variant thereof may be within the ultralong CDR3. Alternatively, the therapeutic polypeptide, or derivative or variant thereof is conjugated to the ultralong CDR3. In some instances, the therapeutic polypeptide is beta- inter feron, or derivative or variant thereof. The antibody may be an immuno conjugate as described herein. The antibody can comprise one or more immunoglobulin domains. The immunoglobulin domain may be an immunoglobulin A, an immunoglobulin D, an immunoglobulin E, an immunoglobulin G, or an immunoglobulin M. The immunoglobulin domain can be an
immunoglobulin heavy chain region or fragment thereof. In some instances, the immunoglobulin domain is from a mammalian antibody. Alternatively, the immunoglobulin domain is from a chimeric antibody. The immunoglobulin domain may be from an engineered antibody or recombinant antibody. The immunoglobulin domain may be from a humanized, human engineered or fully human antibody. The mammalian antibody can be a bovine antibody. The mammalin antibody may be a human antibody. In other instances, the mammalian antibody is a murine antibody. The ultralong CDR3 may be 35 amino acids in length or more. The ultralong CDR3 may comprise at least 3 cysteine residues or more. The ultralong CDR3 may comprise one or more cysteine motifs. The one or more cysteine motifs may be based on or derived from SEQ ID NOS: 45-156. The one or more cysteine motifs may be based on or derived from SEQ ID NOS: 45-99. The one or more cysteine motifs may be based on or derived from SEQ ID NOS: 100-135. The one or more cysteine motifs may be based on or derived from SEQ ID NOS: 136-156. The ultralong CDR3 comprises at least a portion of a knob domain. The knob domain may comprise a conserved motif within the knob domain of an ultralong CDR3. For example, the knob domain may comprise a cysteine motif disclosed herein. The beta-interferon, or a derivative or variant thereof can be attached to the knob domain. Alternatively, or additionally, the ultralong CDR3 comprises at least a portion of a stalk domain. The stalk domain may comprise a conserved motif within the stalk domain of an ultralong CDR3. The conserved motif within the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 157-307 and SEQ ID NOS: 333-336. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 157-224. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 157-161. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 223-234. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 235-239. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 296-299. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 300-303. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from a first sequence selected from the derived from SEQ ID NOS: 300-303. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence basegroup comprising SEQ ID NOS: 157-234 and a second sequence selected from the group comprising SEQ ID NOS: 235-307 and SEQ ID NOS: 333-336. The antibodies disclosed herein may comprise 2 or more, 3 or more, 4 or more, 5 or more sequences based on or derived from SEQ ID NOS: 157-307 and SEQ ID NOS: 333-336. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 304-307 AND SEQ ID NOS: 333-336. For example, the stalk domain may comprise a T(S/T)VHQ motif. The beta-interferon, or a derivative or variant thereof can be attached to the stalk domain. In some instances, the antibody, antibody fragment or immunoglobulin construct further comprises a linker. The linker can attach beta-interferon, or a derivative or variant thereof to the immunoglobulin domain or fragment thereof. In other instances, the linker attaches beta- interferon, or a derivative or variant thereof to the knob domain or stalk domain. In some instances, the pathogenic infection is a viral, bacterial, fungal, or parasitic infection. In some instances, the viral infection is a herpes virus.
[00664] Provided herein is a method of preventing or treating a cancer in a subject in need thereof comprising administering a composition comprising one or more antibodies comprising an ultralong CDR3 as disclosed herein to said subject. The composition can further comprise a pharmaceutically acceptable carrier. The subject may be a mammal. The mammal may be a human. Alternatively, the mammal is a bovine. The antibody may comprise a therapeutic polypeptide, or derivative or variant thereof. The therapeutic polypeptide can be encoded by a non-antibody sequence. The therapeutic polypeptide, or derivative or variant thereof can be attached to the immunoglobulin domain. The therapeutic polypeptide, or derivative or variant thereof may be within the ultralong CDR3. Alternatively, the therapeutic polypeptide, or derivative or variant thereof is conjugated to the ultralong CDR3. In some instances, the therapeutic polypeptide is beta- inter feron, or derivative or variant thereof. The antibody may be an immuno conjugate as described herein. The antibody can comprise one or more immunoglobulin domains. The immunoglobulin domain may be an immunoglobulin A, an immunoglobulin D, an immunoglobulin E, an immunoglobulin G, or an immunoglobulin M. The immunoglobulin domain can be an
immunoglobulin heavy chain region or fragment thereof. In some instances, the immunoglobulin domain is from a mammalian antibody. Alternatively, the immunoglobulin domain is from a chimeric antibody. The immunoglobulin domain may be from an engineered antibody or recombinant antibody. The immunoglobulin domain may be from a humanized, human engineered or fully human antibody. The mammalian antibody can be a bovine antibody. The mammalin antibody may be a human antibody. In other instances, the mammalian antibody is a murine antibody. The ultralong CDR3 may be 35 amino acids in length or more. The ultralong CDR3 may comprise at least 3 cysteine residues or more. The ultralong CDR3 may comprise one or more cysteine motifs. The one or more cysteine motifs may be based on or derived from SEQ ID NOS: 45-156. The one or more cysteine motifs may be based on or derived from SEQ ID NOS: 45-99. The one or more cysteine motifs may be based on or derived from SEQ ID NOS: 100-135. The one or more cysteine motifs may be based on or derived from SEQ ID NOS: 136-156. The ultralong CDR3 comprises at least a portion of a knob domain. The knob domain may comprise a conserved motif within the knob domain of an ultralong CDR3. For example, the knob domain may comprise a cysteine motif disclosed herein. The beta-interferon, or a derivative or variant thereof can be attached to the knob domain. Alternatively, or additionally, the ultralong CDR3 comprises at least a portion of a stalk domain. The stalk domain may comprise a conserved motif within the stalk domain of an ultralong CDR3. The conserved motif within the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 157-307 and SEQ ID NOS: 333-336. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 157-224. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 157-161. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 223-234. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 235-239. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 296-299. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 300-303. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from a first sequence selected from the derived from SEQ ID NOS: 300-303. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence basegroup comprising SEQ ID NOS: 157-234 and a second sequence selected from the group comprising SEQ ID NOS: 235-307 and SEQ ID NOS: 333-336. The antibodies disclosed herein may comprise 2 or more, 3 or more, 4 or more, 5 or more sequences based on or derived from SEQ ID NOS: 157-307 and SEQ ID NOS: 333-336. The conserved motif with the stalk domain of the ultralong CDR3 may comprise a polypeptide sequence based on or derived from SEQ ID NOS: 304-307 AND SEQ ID NOS: 333-336. For example, the stalk domain may comprise a T(S/T)VHQ motif. The beta-interferon, or a derivative or variant thereof can be attached to the stalk domain. In some instances, the antibody, antibody fragment or immunoglobulin construct further comprises a linker. The linker can attach beta-interferon, or a derivative or variant thereof to the immunoglobulin domain or fragment thereof. In other instances, the linker attaches beta- interferon, or a derivative or variant thereof to the knob domain or stalk domain. In some instances, the cancer is a hematological malignancy. The hematological malignancy can be a leukemia or lymphoma. In some instances, the hematological malignancy is a B-cell lymphoma, T-cell lymphoma, follicular lymphoma, marginal zone lymphoma, hairy cell leukemia, chronic myeloid leukemia, mantle cell lymphoma, nodular lymphoma, Burkitt's lymphoma, cutaneous T-cell lymphoma, chronic lymphocytic leukemia, or small lymphocytic leukemia.
[00665] Provided herein is a method of preventing or treating a disease in a mammal in need thereof comprising administering a pharmaceutical composition described herein to said mammal. In some embodiments, the disease is an infectious disease. In certain embodiments, the infectious disease is mastitis. In some embodiments, the infectious disease is a respiratory disease. In certain embodiments, the respiratory disease is bovine respiratory disease of shipping fever. In certain embodiments, the mammal in need is a dairy animal selected from a list comprising cow, camel, donkey, goat, horse, reindeer, sheep, water buffalo, moose and yak. In some embodiments, the mammal in need is bovine.
[00666] Provided is a method of preventing or treating mastitis in a dairy animal, comprising providing to said dairy animal an effective amount of a composition comprising: an
immunoglobulin construct comprising a heavy chain polypeptide comprising a sequence selected from SEQ ID NO: 25 and SEQ ID NO: 26; and a light chain polypeptide comprising the sequence of SEQ ID NO: 23. In an embodiment is provided a method of preventing or treating mastitis in a dairy animal, comprising providing to said dairy animal an effective amount of a composition comprising: an immunoglobulin construct comprising a heavy chain polypeptide comprising a polypeptide sequence encoded by the DNA selected from SEQ ID NO: 4 and SEQ ID NO: 5; and a light chain polypeptide comprising a polypeptide sequence encoded by the DNA of SEQ ID NO: 1. In some embodimetns, the dairy animal is a cow or a water buffalo. Provided are methods of treatment, inhibition and prevention by administration to a subject of an effective amount of an antibody or pharmaceutical composition described herein. The antibody may be substantially purified (e.g., substantially free from substances that limit its effect or produce undesired side- effects). The subject can be an animal, including but not limited to animals such as cows, pigs,sheep, goats, rabbits, horses, chickens, cats, dogs, mice, etc. The subject can be a mammal. In some instances, the subject is a human. Alternatively, the subject is a bovine.
[00667] Various delivery systems are known and can be used to administer an antibody formulation described herein, e.g., encapsulation in liposomes, microparticles, microcapsules, recombinant cells capable of expressing the compound, receptor-mediated endocytosis (see, e.g., Wu and Wu, J. Biol. Chem. 262:4429-4432 (1987)), construction of a nucleic acid as part of a retroviral or other vector, etc. Methods of introduction include but are not limited to intradermal, intramuscular, intraperitoneal, intravenous, subcutaneous, intranasal, epidural, and oral routes. The compounds or compositions may be administered by any convenient route, for example by infusion or bolus injection, by absorption through epithelial or mucocutaneous linings (e.g., oral mucosa, rectal and intestinal mucosa, etc.) and may be administered together with other biologically active agents. Administration can be systemic or local. In addition, in certain embodiments, it is desirable to introduce the heteromultimer compositions described herein into the central nervous system by any suitable route, including intraventricular and intrathecal injection; intraventricular injection may be facilitated by an intraventricular catheter, for example, attached to a reservoir, such as an Ommaya reservoir.
[00668] In a specific embodiment, it is desirable to administer the antibody, or compositions described herein locally to the area in need of treatment; this may be achieved by, for example, and not by way of limitation, local infusion, topical application, e.g., in conjunction with a wound dressing after surgery, by injection, by means of a catheter, by means of a suppository, or by means of an implant, said implant being of a porous, non-porous, or gelatinous material, including membranes, such as sialastic membranes, or fibers. Preferably, when administering a protein, including an antibody, of the invention, care must be taken to use materials to which the protein does not absorb. [00669] In another embodiment, the antibody or pharmaceutical composition is delivered in a vesicle, in particular a liposome (see Langer, Science 249: 1527-1533 (1990); Treat et al, in Liposomes in the Therapy of Infectious Disease and Cancer, Lopez-Berestein and Fidler (eds.), Liss, New York, pp. 353-365 (1989); Lopez-Berestein, ibid., pp. 317-327; see generally ibid.)
[00670] In yet another embodiment, the heteromultimers or composition can be delivered in a controlled release system. In one embodiment, a pump may be used (see Langer, supra; Sefton, CRC Crit. Ref. Biomed. Eng. 14:201 (1987); Buchwald et al, Surgery 88:507 (1980); Saudek et al, N. Engl. J. Med. 321 :574 (1989)). In another embodiment, polymeric materials can be used (see Medical Applications of Controlled Release, Langer and Wise (eds.), CRC Pres., Boca Raton, Fla. (1974); Controlled Drug Bioavailability, Drug Product Design and Performance, Smolen and Ball (eds.), Wiley, New York (1984); Ranger and Peppas, J., Macromol. Sci. Rev. Macromol. Chem. 23:61 (1983); see also Levy et al, Science 228: 190 (1985); During et al, Ann. Neurol. 25:351 (1989); Howard et al, J. Neurosurg. 71 : 105 (1989)). In yet another embodiment, a controlled release system can be placed in proximity of the therapeutic target, e.g., the brain, thus requiring only a fraction of the systemic dose (see, e.g., Goodson, in Medical Applications of Controlled Release, supra, vol. 2, pp. 115-138 (1984)). Other controlled release systems are discussed in the review by Langer (Science 249: 1527-1533 (1990)).
[00671] In a specific embodiment comprising a nucleic acid encoding a antibody decribed herein, the nucleic acid can be administered in vivo to promote expression of its encoded protein, by constructing it as part of an appropriate nucleic acid expression vector and administering it so that it becomes intracellular, e.g., by use of a retroviral vector (see U.S. Pat. No. 4,980,286), or by direct injection, or by use of microparticle bombardment (e.g., a gene gun; Biolistic, Dupont), or coating with lipids or cell-surface receptors or transfecting agents, or by administering it in linkage to a homeobox-like peptide which is known to enter the nucleus (see e.g., Joliot et al, Proc. Natl. Acad. Sci. USA 88: 1864-1868 (1991)), etc. Alternatively, a nucleic acid can be introduced intracellularly and incorporated within host cell DNA for expression, by homologous
recombination.
[00672] In some embodiments are crystals based on or derived from the antibodies disclosed herein. The crystals may have a space group P212121. In some instances, the crystal has the unit cell dimensions of "a" between about 40 to 80 angstroms, between 45 to about 75 angstroms, or between about 50 to about 75 angstroms; "b" between about 40 to 140 angstroms, between about 50 to about 130 angstroms, between about 55 to about 130 angstroms; and "c" between 100 to about 350 angstroms, between 120 to about 340 angstroms, or between about 125 to about 330 angstroms. Alternatively, the crystal has the unit cell dimensions of "a" greater than or equal to 40, 50, 60, 70, or 80 angstroms; "b" greater than or equal to 40, 50, 60, 70, 80, 90, 100, 110, 120, or 130 angstroms; and "c" greater than or equal to 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 220, 230, 240, 250, 260, 270, 280, 290, 300, 310, 320, 330, or 340 angstroms.
[00673] The crystal may comprise a bovine antibody or portion thereof. The crystal may comprise a Fab fragment based on or derived from a bovine antibody. The crystal may comprise a non-antibody sequence, linker, cleave site, non-bovine sequence, or a combination thereof. The crystal may be an isolated crystal. The antibody may be based on or derived from the peptide sequence of any of SEQ ID NOS: 1-44. The antibody may comprise at least a portion of a heavy chain. The portion of the heavy chain may comprise the peptide sequence of any of SEQ ID NOS: 24-44. The antibody may comprise at least a portion of a heavy chain. The portion of the heavy chain may be encoded by a DNA sequence based on or derived from the DNA sequence of any of SEQ ID NOS: 2-22. The antibody may comprise at least a portion of a light chain. The portion of the light chain may comprise the peptide sequence of SEQ ID NO: 23. The antibody may comprise at least a portion of a heavy chain. The portion of the heavy chain may be encoded by a DNA sequence based on or derived from the DNA sequence of SEQ ID NOS: 1.
[00674] In some embodiments, is an isolated crystal comprising a bovine antibody Fab fragment comprising SEQ ID NO: 24 and SEQ ID NO: 23, wherein the crystal has a space group P212121 and unit cell dimensions of a=71.4 angstroms, b=127.6 angstroms and c=127.9 angstroms.
[00675] In some embodiments, is an isolated crystal comprising a bovine antibody Fab fragment comprising SEQ ID NO: 340 and SEQ ID NO: 341, wherein the crystal has a space group P212121 and unit cell dimensions of a=54.6 angstroms, b=53.7 angstroms and c=330.5 angstroms.
Example 1. Purification and Crystallization of Antibodies comprising an Ultralong CDR3
[00676] An antibody that comprises an ultralong CDR3 including, for example, an antibody generated by any of the examples described herein, may be purified and subsequently crystallized to determine the structure of the antibody.
[00677] A. Purification:
[00678] Genes encoding the heavy and light chain Fab regions of BLV1H12 and BLV5B8 were generated by gene synthesis (GenScript, Piscataway, NJ). A DNA fragment derived from the promoter region of pFastBacDual (Invitrogen) was fused to the gp67 and the honey bee mellitin (HBM) signal peptides by overlap PCR, yielding a fragment with head-to-head plO and polyhedrin promoters upstream of the HBM and gp67 signal peptides, respectively (i.e., HBM-plO-pPolyH- gp67). Bovine Fab heavy and light chain regions were fused to the promoter-signal peptide cassette by overlap PCR (heavy chain downstream of pPolyH-gp67 and light chain downstream of plO- HBM), and ligated into the Sfil sites of pDCE361, a derivative of pFastBacDual. Next, a His6-tag was introduced at the C-terminus of the heavy chain to facilitate purification. The resulting baculo virus transfer vectors were used to generate recombinant bacmids using the Bac-to-Bac system (Invitrogen) and virus was rescued by transfecting purified bacmid DNA into Sf9 cells using Cellfectin II (Invitrogen). Both Fab proteins were produced by infecting suspension cultures of Sf9 cells with recombinant baculo virus at an MOI of 5-10 and incubating at 28°C with shaking at 110 RPM. After 72 hours, the cultures were clarified by two rounds of centrifugation at 2000g and 10,000g at 4 °C. The supernatant, containing secreted, soluble Fab were then concentrated and buffer exchanged into lx PBS, pH 7.4. After metal affinity chromatography using Ni-NTA resin, Fabs were purified by protein G affinity chromatography (GE Healthcare), cation exchange chromatography (MonoS, GE healthcare), and gel filtration (Superdex200, GE Healthcare).
[00679] B. Crystallization and Structure Determination
[00680] Gel filtration fractions containing the bovine Fabs were concentrated to ~10 mg/mL in 10 mM Tris, pH 8.0 and 50 mM NaCl. Initial crystallization trials were set up using the automated Rigaku Crystalmation robotic system at the Joint Center for Structural Genomics.
Several hits were obtained for BLV1H12 and BLV5B8, and crystals used for data collection were grown by the sitting drop vapor diffusion method with a reservoir solution (100 μί) containing 0.27 M potassium citrate and 22% PEG 3350 (BLV1H12) and 0.2 M di-sodium tartrate and 20% PEG 3350 (BLV5B8). Drops consisting of 100 nL protein + 100 nL precipitant were set up at 20°C, and crystals appeared within 3-7 days. The resulting crystals were cryoprotected using well solution supplemented with 15% ethylene glycol then flash cooled and stored in liquid nitrogen until data collection.
[00681] Diffraction data were then collected on the GM/CA-CAT 23ID-D beamline at the
Advanced Photon Source at Argonne National Laboratory (BLV1H12) and the 11-1 beamline at the Stanford Synchrotron Radiation Lightsource for BLV5B8. Both datasets were indexed in spacegroup P212121, integrated, scaled, and merged using HKL2000 (BLV5B8; HKL Research) or XPREP (BLV1H12; Bruker). The BLV1H12 structure was solved by molecular replacement to 1.88 A resolution using Phaser (McCoy et al, 2007). Fab variable domains from 1BVK and constant domains from 2FB4 were used as search models and two complete BLV1H12 Fabs were found in the asymmetric unit. The BLV5B8 dataset was also solved by molecular replacement (to 2.20 A), using the refined BLV1H12 coordinates as a model. Rigid body refinement, simulated annealing and restrained refinement (including TLS refinement, with one group for each Ig domain and one for each CDR H3) were carried out in Phenix (Adams et al. (2010) Acta Crystallogr D Biol Crystallogr 66:213-221). Riding hydrogens were used during refinement and are included in the final model.
[00682] Between rounds of refinement, the model was built and adjusted using Coot. Waters were built automatically using the "ordered solvent" modeling function in Phenix (Adams et al. (2010) Acta Crystallogr D Biol Crystallogr 66:213-221). Structures were validated using the JCSG QC Server (publicly available at http://smb.slac.stanford.edu/jcsg/QC/), which includes Molprobity (Chen et al. (2010) Acta Crystallogr D Biol Crystallogr 66:12-21) Table 1
Table 1. Data collection and refinement statistics
Figure imgf000184_0001
hki i ki,i, w ere ki s t e scae ntensty o t e ι measurement o reecton , , <hki> is the average intensity for that reflection, and n is the redundancy (Emsley et al.
(2010) Acta Crystallogr D Biol Crystallogr 66:486-501).
c Za is t ic asymmetric unit.
Figure imgf000185_0001
e Rfree was calculated as for i?cryst, but on a test set comprising 5% of the data
excluded from refinement.
Calculated using Molprobity (Chen et al. (2010) Acta Crystallogr D Biol
Crystallogr 66: 12-21).
g Coordinates and structure factors will be deposited in the PDB prior to publication
and be available immediately on publication.
Example 2. Generation of Libraries of Polynucleotides Encoding Antibodies Comprising an Ultralong CDR3
[00683] Bovine spleen and lymph nodes were obtained from Animal Technologies (Tyler,
TX), or from Texas A&M University. Total RNA was isolated from bovine tissues from three different cows (MIDI , MID 10, and MID 1 1) using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) followed by on column digestion of DNA using the RNeasy Mini Kit (Qiagen, Valencia, CA, USA). Next, RNA quantity and quality were assessed with Nanodrop (Thermal Scientific), Qubit RNA and Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA), following the manufacturer's protocols. Total RNA was used as a template for cDNA synthesis catalyzed by Superscript II (Invitrogen).
[00684] The library of amplified antibody variable regions were then subjected to deep sequencing. Briefly, bar-coded primers (Table 2) for each of the three cows (MIDI , MID 10, and MIDI 1) were used to amplify VH from bovine spleen cDNA.
Table 2. Bar-coded primers for deep sequencing
Figure imgf000185_0002
Figure imgf000186_0001
[00685] Next, the amplicons of VH were purified from 2% agarose gels and deep sequenced according to Roche 454 GS FLX instructions. Multiple alignments were performed with the MUSCLE algorithm (Edgar (2004) Nucleic Acids Research 32: 1792-1797). MUSCLE was executed to generate multiple long CDR H3 nucleotide alignments with relatively high gap open (- 20.0) and gap extend (-10.0) penalties due to the large amount of heterogeneity observed in the sequences. Local alignment was executed using the Smith- Waterman algorithm with the following settings, match score = 2.0, mismatch penalty = -1.0, gap opening penalty = -2.0, and gap extension penalty = -0.5. CDR H3s were defined by the third residue following the conserved cysteine in framework 3 to the residue immediately preceding the conserved tryptophan in framework 4. VHBUL was identified by BLAST searching the bovine genome (assembly Btau_4.6.1) with multiple ultralong VH sequences identified by deep sequencing. The deep sequencing identified a total of 11,728 ultralong CDR3 sequences with having a length between 44 and 69 amino acid residues. The results of the deep sequencing are summarized in Table 3 below.
Table 3. Summary of deep sequencing results from bovine spleen
Figure imgf000186_0002
[00686] The results of the deep sequencing also revealed that ultralong CDR3 comprise a cysteine motif (e.g., a pattern of cysteine residues) that comprises between 3 and 12 cysteine residues. Representative examples of cysteine patterns are shown for the deep sequencing run for three different cows (MIDI, MID 10, and MIDI 1) as well as their abundance in the run (Table 4-6; SEQ ID NOS: 45-156). The cysteines in the ultralong CDR3 regions are symbolized as "C". The amino acids between two cysteines are symbolized as "Xn". Additional exemplary cysteine motifs are shown in the ultralong CDR3 sequences set forth in Table 23. Table 4. Cysteine patterns identified in ultralong CDR3s from MIDI
Figure imgf000187_0001
Table 5. Cysteine patterns identified in ultralong CDR3s from MID 10
Figure imgf000187_0002
Table 6. Cysteine patterns identified in ultralong CDR3s from MIDI 1
Figure imgf000188_0001
[00687] Bovine VH regions were amplified from cDNA prepared in example 9 using primers
5 '-TTGAGCGACAAGGCTGTAGGCTG-3 ' (SEQ ID NO: 314) and 5'- CTTTCGGGGCTGTGGTGG-AGGC-3 ' (SEQ ID NO: 315) producing a library of antibody variable region cDNA biased for ultralong CDRs. Next, the mixture of VH regions was assembled by overlap PCR with bovine CHI and human IgG Fc. Briefly, EcoRI and Nhel sites were incorporated for ligation into pFUSE expression vector, to afford a full-length heavy chain library ready for expression in mammalian cells. The ligation product was transformed into E. coli and 500 single E. coli transformants were picked. Each transformant was then grown overnight in a separate vessel and DNA from each colony was extracted using Qiagen minprep kits (Qiagen, Inc.) and sequenced by BATJ, Inc. (San Diego, CA) using the oligo 5 '-AGATCCAAGCTGTGACCGGC-3 ' (SEQ ID NO: 316). Sequences were analyzed using VectorNTI (Invitrogen, Inc. Carlsbad, CA). Duplicative sequences, sequences with no insert, and sequences encoding a CDR shorter than 35 residues were excluded. 132 clones containing unique long CDR heavy chain sequences were selected. Each heavy chain in the 132 member library was then co-transfected in parallel with pFUSE expression vector encoding the invariant bovine light chain (SEQ ID NO: N) into 293T cells, to generate a small spatially addressed library (Mao et al. (2010) Nat Biotech 28: 1195-1202). 130,000 293T cells per well were plated in 24 well plates and grown overnight in 500ul DMEM media (Invitrogen) with 10% FBS (Invitrogen), and Penicillin/streptomycin/ glutamine (Invitrogen) at 37°C and 5% C02. 0.5μ§ of Hc-encoding pFuse vector and 0.5μ§ of Lc-encoding pFuse vector were added to 25μ1 of optimem (Invitrogen). Ιμΐ of Lipofectamine 2000 or 293Fectin transfection reagent (Invitrogen) was added to 25 μΐ of optimem, and incubated 5 minutes. Next, the DNA- optimem mix and transfection reagent-optimem mix were combined and incubated 15 minutes, added to 293T cells, and allowed to incubate on cells 4-6 hours. Then media was then aspirated from wells and replaced with fresh media, and cells were allowed to grow and secrete IgG into the media for 4 days. Cell-culture supernatants containing IgG were harvested in 96 well format for further testing. The chimeric antibodies were quantified by sandwich ELISA detecting human Fc and screened for binding to BVDV by ELISA.
[00688] Antibodies were then secreted into culture media and harvested in a 96 well format to generate a small spatially addressed library for further testing including, screening for binding to BVDV by ELISA. For example, an ELISA was conducted to screen the antibody library for binding to BVDV. Briefly, killed BVDV (0.2 μg) in 100 μΐ, DPBS was coated on 96-well
MaxiSorp ELISA plates (Nunc) for 1 hour at 37°C. Next, the plates were blocked with 200 μΐ, 3% BSA solution in DPBST, Dulbecco's phosphate buffered saline, 0.25% Tween 20) for 1 hour at 37°C. Samples were then incubated with 3% BSA in DPBST for 1 hour at 37°C. Subsequently, wells were washed 5 times with 200 μΐ, DPBST. Next, Goat Anti-Human IgG (Fc) - HRP conjugated antibody (KPL Inc.) was added at a 1 : 1,000 dilution in blocking solution and incubated for 1 hour at 37°C. Wells were then washed 10 times with 200 μΐ, DPBST. A 100 μί working solution of QuantaBlu (Pierce) was added to each well and incubated for 5 minutes at room temperature before plates were read in a SpectraMax M5 plate reader at ex325/em420 nm. Several candidate binders were identified (Figure IB, left). Clone H12 has a 63-residue CDR3 with 6 cysteine residues and was able to strongly bind BVDV in a dose dependent fashion (Figure IB, right; and 1C).
[00689] Additionally, binding of the chimeric recombinant antibodies to BVDV antigens was evaluated by immuno cytometric analysis of transfected human embryonic kidney (HEK) 293A cells (Invitrogen), as previously described (see, e.g., Njongmeta et al. (2012) Vaccine 30: 1624- 1635). Briefly, HEK 293 A monolayers grown in 6-well tissue culture plates were transfected with 2 μg/well of plasmid (pCDNA3.3, Invitrogen) encoding BVDV antigens (Npro, E2, or non-structural proteins NS2-3) using Lipofectamine 2000 reagent (Invitrogen), and incubated for 48 hr at 37 °C with 5 % C02. The monolayers were fixed with ice-cold 100% methanol for 10 minutes, rinsed with PBS, and after blocking for 1 hr with PBS containing 5% fetal bovine serum (blocking buffer), the monolayers were incubated at room temperature for 1 hr with 10 μg/ml of a mouse anti-FLAG M2-alkaline phosphatase (AP)-conjugate (Sigma) in blocking buffer or 10 μg/ml of the chimeric recombinant antibodies (HI 2 or B8). Monolayers transfected with empty vector were similarly reacted to serve as negative controls and, following washes in blocking buffer, the monolayers probed with the chimeric recombinant antibodies were incubated with a 1/200 dilution of AP- conjugated goat anti-Human IgG (Fc specific) mAb (Sigma) in blocking buffer for 1 fir. Following washes in blocking buffer, the AP activity in all the wells was detected using Fast Red AS-MX substrate (Sigma). Stained cells were visualized and photographed using an IS70 inverted optical microscope (Olympus, Japan) equipped with a camera. H12 strongly binds HEK293A cells transfected with the NS2-3 non-structural proteins of BVDV but weakly bound to untransfected cells while B8 had weak binding to both HEK293A cells transfected with the NS2-3 non-structural proteins of BVDV and untransfected cells (Figure ID).
Example 3. Generation and Testing of Libraries of Antibodies Comprising an Ultralong CDR3
[00690] A library of polynucleotides coding for antibodies that comprise an ultralong CDR3 is generated by immunization of cattle with whole killed bovine viral diarrhea virus (BVDV) (Figure 1 A). Briefly, a four month-old Holstein steer was immunized by intradermal inoculation of a mixture of heat killed BVDV-1 and BVDV-2 (100 μg of each). The inactivated virus mixture was suspended in 500 μΐ PBS and emulsified in 500 μΐ Freund's Complete Adjuvant by repeated passage through a double barrel needle. Next, the immunogen was inoculated intradermally (200 μΐ/injection) at the neck region using a 26 x 1 ½ G needle. The steer was then boosted three times at monthly intervals with the same amount of antigen but formulated in Freund's Incomplete
Adjuvant. Sero-conversion was tested by ELISA using plates coated with the inactivated virus and by immuno cytometric analysis of MDBK cells infected with either BVDV-1 or BVDV-2. The steer was then bled from the jugular vein and blood was collected in heparin. Lymphocytes were purified through Lymphocyte Separation Media (Mediatech) centrifugation and stored in RNAlater. A cDNA library was then made from the plurality of lymphocyte RNA as described in Example 2. Example 4. Constructing vectors of BLVlH12-bGCSF fusion proteins for expression in mammalian cells.
[00691] A gene encoding bovine G-CSF (bGCSF) was synthesized by Genscript (NJ, USA) and amplified by polymerase chain reaction (PCR). To optimize the folding and stability of the immunoglobulin constructs, flexible linkers of (GGGGS)n (n=0, 1) were added on both ends of the bGCSF fragment. Subsequently, PCR fragments of bGCSF with varied lengths of linkers were grafted into the complementarity determining region 3 of the heavy chain (CDR3H) of BLV1H12 antibody by exploiting overlap extension PCR, to replace the 'knob' domain as shown in the crystal structure of BLV1H12. The expression vectors of BLVlH12-bGCSF fusion proteins were generated by in- frame ligation of the amplified BLVlH12-bGCSF fusion genes to the pFuse- hlgGl-Fc backbone vector (InvivoGen, CA). Similarly, the gene encoding the light chain of BLV1H12 antibody was cloned into the pFuse vector without hlgGl Fc fragment. The obtained expression vectors were confirmed by sequencing. Figures 8F, and 8G provide depictions of the bovine G-CSF inserted into or replacing at least a portion of the knob domain of a heavy chain region of bovine BLV1H12 antibody. Figure 14 shows vectors for expression of the BLV1H12- bGCSF fusion protein. DNA sequences encoding the heavy and light chain immunoglobulin constructs Ab-bGCSF L0 (n = 0) and Ab-bGCSF LI (n = 1) are shown in Table 19. Amino acid sequences encoding the heavy and light chain immunoglobulin constructs Ab-bGCSF L0 and Ab- bGCSF LI are shown in Table 21.
Example 5. Expression and purification of BLVlH12-bGCSF fusion antibodies.
[00692] BLVlH12-bGCSF fusion antibodies were expressed through transient transfections of free style HEK 293 cells with vectors encoding BLVlH12-bGCSF fusion heavy chain and BLVH1H12 light chain. Expressed BLVlH12-bGCSF fusion antibodies were secreted into the culture medium and harvested at 48 hours and 96 hours after transfection. The BLVlH12-bGCSF fusion antibodies were purified by Protein A/G chromatography (Thermo Fisher Scientific, IL), and analyzed by SDS-PAGE gel. Figure 15A shows SDS-PAGE gel of purified Ab-bGCSF L0 and Ab- bGCSF LI fusion antibodies from HEK 293 cells.
Example 6. In vitro study of proliferative activities of the BLVlH12-bGCSF fusion antibodies on mouse NFS-60 cells.
[00693] Mouse NFS-60 cells were obtained from American Type Culture Collection
(ATCC), VA, and cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS), 0.05 mM 2-mercapoethanol and 62 ng/ml human macrophage colony stimulating factor (M- CSF). For proliferation assay, mouse NFS-60 cells were washed three times with RPMI-1640 medium and resuspended in RPMI-1640 medium with 10% FBS and 0.05 mM 2-mercapoethanol at a density of 1.5x 105 cells/ml. In 96-well plates, 100 μΐ of cell suspension was added into each well, followed by the addition of varied concentrations of bGCSF, BLV1H12 antibody, and the immunoglobulin constructs described herein, Equal volume of PBS buffer was added into the control wells. The plates were incubated at 37°C in a 5% C02 incubator for 72 hours. Cells were then treated with AlamarBlue (Invitrogen) (1/10 volume of cell suspension) for 4 hours at 37°C. Fluorescence at 595 nm for each well was read to indicate the cell viability. As seen in Figures 9A- 9E and Tables 7-8, the immunoglobulin constructs Ab-bGCSF L0 and Ab-bGCSF LI display similar activity as the bovine G-CSF and human G-CSF. Table 7.
Figure imgf000192_0001
Table 8.
Figure imgf000192_0002
Example 7. In vitro study of proliferative activities of BLVlH12-bGCSF fusion antibodies on human granulocyte progenitors
[00694] Human mPB CD34+ cells were purchased from AllCells. Cells were resuspended in HSC expansion medium (StemSpan SFEM, StemCell Technologies) supplemented with lx antibiotics and the following recombinant human cytokines: thrombopoietin, IL6, Flt3 ligand, and stem cell factor (100 ng/mL, R & D Systems), then plated in 96-well plates (1000 cells per well), with varied concentrations of BLVlH12-bGCSF fusion antibodies. Cells were cultured for 7 days at 37°C in a 5% C02 incubator, then analyzed by flow cytometry to measure cell number and expression of CD45ra and CD41. Cells were stained in staining medium (HBSS supplemented with 2% FBS and 2mM EDTA) at 4°C for 1 h with PECy7 anti-CD45ra and eFluor 450 anti-CD41 (eBiosciences), then washed with staining medium and analyzed. Multicolor analysis for cell pheno typing was performed on a LSR II flow cytometer (Becton Dickinson). Figures 10A-10E and Tables 9-10 show the human granulocyte progenitor cell proliferative activities of the Ab-GCSF fusion antibodies.
Table 9.
Figure imgf000193_0001
Table 10.
Figure imgf000193_0002
Example 8. Pharmacokinetics of BLVlH12-bGCSF fusion antibodies in mice.
[00695] For PK study in mice, 70 μg of the immunoglobulin constructs described herein were injected into 3 BALB/c mice per group. Blood samples were drawn from time 0 to 14 days with extended intervals and analyzed by ELISA using anti-human IgG Fc antibody with horseradish peroxidase (HRP) labeled (KPL) and anti-6xHis antibody with HRP labeled
(Clontech). Data were normalized by taking maximal concentration at the first time point (30 min). As seen in Figures 1 lA-1 IB and Table 11, the half-life for bovine G-CSF was significantly increased when provided in the form of an immunoglobulin construct described herein.
Table 11.
Figure imgf000194_0001
Example 9. Neutrophils counts in mice.
[00696] On the 10th day after injection of BLV 1 H 12-bGCSF fusion antibodies into mice for
PK study, blood samples were drawn from the mice and stained using the Diff Quick Staining Kit (Thermo Fisher Scientific, IL). Neutrophils and white blood cells were counted under microscope and the percentages of neutrophils were analyzed. Figures 12A-12B and Table 12 show
proliferative activities of BLVlH12-bGCSF fusion antibodies on mice neutrophils that are blood stained and counted at the 10th day post-injection. Table 12.
Figure imgf000195_0001
Example 10. Construction of vectors of BLVlH12-bGCSF fusion proteins for expression in Pichia pastoris.
[00697] Gene fragments encoding BLV 1 H 12-bGCSF chain heavy chain and BLV 1 H 12 light chain were amplified from the pFuse expression vectors and subsequently ligated into the same pPICZa vector (Invitrogen). The expressions of the heavy and light chains were under the control of AOX1 promoter.
Example 11. Expression and purification of BLVlH12-bGCSF fusion antibodies in Pichia.
[00698] The Pichia GS190 cells were transformed with the pPICZa vectors encoding immunoglobulin construct heavy and light chains by electroporation. Positive transformants were selected based on zeocin resistance and confirmed by PCR. Pichia cells with integrated BLV1H12- bGCSF fusion genes were grown in BMGY medium till OD6oo = 2-6. The cells were then transferred into BMMY medium in 1/5 of its original volume for induction of the proteins expression. For every 24 hours, a final concentration of 0.5% methanol was added into the medium to maintain the induction. Medium containing the secreted immunoglobulin constructs were harvested after 96-hour induction. The BLVlH12-bGCSF fusion antibodies were purified by Protein A G chromatography (Thermo Fisher Scientific, IL) and analyzed by SDS-PAGE gel. Figures 13A-13C show expression and purification of BLVlH12-bGCSF fusion antibodies in Pichia pastoris.
Example 12. Constructing vectors of BLVlH12-Mokal fusion proteins for expression in mammalian cells.
[00699] A gene encoding Mokal was synthesized by Genscript or IDT, and amplified by polymerase chain reaction (PCR). To optimize the folding and stability of fusion proteins, flexible linkers of (GGGGS)n (n=0, 1) were added on both ends of the Mokal fragment. Subsequently, PCR fragments of Mokal with and without the linker were grafted into the complementarity determining region 3 of the heavy chain (CDR3H) of BLV1H12 antibody by exploiting overlap extension PCR, to replace the 'knob' domain as shown in the crystal structure of BLV1H12. The expression vectors of BLVlH12-Mokal fusion proteins were generated by in-frame ligation of the amplified BLVlH12-Mokal fusion genes to the pFuse-hlgGl-Fc backbone vector (InvivoGen, CA). Similarly, the gene encoding the light chain of BLV1H12 antibody was cloned into the pFuse vector without hlgGl Fc fragment. The obtained expression vectors were confirmed by sequencing. Figures 8F and 8H provide depictions of a Mokal peptide inserted into or replacing at least a portion of the knob domain of a heavy chain region of bovine BLV1H12 antibody.
Example 13. Expression and purification of BLV1H12 Ab-Mokal fusion antibodies.
[00700] BLVlH12-Mokal fusion antibodies were expressed through transient transfections of free style HEK 293 cells with vectors encoding BLVlH12-Mokal fusion heavy chain and the BLV1H12 light chain. BLVlH12-Mokal fusion antibodies were secreted into the culture medium and harvested at 48 hours and 96 hours after transfection. The BLVlH12-Mokal fusion antibodies were purified by Protein A/G chromatography (Thermo Fisher Scientific, IL), and analyzed by SDS-PAGE gel. Figure 16A shows a SDS PAGE of the immunoglobulin fusion antibodiess Ab- Mokal L0 (n = 0) and Ab-Mokal LI (n = 1).
Example 14. In vitro study of BLVlH12-Mokal fusion antibodies inhibitory activities on human peripheral blood mononuclear cells (PBMCs)/T cells activation.
[00701] Human PBMCs were isolated from fresh venous blood of healthy donors through ficoll gradient centrifugation, followed by resuspension in RPMI1640 medium with 10% FBS and plating in 96-well plates at a density of 1 x 106 cells/mL. Human T cells were purified from the isolated PBMCs using T cell enrichment kit. Purified PBMCs and T cells were pretreated for 1 h at 37°C with 5% C02 with various concentrations of purified BLVlH12-Mokal fusion antibodies and then activated by anti-CD3 and CD28 antibodies. After 24 h treatment, supernatant was collected for measurement of the levels of secreted TNF-a using ELISA kit. Figure 17 and Table 13 shows BLVlH12-Mokal fusion antibodies inhibitory activities on human peripheral blood mononuclear cells (PBMCs). Figure 16B and Table 14 shows BLVlH12-Mokal fusion antibodies inhibitory activities on T cells activation.
Table 13.
Figure imgf000196_0001
20 2186.372667 1441.220667 1294.799333
200 1981.540333 928.0533333 773.3666667
400 1732.831333 664.9696667 505.102
N.A. 183.3106667 183.3106667 183.3106667
Table 14.
[Ab-Moka-Ll]
F.I.
nM
0.3658 479.8675
1.09739 498.558
3.29218 452.342
9.87654 445.013
29.62963 467.268
88.88889 360.2535
266.66667 233.809
800 226.155
Example 15. Constructing vectors of BLV1H12-VM24 fusion proteins for expression in mammalian cells.
[00702] A gene encoding Vm24 was synthesized by Genscript or IDT, and amplified by polymerase chain reaction (PCR). To optimize the folding and stability of BLV1H12-VM24 fusion proteins, flexible linkers of GGGGS or GGGSGGGGS were added on both ends of the Vm24 fragment. Subsequently, PCR fragments of VM24 with varied lengths of linkers were grafted into the complementarity determining region 3 of the heavy chain (CDR3H) of BLV1H12 antibody by exploiting overlap extension PCR, to replace the 'knob' domain as shown in the crystal structure of BLV1H12. The expression vectors of BLV1H12-VM24 fusion proteins were generated by in-frame ligation of the amplified BLV1H12-VM24 fusion genes to the pFuse-hlgGl-Fc backbone vector (InvivoGen, CA). Similarly, the gene encoding the light chain of BLV1H12 antibody was cloned into the pFuse vector without hlgGl Fc fragment. The obtained expression vectors were confirmed by sequencing. Figures 8F, and 8H provide depictions of a VM24 peptide inserted into or replacing at least a portion of the knob domain of a heavy chain region of bovine BLV1H12 antibody.
Example 16. Expression and purification of BLV1H12-VM24 fusion antibodies.
[00703] BLV1H12-VM24 fusion antibodies were expressed through transient transfections of free style HEK 293 cells with vectors encoding BLV1H12-VM24 fusion heavy chain and the BLV1H12 light chain. Expressed BLV1H12-VM24 fusion antibodies were secreted into the culture medium and harvested every 48 hours for twice after transfection. The BLV1H12-VM24 fusion antibodies were purified by Protein A/G chromatography (Thermo Fisher Scientific, IL), and analyzed by SDS-PAGE gel. Figure 18A shows a SDS PAGE of the immunoglobulin constructs Ab-VM24 LI (linker = GGGGS) and Ab-VM24 L2 (first linker = GGGSGGGGS and second linker = GGGGSGGGS).
Example 17. In vitro study of BLV1H12-Vm24 fusion antibodies inhibitory activities on T cells activation.
[00704] Human T cells were purified from the isolated PBMCs using T cell enrichment kit.
Purified T cells were pretreated for 1 h at 37°C with 5% C02 with various concentrations of purified BLV1H12-VM24 fusion antibodies and then activated by anti-CD3 and CD28 antibodies. After 24 h treatment, supernatant was collected for measurement of the levels of secreted TNF-a using ELISA kit. Figures 18B-C and Table 15 show the BLV1H12-VM24 fusion antibodies inhibitory activities on T cells activation.
Table 15.
Figure imgf000198_0001
Example 18. Constructing vectors of BLVlH12-Ex-4 fusion proteins for expression in mammalian cells.
[00705] A gene encoding Exendin-4 (Ex-4) was synthesized by Genscript or IDT, and amplified by polymerase chain reaction (PCR). A cleavage site of Factor Xa was placed in front of the N-terminal of Exendin-4. In addition to this protease cleavage site, GGGGS linker followed with a cysteine were also added on both ends of the Exendin-4 fragment. Subsequently, PCR fragments of Exendin-4 were grafted into the complementarity determining region 3 of the heavy chain (CDR3H) of BLV1H12 antibody by exploiting overlap extension PCR, to replace the 'knob' domain as shown in the crystal structure of BLV1H12. The expression vectors of BLVlH12-Ex-4 clip fusion proteins were generated by in- frame ligation of the amplified BLVlH12-fusion genes to the pFuse-hlgGl-Fc backbone vector (InvivoGen, CA). Similarly, the gene encoding the light chain of BLV1H12 antibody was cloned into the pFuse vector without hlgGl Fc fragment. The obtained expression vectors were confirmed by sequencing. Figures8F, and 81 show cartoons depicting Exendin-4 peptide inserted into or replacing at least a portion of the knob domain of an
immunoglobulin heavy chain region. Figure 81 also depicts the clipped version of the BLV1H12- Exendin-4 fusion protein, wherein Exendin-4 has a free N-terminus.
Example 19. Expression and purification of BLVlH12-Ex-4 clip fusion proteins.
[00706] BLVlH12-Ex-4 fusion antibodies were expressed through transient transfections of free style HEK 293 cells with vectors encoding BLVlH12-Ex-4 fusion heavy chain and the BLV1H12 light chain. Expressed BLVlH12-Ex-4 fusion antibodies were secreted into the culture medium and harvested at 48 hours and 96 hours after transfection. The BLVlH12-Ex-4 fusion antibodies were purified by Protein A/G chromatography (Thermo Fisher Scientific, IL).
BLVlH12-Ex-4 fusion antibodies were further treated with Factor Xa protease (GE Healthcare) following manufacture's protocol to release N-terminal of Ex-4 peptides fused to the BLV1H12 antibody. After treatment, BLVlH12-Ex-4 fusion antibodies were re-purified by Protein A/G affinity column to remove protease and analyzed by SDS-PAGE gel. Figure 19 shows a western blot of expression of the immunoglobulin construct Ab-Exendin-4.
Example 20. In vitro study of BLVlH12-Ex-4 clip fusion antibodies activation activities on GLP-1 receptor (GLP-1R).
[00707] HEK293 cells expressing surface GLP-1 R and cAMP responsive luciferase reporter gene were seeded in 384 well plates at a density of 5000 cells per well. After 24 h incubation at 37°C with 5% C02, cells were treated with various concentrations of Exendin-4 peptides and BLVlH12-Ex-4 clip fusion antibodies and incubated for another 24 h. Subsequently, luciferase assay was performed using One-Glo luciferase reagent according manufacture's instruction (Promega). Figure 20 and Tables 16-17 show the activity of Ab-Ex4 fusion antibodies on HEK293 cells expressing GLP-1 receptor.
Table 16.
Figure imgf000199_0001
10.15625 5500 10.15625 66560 10.15625 10420 10.15625 5200
20.3125 5380 20.3125 105040 20.3125 19340 20.3125 7780
40.625 4600 40.625 143780 40.625 27960 40.625 13600
81.25 6140 81.25 151060 81.25 54800 81.25 33760
162.5 5760 162.5 166640 162.5 90660 162.5 65800
325 5600 325 171400 325 117900 325 100920
650 5800 650 159780 650 134760 650 140640
1300 14000 1300 184960 1300 159660 1300 169060
Table 17.
Figure imgf000200_0001
Example 21. Constructing vectors of BLV1H12-GLP-1 clip fusion proteins for expression in mammalian cells.
[00708] A gene encoding GLP-1 was synthesized by Genscript or IDT, and amplified by polymerase chain reaction (PCR). To optimize the folding and stability of fusion proteins, flexible linkers of (GGGGS)n (n=0, 1) were added on both ends of the Mokal fragment. Linkers of GGGGS or GGGSGGGGS were added on both ends of the GLP-1 fragment. A cleavage site of Factor Xa was placed in front of the N-terminal of GLP-1. In addition to this protease cleavage site, GGGGS linker followed with a cysteine were also added on both ends of the GLP-1 fragment. Subsequently, PCR fragments of GLP-1 were grafted into the complementarity determining region 3 of the heavy chain (CDR3H) of BLV1H12 antibody by exploiting overlap extension PCR, to replace the 'knob' domain as shown in the crystal structure of BLV1H12. The expression vectors of BLV1H12-GLP-1 clip fusion proteins were generated by in-frame ligation of the amplified
BLV1H12-GLP-1 fusion genes to the pFuse-hlgGl-Fc backbone vector (InvivoGen, CA).
Similarly, the gene encoding the light chain of BLV1H12 antibody was cloned into the pFuse vector without hlgGl Fc fragment. The obtained expression vectors were confirmed by sequencing. Figures 8F and 81 show cartoons depicting a GLP1 peptide inserted into or replacing at least a portion of the knob domain of an immunoglobulin heavy chain region. Figure 81 also shows shows a clipped version of the BLV1H12-GLP-1 fusion protein, wherein GLP-1 has a free N-terminus. Example 22. Expression and purification of BLV1H12-GLP-1 clip fusion antibodies.
[00709] BLV1H12-GLP-1 fusion antibodies were expressed through transient transfections of free style HEK 293 cells with vectors encoding BLV1H12-GLP-1 fusion heavy chain and the BLV1H12 light chain. Expressed BLV1H12-GLP-1 fusion antibodies were secreted into the culture medium and harvested at 48 hours and 96 hours after transfection. The BLV1H12-GLP-1 fusion antibodies were purified by Protein A/G chromatography (Thermo Fisher Scientific, IL).
BLV1H12-GLP-1 fusion antibodies were further treated with Factor Xa protease (GE Healthcare) following manufacture's protocol to release N-terminal of GLP-1 peptide fused to the BLV1H12 antibody. After treatment, BLV1H12-GLP-1 clip fusion antibodies were re-purified by Protein A/G affinity column to remove protease and analyzed by SDS-PAGE gel. Figure 19 provides a western blot of expression of the immunoglobulin construct Ab-GLP-1.
Example 23. In vitro study of BLV1H12-GLP-1 clip fusion antibodies activation activities on GLP-1 recepto (GLP-1R).
[00710] HEK293 cells expressing surface GLP-1R and cAMP responsive luciferase reporter gene were seeded in 384 well plates at a density of 5000 cells per well. After 24 h incubation at 37°C with 5% C02, cells were treated with various concentrations of peptides and BLV1H12-GLP- 1 clip fusion proteins and incubated for another 24 h. Subsequently, luciferase assay was performed using One-Glo luciferase reagent according manufacture's instruction (Promega). Figure 20 and Table 16 show the activity of Ab-GLP-1 f fusion antibodies on HEK293 cells expressing GLP-1 receptor.
Example 24. Constructing vectors of BLVlH12-hEPO fusion proteins for expression in mammalian cells.
[00711] A gene encoding human EPO was synthesized by Genscript or IDT, and amplified by polymerase chain reaction (PCR). To optimize the folding and stability of fusion proteins, flexible linkers of (GGGGS) were added on both ends of human EPO. Subsequently, PCR fragments of hEPO were grafted into the complementarity determining region 3 of the heavy chain (CDR3H) of BLV1H12 antibody by exploiting overlap extension PCR, to replace the 'knob' domain as shown in the crystal structure of BLV1H12. The expression vectors of BLVlH12-hEPO fusion proteins were generated by in- frame ligation of the amplified BLVlH12-fusion genes to the pFuse-hlgGl-Fc backbone vector (InvivoGen, CA). Similarly, the gene encoding the light chain of BLV1H12 antibody was cloned into the pFuse vector without hlgGl Fc fragment. The obtained expression vectors were confirmed by sequencing. Figures 8F and 8J show cartoons depicting hEPO peptide attached to the knob domain of an immunoglobulin heavy chain region.
Example 25. Expression and purification of BLVlH12-hEPO fusion antibodies.
[00712] BLVlH12-hEPO fusion antibodies were expressed through transient transfections of free style HEK 293 cells with vectors encoding BLVlH12-hEPO fusion heavy chain and the BLV1H12 light chain. Expressed BLVlH12-hEPO fusion antibodies were secreted into the culture medium and harvested at 48 hours and 96 hours after transfection. The BLVlH12-hEPO fusion antibodies were purified by Protein A/G chromatography (Thermo Fisher Scientific, IL), and analyzed by SDS-PAGE gel.
Example 26. In vitro study of BLVlH12-hEPO fusion antibody proliferative activities on TF- 1 cells.
[00713] TF-1 cells were obtained from American Type Culture Collection (ATCC), VA, and cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS), penicillin, streptomycin and 2 ng/mL granulocyte-macrophage colony- stimulating factor (GM-CSF). For proliferation assay, TF-1 cells were washed three times with RPMI-1640 medium and resuspended in RPMI-1640 medium with 10% FBS and penicillin and streptomycin at a density of 1.5χ 105 cells/ml. Cells were plated in 96-well plates and treated with varied concentrations of BLV1H12- hEPO fusion antibodies. After 72 h of incubation at 37°C with 5% C02, cells viabilities were measured using AlamarBlue (Invitrogen) assay following manufacture's instruction. Figure 21 and Table 18 show the proliferative activity of Ab-hEPO fusion antibodies on TF1 cells.
Table 18.
Figure imgf000203_0001
Example 27. Constructing vectors of BLVlH12-hFGF21fusion proteins for expression in mammalian cells.
[00714] A gene encoding human FGF21 (hFGF21) was synthesized by Genscript or IDT, and amplified by polymerase chain reaction (PCR). To optimize the folding and stability of fusion proteins, flexible linkers of (GGGGS) were added on both ends of human FGF21. Subsequently, PCR fragments of hFGF21 were grafted into the complementarity determining region 3 of the heavy chain (CDR3H) of BLV1H12 antibody by exploiting overlap extension PCR, to replace the 'knob' domain as shown in the crystal structure of BLV1H12. The expression vectors of
BLVlH12-hFGF21 fusion proteins were generated by in- frame ligation of the amplified
BLVlH12-fusion genes to the pFuse-hlgGl-Fc backbone vector (InvivoGen, CA). Similarly, the gene encoding the light chain of BLV1H12 antibody was cloned into the pFuse vector without hlgGl Fc fragment. The obtained expression vectors were confirmed by sequencing.
Example 28. Expression and purification of BLVlH12-hFGF21 fusion antibody.
[00715] BLVlH12-hFGF21 fusion antibodies were expressed through transient transfections of free style HEK 293 cells with vectors encoding BLVlH12-hFGF21 fusion heavy chain and the BLV1H12 light chain. Expressed BLVlH12-hFGF21 fusion antibodies were secreted into the culture medium and harvested every 48 hours for twice after transfection. The BLVlH12-hFGF21 fusion antibodies were purified by Protein A/G chromatography (Thermo Fisher Scientific, IL), and analyzed by SDS-PAGE gel.
Example 29. Constructing vectors of BLVlH12-hGMCSF fusion proteins for expression in mammalian cells.
[00716] A gene encoding human GMCSF (hGMCSF) was synthesized by Genscript or IDT, and amplified by polymerase chain reaction (PCR). To optimize the folding and stability of fusion proteins, flexible linkers of (GGGGS) were added on both ends of human GMCSF. Subsequently, PCR fragments of hGMCSF were grafted into the complementarity determining region 3 of the heavy chain (CDR3H) of BLV1H12 antibody by exploiting overlap extension PCR, to replace the 'knob' domain as shown in the crystal structure of BLV1H12. The expression vectors of
BLVlH12-hGMCSF fusion proteins were generated by in- frame ligation of the amplified
BLVlH12-hGMCSF fusion genes to the pFuse-hlgGl-Fc backbone vector (InvivoGen, CA).
Similarly, the gene encoding the light chain of BLV1H12 antibody was cloned into the pFuse vector without hlgGl Fc fragment. The obtained expression vectors were confirmed by sequencing. Example 30. Expression and purification of BLVlH12-hGMCSF fusion antibodies.
[00717] BLVlH12-hGMCSF fusion antibodies can be expressed through transient transfections of free style HEK 293 cells with vectors encoding BLVlH12-hGMCSF fusion heavy chain and the BLV1H12 light chain. Expressed BLVlH12-hGMCSF fusion antibodies can be secreted into the culture medium and harvested at 48 hours and 96 hours after transfection. The BLVlH12-hGMCSF fusion antibodies can be purified by Protein A G chromatography (Thermo Fisher Scientific, IL), and analyzed by SDS-PAGE gel.
Example 31. Constructing vectors of BLVlH12-hIFN-b proteins for expression in
mammalian cells.
[00718] A gene encoding human interferon-beta (hlFN-b) was synthesized by Genscript or
IDT, and amplified by polymerase chain reaction (PCR). To optimize the folding and stability of fusion proteins, flexible linkers of (GGGGS) were added on both ends of human interferon-beta. Subsequently, PCR fragments of hlFN-b were grafted into the complementarity determining region 3 of the heavy chain (CDR3H) of BLV1H12 antibody by exploiting overlap extension PCR, to replace the 'knob' domain as shown in the crystal structure of BLV1H12. The expression vectors of BLVlH12-hIFN-b fusion proteins were generated by in- frame ligation of the amplified BLV1H12- hlFN-b fusion genes to the pFuse-hlgGl-Fc backbone vector (InvivoGen, CA). Similarly, the gene encoding the light chain of BLV1H12 antibody was cloned into the pFuse vector without hlgGl Fc fragment. The obtained expression vectors were confirmed by sequencing. Example 32. Expression and purification of BLVlH12-hIFN-b fusion antibodies.
[00719] BLVlH12-hIFN-b fusion antibodies can be expressed through transient
transfections of free style HEK 293 cells with vectors encoding BLVlH12-hIFN-b fusion heavy chain and the BLV1H12 light chain. Expressed BLVlH12-hIFN-b fusion antibodies can be secreted into the culture medium and harvested at 48 hours and 96 hours after transfection. The BLVlH12-hIFN-b fusion antibodies can be purified by Protein A/G chromatography (Thermo Fisher Scientific, IL), and analyzed by SDS-PAGE gel.
Example 33. Constructing vectors of BLVlH12-fusion proteins for expression in mammalian cells.
[00720] Genes encoding encoding various genes were synthesized by Genscript (NJ, USA) and amplified by polymerase chain reaction (PCR). To optimize the folding and stability of the immunoglobulin constructs, one or more flexible linkers of (GGGGS)n (n=0, 1), GGGSGGGGS, and/or GGGGSGGGS were added on both ends of the gene fragment. Subsequently, PCR fragments of the genes with varied lengths of linkers were grafted into the complementarity determining region 3 of the heavy chain (CDR3H) of BLV1H12 antibody by exploiting overlap extension PCR, to replace at least a portion of the 'knob' domain as shown in the crystal structure of BLV1H12 (Figures 8A-8J). The expression vectors of BLVlH12-fusion proteins were generated by in- frame ligation of the amplified BLVlH12-fusion genes to the pFuse-hlgGl-Fc backbone vector (InvivoGen, CA). Similarly, the gene encoding the light chain of BLV1H12 antibody was cloned into the pFuse vector without hlgGl Fc fragment. The obtained expression vectors were confirmed by sequencing.
[00721] Nucleic acid sequences of the BLVlH12-fusion proteins are displayed in Table 19
(SEQ ID NOS: 1-15). Peptide sequences of the BLVH12-fusion proteins are displayed in Table 21 (SEQ ID NOS: 23-37). As shown in the Table 19 and Table 21, the bovine heavy chain sequence is in bold font; the human heavy chain sequence is highlighted with a dashed under linei the non- antibody sequence is in italicized font; the_stalk domain is in bold font and underlined; the knob domain is in hold font and double underlined: the linker sequence is in i aUcized bntjmd s uiggl underJ ed
Example 34. Constructing vectors of BLV1H12-IL8 fusion proteins for expression in mammalian cells.
[00722] Gene encoding a human IL-8 sequence (see, e.g., SEQ ID NO: 317 corresponding to amino acids 26-99 of IL-8, designated IL8 herein) was amplified from cDNA (OriGene) by polymerase chain reaction (PCR). In some constructs, a linker (e.g., GSG or repeats of GSG) may be added on one or both ends of the IL8 fragment. Subsequently, PCR fragments of IL8 with or without a linker were grafted into the complementarity determining region 3 of the heavy chain (CDR3H) of BLV1H12 antibody by PCR, to replace the 'knob' domain as shown in the crystal structure of BLV1H12. The expression vectors of BLV1H12-IL8 fusion proteins were generated by in- frame ligation of the amplified BLV1H12-IL8 fusion genes to CH1-CH2-CH3 in a pFuse- backbone vector (InvivoGen, CA). The BLV1H12-IL8 heavy chain variable region sequence is shown as SEQ ID NO: 16 (nucleotide) and SEQ ID NO: 38 (amino acid). Similarly, the gene encoding the light chain of BLV1H12 antibody was cloned into a pFuse vector without hlgGl Fc fragment. The obtained expression vectors were confirmed by sequencing.
Example 35. Expression of BLV1H12-IL8 fusion proteins.
[00723] BLV1H12-IL8 fusion proteins were expressed through transient transfections of
293T cells or Freestyle™ 293-F cells with vectors encoding BLV1H12-IL8 heavy and light chains. Expressed fusion proteins were secreted into the culture medium and culture supernatants obtained after 2days of cell culture. The expression of BLV1H12-IL8 fusion proteins in the supernatants was determined by ELISA to be 37.2 nM
Example 36. In vitro study of activities of the BLV1H12-IL8 fusion proteins on CXCR1 expressing cells.
[00724] Briefly, a cell line expressing functionally validated CXCR1 derived from U20S cells was obtained from DiscoveRx and cultured per manufacturer's instructions (Cat# 93-0226C3, DiscoveRx Corporation, Freemont, CA). The parental cell line U20S was obtained from ATCC and cultured under the same conditions as the CXCR1 cells. Cell culture supernatants from
Example 2 above were then tested for binding to cells by flow cytometry. The adherent U20S or CXCR1-U20S cells were dissociated with Accutase (Innovative Cell Technologies, Inc., San Diego, CA), neutralized with an equal volume of media containing 10% serum, centrifuged at 1000 g, and resuspended in PBS with 2%BSA. Next, cells were dispensed into microtiter plates to achieve between 30,000 to 300,000 cells per well, centrifuged again, and resuspended in cell culture supernatant containing expressed IgG, or a dilution of IgG-containing cell culture supernatant. A fluorescent-conjugated anti-Human Fc antibody was used to detect binding of the expressedBLVlH12-IL8 fusion proteins to cells. Subsequently, cell fluorescence was measured by flow cytometry (e.g., FACS), and median Arbitrary Fluorescence Units (AFU) were calculated, revealing the extent of IgG binding to those cells. The ratio of median fluorescence (IgG binding) of CXCR1-U20S cells versus U20S parental cells shows that the BLV1H12-IL8 fusion protein has specificity for CXCR1 (Table 27). Table 27.
Figure imgf000207_0001
Example 37. Constructing vectors of BLVlH12-ziconotide fusion proteins for expression in mammalian cells.
[00725] Gene encoding a ziconotide sequence (see, e.g., SEQ ID NO: 318) was prepared from multiple oligonucleotides and then amplified by polymerase chain reaction (PCR). In some constructs, a linker (e.g., GSG or repeats of GSG) may be added on one or both ends of the ziconotide fragment. Subsequently, PCR fragments of ziconotide with or without a linker were grafted into the complementarity determining region 3 of the heavy chain (CDR3H) of BLV1H12 antibody by PCR, to replace the 'knob' domain as shown in the crystal structure of BLV1H12. The expression vectors of BLVlH12-ziconotide fusion proteins were generated by in- frame ligation of the amplified BLVlH12-ziconotide fusion genes to CH1-CH2-CH3 in a pFuse-backbone vector (InvivoGen, CA). The BLVlH12-ziconotide heavy chain variable region sequence is shown as SEQ ID NO: 17 (nucleotide) and SEQ ID NO: 39 (amino acid). Similarly, the gene encoding the light chain of BLV1H12 antibody was cloned into a pFuse vector without hlgGl Fc fragment. The obtained expression vectors were confirmed by sequencing.
Example 38. Expression of BLVlH12-ziconotide fusion proteins.
[00726] BLVlH12-ziconotide fusion proteins were expressed through transient trans fections of 293T cells or Freestyle™ 293-F cells with vectors encoding BLVlH12-ziconotide heavy and light chains. Expressed fusion proteins were secreted into the culture medium and culture supernatants obtained after 2days of cell culture. The expression of BLVlH12-ziconotide fusion proteins in the supernatants was determined by ELISA and normalized as compared to the IL8 construct in Example 35 above to be 94.7% of the IL8 construct.
Example 39. Constructing vectors of BLVlH12-somatostatin fusion proteins for expression in mammalian cells.
[00727] Gene encoding a somatostatin sequence (see, e.g., SEQ ID NO: 319) was prepared from multiple oligonucleotides and then amplified by polymerase chain reaction (PCR). In some constructs, a linker (e.g., GSG or repeats of GSG) may be added on one or both ends of the somatostatin fragment. Subsequently, PCR fragments of somatostatin with or without a linker were grafted into the complementarity determining region 3 of the heavy chain (CDR3H) of BLV1H12 antibody by PCR, to replace the 'knob' domain as shown in the crystal structure of BLV1H12. The expression vectors of BLVlH12-somatostatin fusion proteins were generated by in- frame ligation of the amplified BLVlH12-somatostatin fusion genes to CH1-CH2-CH3 in a pFuse-backbone vector (InvivoGen, CA). The BLVlH12-somatostatin heavy chain variable region sequence is shown as SEQ ID NO: 18 (nucleotide) and SEQ ID NO: 40 (amino acid). Similarly, the gene encoding the light chain of BLV1H12 antibody was cloned into a pFuse vector without hlgGl Fc fragment. The obtained expression vectors were confirmed by sequencing.
Example 40. Expression of BLVlH12-somatostatin fusion proteins.
[00728] BLVlH12-somatostatin fusion proteins were expressed through transient transfections of 293T cells or Freestyle™ 293-F cells with vectors encoding BLV1H12- somatostatin heavy and light chains. Expressed fusion proteins were secreted into the culture medium and culture supernatants obtained after 2days of cell culture. The expression of BLV1H12- somatostatin fusion proteins in the supernatants was determined by ELISA and normalized as compared to the IL8 construct in Example 35 above to be 46.5% of the IL8 construct.
Example 41. Constructing vectors of BLVlH12-chlorotoxin fusion proteins for expression in mammalian cells.
[00729] Gene encoding a chlorotoxin sequence (see, e.g., SEQ ID NO: 320) was prepared from multiple oligonucleotides and then amplified by polymerase chain reaction (PCR). In some constructs, a linker (e.g., GSG or repeats of GSG) may be added on one or both ends of the chlorotoxin fragment. Subsequently, PCR fragments of chlorotoxin with or without a linker were grafted into the complementarity determining region 3 of the heavy chain (CDR3H) of BLV1H12 antibody by PCR, to replace the 'knob' domain as shown in the crystal structure of BLV1H12. The expression vectors of BLVlH12-chloro toxin fusion proteins were generated by in- frame ligation of the amplified BLVlH12-chlorotoxin fusion genes to CH1-CH2-CH3 in a pFuse-backbone vector (InvivoGen, CA). The BLVlH12-chlorotoxin heavy chain variable region sequence is shown as SEQ ID NO: 19 (nucleotide) and SEQ ID NO: 41 (amino acid). Similarly, the gene encoding the light chain of BLV1H12 antibody was cloned into a pFuse vector without hlgGl Fc fragment. The obtained expression vectors were confirmed by sequencing.
Example 42. Expression of BLVlH12-chlorotoxin fusion proteins.
[00730] BLV 1 H 12-chlorotoxin fusion proteins were expressed through transient
transfections of 293T cells or Freestyle™ 293-F cells with vectors encoding BLVlH12-chlorotoxin heavy and light chains. Expressed fusion proteins were secreted into the culture medium and culture supernatants obtained after 2days of cell culture. The expression of BLVlH12-chloro toxin fusion proteins in the supernatants was determined by ELISA and normalized as compared to the IL8 construct in Example 35 above to be 39.7% of the IL8 construct.
Example 43. Constructing vectors of BLV1H12-SDF-1 (alpha) fusion proteins for expression in mammalian cells.
[00731] Gene encoding a SDF-1 alpha sequence (see, e.g., SEQ ID NO: 321) was amplified from cDNA (OriGene) by polymerase chain reaction (PCR). In some constructs, a linker (e.g., GSG or repeats of GSG) may be added on one or both ends of the SDF-1 (alpha) fragment.
Subsequently, PCR fragments of SDF-1 (alpha) with or without a linker were grafted into the complementarity determining region 3 of the heavy chain (CDR3H) of BLV1H12 antibody by PCR, to replace the 'knob' domain as shown in the crystal structure of BLV1H12. The expression vectors of BLV1H12-SDF-1 (alpha) fusion proteins were generated by in- frame ligation of the amplified BLV1H12-SDF-1 (alpha) fusion genes to CH1-CH2-CH3 in a pFuse-backbone vector (InvivoGen, CA). The BLV1H12-SDF-1 (alpha) heavy chain variable region sequence is shown as SEQ ID NO: 20 (nucleotide) and SEQ ID NO: 42 (amino acid). Similarly, the gene encoding the light chain of BLV1H12 antibody was cloned into a pFuse vector without hlgGl Fc fragment. The obtained expression vectors were confirmed by sequencing.
Example 44. Expression of BLV1H12-SDF-1 (alpha) fusion proteins.
[00732] BLV1H12-SDF-1 (alpha) fusion proteins were expressed through transient transfections of 293T cells or Freestyle™ 293-F cells with vectors encoding BLV1H12-SDF-1
(alpha) heavy and light chains. Expressed fusion proteins were secreted into the culture medium and culture supernatants obtained after 2days of cell culture. The expression of BLV1H12-SDF-1
(alpha) fusion proteins in the supernatants was determined by ELISA and normalized as compared to the IL8 construct in Example 35 above to be 38.9% of the IL8 construct.
Example 45. Constructing vectors of BLV1H12-IL21 fusion proteins for expression in mammalian cells.
[00733] Gene encoding an IL21 sequence (see, e.g., SEQ ID NO: 322) was amplified from cDNA (OriGene) by polymerase chain reaction (PCR). In some constructs, a linker (e.g., GSG or repeats of GSG) may be added on one or both ends of the IL21 fragment. Subsequently, PCR fragments of IL21 with or without a linker were grafted into the complementarity determining region 3 of the heavy chain (CDR3H) of BLV1H12 antibody by PCR, to replace the 'knob' domain as shown in the crystal structure of BLV1H12. The expression vectors of BLV1H12-IL21 fusion proteins were generated by in- frame ligation of the amplified BLV1H12-IL21 fusion genes to CH1- CH2-CH3 in a pFuse-backbone vector (InvivoGen, CA). The BLV1H12-IL21 heavy chain variable region sequence is shown as SEQ ID NO: 21 (nucleotide) and SEQ ID NO: 43 (amino acid). Similarly, the gene encoding the light chain of BLV1H12 antibody was cloned into a pFuse vector without hlgGl Fc fragment. The obtained expression vectors were confirmed by sequencing.
Example 46. Expression of BLV1H12-IL21 fusion proteins.
[00734] BLV1H12-IL21 fusion proteins were expressed through transient transfections of
293T cells or Freestyle™ 293-F cells with vectors encoding BLV1H12-IL21 heavy and light chains. Expressed fusion proteins were secreted into the culture medium and culture supernatants obtained after 2days of cell culture. The expression of BLV1H12-IL21 fusion proteins in the supernatants was determined by ELISA and normalized as compared to the IL8 construct in Example 35 above to be 32.3% of the IL8 construct.
Example 47. Constructing vectors of BLVlH12-protoxin2 fusion proteins for expression in mammalian cells.
[00735] Gene encoding protoxin2 was synthesized by Genscript or IDT, and amplified by polymerase chain reaction (PCR). To optimize the folding and stability of fusion proteins, flexible linkers of GGGGS were added on both ends of protoxin2 fragments. Subsequently, PCR fragments of protoxin2 (called protoxin2-Ll) were grafted into the complementarity determining region 3 of the heavy chain (CDR3H) of BLV1H12 antibody by exploiting overlap extension PCR, to replace the 'knob' domain as shown in the crystal structure of BLV1H12. The expression vectors of BLVlH12-fusion proteins were generated by in- frame ligation of the amplified BLV1H12- protoxin2-Ll fusion genes (SEQ ID NO: 15) to the pFuse-hlgGl-Fc backbone vector (InvivoGen, CA). Similarly, the gene encoding the light chain of BLV1H12 antibody was cloned into the pFuse vector without hlgGl Fc fragment. The obtained expression vectors were confirmed by sequencing. Example 48. Expression and purification of BLVlH12-protoxin2-Ll fusion proteins.
[00736] BLVlH12-protoxin2-Ll fusion antibodies were expressed through transient transfections of free style HEK 293 cells with vectors encoding BLVlH12-protoxin2 fusion heavy chain and the BLV1H12 light chain. Expressed BLVlH12-protoxin2-Ll fusion antibodies were secreted into the culture medium and harvested at 48 hours and 96 hours after transfection. The BLVlH12-protoxin2-Ll fusion antibodies were purified by Protein A/G chromatography (Thermo Fisher Scientific, IL), and analyzed by SDS-PAGE gel (Figure 15B).
Example 49. Constructing vectors of BLVlH12-ProTxII fusion proteins for expression in mammalian cells.
[00737] Gene encoding a ProTxII sequence (see, e.g., SEQ ID NO: 323) was prepared from multiple oligonucleotides and then amplified by polymerase chain reaction (PCR). In some constructs, a linker (e.g., GSG or repeats of GSG) may be added on one or both ends of the ProTxII fragment. Subsequently, PCR fragments of ProTxII with or without a linker were grafted into the complementarity determining region 3 of the heavy chain (CDR3H) of BLV1H12 antibody by PCR, to replace the 'knob' domain as shown in the crystal structure of BLV1H12. The expression vectors of BLV1H12- ProTxII fusion proteins were generated by in- frame ligation of the amplified BLV1H12- ProTxII fusion genes to CH1-CH2-CH3 in a pFuse- backbone vector (InvivoGen, CA). The BLV1H12- ProTxII heavy chain variable region sequence is shown as SEQ ID NO: 22 (nucleotide) and SEQ ID NO: 44 (amino acid). Similarly, the gene encoding the light chain of BLV1H12 antibody was cloned into a pFuse vector without hlgGl Fc fragment. The obtained expression vectors were confirmed by sequencing.
Example 50. Expression of BLV1H12- ProTxII fusion proteins.
[00738] BLVlH12-ProTxII fusion proteins were expressed through transient transfections of
293T cells or Freestyle™ 293-F cells with vectors encoding BLV1H12- ProTxII heavy and light chains. Expressed fusion proteins were secreted into the culture medium and culture supernatants obtained after 2 days of cell culture. The expression of BLV1H12- ProTxII fusion proteins in the supernatants was determined by ELISA and normalized as compared to the IL8 construct in Example 35 above to be 2.1% of the IL8 construct.
[00739] For the disclosure herein, the very least, and not as an attempt to limit the application of the doctrine of equivalents to the scope of the claims, each numerical parameter should at least be construed in light of the number of reported significant digits and by applying ordinary rounding techniques. Notwithstanding that the numerical ranges and parameters setting forth the broad scope of the disclosure are approximations, the numerical values set forth in the specific examples are reported as precisely as possible. Any numerical value, however, inherently contains certain errors necessarily resulting from the standard deviation found in their respective testing measurements.
Table 19.
Description SEQ ID Sequence
NO:
Light Chain 1 CAGGCCGTCCTGAACCAGCCAAGCAGCGTCTCCGGGTCT
CTGGGGCAGCGGGTCTCAATCACCTGTAGCGGGTCTTCCT
CCAATGTCGGCAACGGCTACGTGTCTTGGTATCAGCTGAT
CCCTGGCAGTGCCCCACGAACCCTGATCTACGGCGACAC
ATCCAGAGCTTCTGGGGTCCCCGATCGGTTCTCAGGGAGC
AGATCCGGAAACACAGCTACTCTGACCATCAGCTCCCTG
CAGGCTGAGGACGAAGCAGATTATTTCTGCGCATCTGCC
GAGGACTCTAGTTCAAATGCCGTGTTTGGAAGCGGCACC ACACTGACAGTCCTGGGGCAGCCCAAGAGTCCCCCTTCA
GTGACTCTGTTCCCACCCTCTACCGAGGAACTGAACGGA
AACAAGGCCACACTGGTGTGTCTGATCAGCGACTTTTACC
CTGGATCCGTCACTGTGGTCTGGAAGGCAGATGGCAGCA
CAATTACTAGGAACGTGGAAACTACCCGCGCCTCCAAGC
AGTCTAATAGTAAATACGCCGCCAGCTCCTATCTGAGCCT
GACCTCTAGTGATTGGAAGTCCAAAGGGTCATATAGCTG
CGAAGTGACCCATGAAGGCTCAACCGTGACTAAGACTGT
GAAACCATCCGAGTGCTCC
Heavy Chain - 2 CAGGTCCAGCTGAGAGAGAGCGGCCCTTCACTGGTCA no insertion AGCCATCCCAGACACTGAGCCTGACATGCACAGCAAG
CGGGTTTTCACTGAGCGACAAGGCAGTGGGATGGGTC
CGACAGGCACCAGGAAAAGCCCTGGAATGGCTGGGC
AGCATCGATACCGGCGGGAACACAGGGTACAATCCCG
GACTGAAGAGCAGACTGTCCATTACCAAGGACAACTC
TAAAAGTCAGGTGTCACTGAGCGTGAGCTCCGTCACC
ACAGAGGATAGTGCAACTTACTATTGCACCTCTGTGC
ACCAGGAAACTAAGAAATACCAGAGCTGTCCTGACGG
CTATCGGGAGAGATCTGATTGCAGTAATAGGCCAGCT
TGTGGCACATCCGACTGCTGTCGCGTGTCTGTCTTCG
GGAACTGCCTGACTACCCTGCCTGTGTCCTACTCTTAT
ACCTACAATTATGAATGGCATGTGGATGTCTGGGGAC AGGGCCTGCTGGTGACAGTCTCTAGT
IFN-beta 3 CAGGTCCAGCTGAGAGAGAGCGGCCCTTCACTGGTCA
AGCCATCCCAGACACTGAGCCTGACATGCACAGCAAG
CGGGTTTTCACTGAGCGACAAGGCAGTGGGATGGGTC
CGACAGGCACCAGGAAAAGCCCTGGAATGGCTGGGC
AGCATCGATACCGGCGGGAACACAGGGTACAATCCCG
GACTGAAGAGCAGACTGTCCATTACCAAGGACAACTC
TAAAAGTCAGGTGTCACTGAGCGTGAGCTCCGTCACC
ACAGAGGATAGTGCAACTTACTATTGCACCTCTGTGC
ACCAGGAAACTAAGAAATACCAGAGCGGGGGrGGCGGJ
AGCA TGA GCTA CAA CTTGCTTGGA TTCCTA CAAA GAA GCAGC AA TTTTCA GTGTCA GAA GCTCCTGTGGCAA TTGAA TGGGAGG CTTGAA TA CTGCCTCAA GGA CA GGA TGA A CTTTGA CA TCCCT GA GGA GA TTAA GCA GCTGCA GCA GTTCCA GAA GGAGGACGC CGCA TTGA CCA TCTA TGA GA TGCTCCA GAA CA TCTTTGCTA TT TTCA GA CAA GA TTCA TCTA GCA CTGGCTGGAA TGA GA CTA TTG
TTGA GAA CCTCCTGGCTAA TGTCTA TCA TCA GA TAAA CCA TCT
GAA GA CA GTCCTGGAA GAAAAA CTGGA GAAA GAA GA TTTCA C
CA GGGGAAAA CTCA TGA GCA GTCTGCA CCTGAAAA GA TA TTA
TGGGA GGA TTCTGCA TTA CCTGAA GGCCAA GGA GTA CA GTCA
CTGTGCCTGGA CCA TA GTCA GA GTGGAAA TCCTAA GGAA CTT
TTA CTTCA TTAA CA GA CTT A CA GGTTA CCTCCGAAA CQGCGQA
GGTGGGAG 7TCTTATACCTACAATTATGAATGGCATGT
GGATGTCTGGGGACAGGGCCTGCTGGTGACAGTCTCT
AGTGCTTCCACAACTGCACCAAAGGTGTACCCCCTGT
CAAGCTGCTGTGGGGACAAATCCTCTAGTACCGTGAC
ACTGGGATGCCTGGTCTCAAGCTATATGCCCGAGCCT
GTGACTGTCACCTGGAACTCAGGAGCCCTGAAAAGCG
GAGTGCACACCTTCCCAGCTGTGCTGCAGTCCTCTGG
CCTGTATAGCCTGAGTTCAATGGTGACAGTCCCCGGCA
GTACTTCAGGGCAGACCTTCACCTGTAATGTGGCCCATCC
TGCCAGCTCCACCAAAGTGGACAAAGCAGTGGAACCCAA
ATCTTGCGACAAAA TCA ACA
A^CTG^CTCCJGGGGGGACCGTCAGTC
Figure imgf000213_0001
GAGGXCAC VTGjCGTGGTGG
CCTGAGGTCAACT^
GXGCATAAXGC^AAGACAAAGCCG
AACAGCA^GTACCGXGTGGTCAGCG
A^CAGGACTGGCTGA^TGGCAAGGACT
TCTCCAACAAAGCCCTC
TCTCCAAAGJ AAAGGG^
ACACCCTGJCCCCJ^^^
AGGTCAGCCTGACCTGCCT^
CGACATCGJ GXGGAGTGGG
GAACAACTACAAGAC
CGGCXCCTTCTTCCT
AGCAGGTGGCAGCAG
AXGCAXGAGGCXCTGjCACAAQ^ACXAC
CTCTCCCTGTCTCCGGGTAAA
bGCSF-LO CAGGTCCAGCTGAGAGAGAGCGGCCCTTCACTGGTCA
AGCCATCCCAGACACTGAGCCTGACATGCACAGCAAG CGGGTTTTCACTGAGCGACAAGGCAGTGGGATGGGTC
CGACAGGCACCAGGAAAAGCCCTGGAATGGCTGGGC
AGCATCGATACCGGCGGGAACACAGGGTACAATCCCG
GACTGAAGAGCAGACTGTCCATTACCAAGGACAACTC
TAAAAGTCAGGTGTCACTGAGCGTGAGCTCCGTCACC
ACAGAGGATAGTGCAACTTACTATTGCACCTCTGTGC
ACCAGGAAACTAAGAAATACCAGAG 4 CCCCCCTTGGC
CCTGCCCGA TCCCTGCCCCA GA GCTTCCTGCTCAA GTGCTTA
GA GCAA GTGA GGAAAA TCCA GGCTGA TGGCGCCGA GCTGCA
GGA GA GGCTGTGTGCCGCCCA CAA GCTGTGCCA CCCGGA G
GA GCTGA TGCTGCTCA GGCA CTCTCTGGGCA TCCCCCA GGC
TCCCCTAA GCA GCTGCTCCA GCCA GTCCCTGCA GCTGA CGA
GCTGCCTGAA CCAA CTA CA CGGCGGCCTCTTTCTCTA CCA GG
GCCTCCTGCA GGCCCTGGCGGGCA TCTCCCCA GA GCTGGCC
CCCA CCTTGGA CA CA CTGCA GCTGGA CGTCA CTGA CTTTGCC
A CGAA CA TCTGGCTGCA GA TGGA GGA CCTGGGGGCGGCCCC
CGCTGTGCA GCCCA CCCA GGGCGCCA TGCCGA CCTTCA CTT
CA GCCTTCCAA CGCA GA GCAGGA GGGGTCCTGGTTGCTTCC
CA GCTGCA TCGTTTCCTGGA GCTGGCA TA CCGTGGCCTGCG
CTA CCTTGCTGA (7CCCTCTTATACCTACAATTATGAATG
GCATGTGGATGTCTGGGGACAGGGCCTGCTGGTGACA
GTCTCTAGTGCTTCCACAACTGCACCAAAGGTGTACC
CCCTGTCAAGCTGCTGTGGGGACAAATCCTCTAGTAC
CGTGACACTGGGATGCCTGGTCTCAAGCTATATGCCC
GAGCCTGTGACTGTCACCTGGAACTCAGGAGCCCTGA
AAAGCGGAGTGCACACCTTCCCAGCTGTGCTGCAGTC
CTCTGGCCTGTATAGCCTGAGTTCAATGGTGACAGTC
CCCGGCAGTACTTCAGGGCAGACCTTCACCTGTAATG
TGGCCCATCCTGCCAGCTCCACCAAAGTGGACAAAGC
AGTGGAACCCAAATCTTGCGACAAAACTCACACATGCC
CACCCTGC_CCAGCA^
Figure imgf000214_0001
CJj CCGGAC_CCCTGAGGTCACA
GAGCC_ACGAAGACj CTGAGGTC
GGACGGCGTGGAGGTG^
Figure imgf000214_0002
CCTCACCGTCCTGCACCAGGACTGGCTGAATGGCAAGGA GTACAAGJGC GCTCTCC
CAXCGAGAAAACCATCTCJCAAAGCJ^
AGAACCA£AGGTC
GCTGACC GAACCAGGTCAGCCT
AGGCTTCTATCCCAGCGACAT^
CAATGGGCAGCCGGAGAACA^
CGTGCTGGACTCj GAj GGCTCCTTC^
CJ£AC(1GTGGACAA^
TTCTCAXGCJi^CGXGAJGCAXGAG
ACACGCAGAAGAGCCTCTCCCTGTCTCCGGGTAAA
bGCSF-Ll CAGGTCCAGCTGAGAGAGAGCGGCCCTTCACTGGTCA
AGCCATCCCAGACACTGAGCCTGACATGCACAGCAAG CGGGTTTTCACTGAGCGACAAGGCAGTGGGATGGGTC CGACAGGCACCAGGAAAAGCCCTGGAATGGCTGGGC AGCATCGATACCGGCGGGAACACAGGGTACAATCCCG GACTGAAGAGCAGACTGTCCATTACCAAGGACAACTC TAAAAGTCAGGTGTCACTGAGCGTGAGCTCCGTCACC ACAGAGGATAGTGCAACTTACTATTGCACCTCTGTGC ACCAGGAAACTAAGAAATACCAGAGC(7(7r(7(7r(7(7^(7(7^ TCTA CCCCCCTTGGCCCTGCCCGA TCCCTGCCCCA GA GCTTC CTGCTCAA GTGCTTA GA GCAA GTGA GGAAAA TCCA GGCTGA T GGCGCCGA GCTGCA GGA GA GGCTGTGTGCCGCCCA CAA GC TGTGCCA CCCGGA GGA GCTGA TGCTGCTCA GGCA CTCTCTG GGCA TCCCCCA GGCTCCCCTAA GCA GCTGCTCCA GCCA GTC CCTGCA GCTGA CGA GCTGCCTGAA CCAA CTA CA CGGCGGCC TCTTTCTCTA CCA GGGCCTCCTGCA GGCCCTGGCGGGCA TCT CCCCA GA GCTGGCCCCCA CCTTGGA CA CA CTGCA GCTGGA C GTCA CTGA CTTTGCCA CGAA CA TCTGGCTGCA GA TGGA GGAC CTGGGGGCGGCCCCCGCTGTGCA GCCCA CCCA GGGCGCCA TGCCGA CCTTCA CTTCA GCCTTCCAA CGCAGAGCAGGAGGG GTCCTGGTTGCTTCCCA GCTGCA TCGTTTCCTGGA GCTGGCA TA CCGTGGCCTGCGCTA CCTTGCTGA GCCCGGIGGCGGAGG
/47 7TCTTATACCTACAATTATGAATGGCATGTGGATG TCTGGGGACAGGGCCTGCTGGTGACAGTCTCTAGTGC TTCCACAACTGCACCAAAGGTGTACCCCCTGTCAAGC TGCTGTGGGGACAAATCCTCTAGTACCGTGACACTGG GATGCCTGGTCTCAAGCTATATGCCCGAGCCTGTGAC TGTCACCTGGAACTCAGGAGCCCTGAAAAGCGGAGTG
CACACCTTCCCAGCTGTGCTGCAGTCCTCTGGCCTGT
ATAGCCTGAGTTCAATGGTGACAGTCCCCGGCAGTAC
TTCAGGGCAGACCTTCACCTGTAATGTGGCCCATCCT
GCCAGCTCCACCAAAGTGGACAAAGCAGTGGAACCCA
AATCTTGCGACAAAACTCA^
CACCTGAACTCCTGGG^
COCAAAACCC GGACACCCT
TGAGGTCACATGCGXGGJGGTG^
CCCTGAGGXCAAGTJ^AACTGCTAm
GGTG^ATAATGi^CAAGA^AAAGCj^
A^AAC_AGi:ACGTACjCGJGTG
GCACCAGGACTGGCTG IGGC G
GGTCTCCAACAAAGCCCTCCC^
CATCTCCAAAGCC.AAAGGGCAGCC
GTACACCCTGCCCCCATCCCGGG^
CCAGGTCAGCCTGACCTGCCTGGT
AGCGACATCGCCGTGGAGTGGG
GAG C CTAC GACCACGCCTCCC
GACGGCTCCTTCTTCCTCT^
AGAGCAGGTGGCAGCAGGGGAAC
TGATGCATGAGGCTCTGCACAACCA
GCCTCTCCCTGTCTCCGGGTAAA
GMCSF CAGGTCCAGCTGAGAGAGAGCGGCCCTTCACTGGTCA
AGCCATCCCAGACACTGAGCCTGACATGCACAGCAAG
CGGGTTTTCACTGAGCGACAAGGCAGTGGGATGGGTC
CGACAGGCACCAGGAAAAGCCCTGGAATGGCTGGGC
AGCATCGATACCGGCGGGAACACAGGGTACAATCCCG
GACTGAAGAGCAGACTGTCCATTACCAAGGACAACTC
TAAAAGTCAGGTGTCACTGAGCGTGAGCTCCGTCACC
ACAGAGGATAGTGCAACTTACTATTGCACCTCTGTGC
ACCAGGAAACTAAGAAATACCAGAGC(7(7(7(7(77r7(7C(7(7
AAGCGCA CCCGCCCGCTCGCCCA GCCCCA GCA CGCA GCCCT
GGGAGCA TGTGAA TGCCA TCCA GGA GGCCCGGCGTCTCCTG
AA CCTGA GTA GA GA CA CTGCTGCTGA GA TGAA TGAAA CA GTA
GAA GTCA TCTCA GAAA TGTTTGA CCTCCA GGA GCCGA CCTGC
CTA CA GA CCCGCCTGGA GCTGTA CAA GCA GGGCCTGCGGGG CA GCCTCA CCAA GCTCAA GGGCCCCTTGA CCA TGA TGGCCA
GCCA CTA CAA GCA GCA CTGCCCTCCAA CCCCGGAAA CTTCCT
GTGCAA CCCA GA TTA TCA CCTTTGAAA GTTTCAAA GA GAA CCT
GAA GGA CTTTCTGCTTGTCA TCCCCTTTGA CTGCTGGGA GCC
A GTCCA GGA GGGCGGA GGTGGGA 77TCTT AT ACCTACAA
TTATGAATGGCATGTGGATGTCTGGGGACAGGGCCTG
CTGGTGACAGTCTCTAGTGCTTCCACAACTGCACCAA
AGGTGTACCCCCTGTCAAGCTGCTGTGGGGACAAATC
CTCTAGTACCGTGACACTGGGATGCCTGGTCTCAAGC
TATATGCCCGAGCCTGTGACTGTCACCTGGAACTCAG
GAGCCCTGAAAAGCGGAGTGCACACCTTCCCAGCTGT
GCTGCAGTCCTCTGGCCTGTATAGCCTGAGTTCAATG
GTGACAGTCCCCGGCAGTACTTCAGGGCAGACCTTCA
CCTGTAATGTGGCCCATCCTGCCAGCTCCACCAAAGT
GGACAAAGCAGTGGAACCCAAATCTTGCGACAAAACT
CACACATGJ CACCGT^
GGACCJJTCAGTCTO
CCCTCATGATCTCJ
GGTGGACGTGAGCC CG
CTGGTACGTGGACGGCGTGGAG
AAAGJXGJ:GGGAGGAGC^
GGTCAGCGTCCTCAC^GTCCTGCA^
GGCAAGGAGTACAAGTGCAAGG
CCAGCCCQ:ATCG^^
CAGCCCCGAGAACCACAGGTCT
CGGGATGAGCTGACJCAAGAACCAGGX^
Figure imgf000217_0001
GGGAGAGCAAIGGGCAGCCGGAGAA
A^GCCTCC^GTGCTGGACTCCGACGGC
ACAGC_AAGCTCA^
GGGAACGXCTTCTCAXGCTCCGJj AJG
A^AAC_CACTACACGi:AGAAGA^
GTAAA
hFGF21 CAGGTCCAGCTGAGAGAGAGCGGCCCTTCACTGGTCA
AGCCATCCCAGACACTGAGCCTGACATGCACAGCAAG CGGGTTTTCACTGAGCGACAAGGCAGTGGGATGGGTC CGACAGGCACCAGGAAAAGCCCTGGAATGGCTGGGC AGCATCGATACCGGCGGGAACACAGGGTACAATCCCG GACTGAAGAGCAGACTGTCCATTACCAAGGACAACTC TAAAAGTCAGGTGTCACTGAGCGTGAGCTCCGTCACC ACAGAGGATAGTGCAACTTACTATTGCACCTCTGTGC ACCAGGAAACTAAGAAATACCAGAGC(7(7(7(7(77r7(7C(7(7 AAGCCA CCCCA TCCCTGA CTCCA GTCCTCTCCTGCAA TTCGG GGGCCAA GTCCGGCA GCGGTA CCTCTA CA CA GA TGA TGCCC AGCAGA CA GAA GCCCA CCTGGA GA TCA GGGAGGATGGGA CG GTGGGGGGCGCTGCTGA CCA GA GCCCCGAAA GTCTCCTGCA GCTGAAA GCCTTGAA GCCGGGA GTTA TTCAAA TCTTGGGA GT CAA GA CA TCCA GGTTCCTGTGCCA GCGGCCA GA TGGGGCCC TGTA TGGA TCGCTCCA CTTTGA CCCTGA GGCCTGCA GCTTCC GGGA GCTGCTTCTTGA GGA CGGA TA CAA TGTTTA CCA GTCCG AA GCCCA CGGCCTCCCGCTGCA CCTGCCA GGGAA CAA GTCC CCA CA CCGGGA CCCTGCA CCCCGA GGA CCA GCTCGCTTCCT GCCA CTA CCA GGCCTGCCCCCCGCA CCCCCGGA GCCA CCC GGAA TCCTGGCCCCCCA GCC CCCCGA TGTGGGCTCCTCGGA CCCTCTGA GCA TGGTGGGA CCTTCCCA GGGCCGAA GCC CCA GCTA CGCTTCCGGCGGA GGTGGGA 77TCTT AT ACCT AC A A TTATGAATGGCATGTGGATGTCTGGGGACAGGGCCTG CTGGTGACAGTCTCTAGTGCTTCCACAACTGCACCAA AGGTGTACCCCCTGTCAAGCTGCTGTGGGGACAAATC CTCTAGTACCGTGACACTGGGATGCCTGGTCTCAAGC TATATGCCCGAGCCTGTGACTGTCACCTGGAACTCAG GAGCCCTGAAAAGCGGAGTGCACACCTTCCCAGCTGT GCTGCAGTCCTCTGGCCTGTATAGCCTGAGTTCAATG GTGACAGTCCCCGGCAGTACTTCAGGGCAGACCTTCA CCTGTAATGTGGCCCATCCTGCCAGCTCCACCAAAGT GGACAAAGCAGTGGAACCCAAATCTTGCGACAAAACT CACACATGJ CACCGTGC^
GGACC_GTCAGTCTTCCT^
CCCTCAIGATCTCCCGGA^^^
GGTGGACGTGAGCC CG ^
CJGGTACGTGGACGGCGTGGAQGTGC^
AAAG£CG GGGAGj AGCACT
GGTCAQCGTCCTCAa:GTC
GGC ^GGAGTACAAGTGC ^GG CTC^^ C_ AGCJ£CC£ATCG^
CAQCCCCGAGAACCACAGGJGT^
CGGGATGAGCXGAOCAAGAACCAG
Figure imgf000219_0001
GGGAGAGCAATGGj CA
A^GCCTCC^GTGCTGGACTCCGACGGC
A^AGC_AAGCTCACCGTGGACA^
GGG CGXCTTCTCAT_GCJC_CGJGAJG^
A^AAC_CACTACACGi:AGA GA^
GTAAA
Ex-4 CAGGTCCAGCTGAGAGAGAGCGGCCCTTCACTGGTCA
AGCCATCCCAGACACTGAGCCTGACATGCACAGCAAG
CGGGTTTTCACTGAGCGACAAGGCAGTGGGATGGGTC
CGACAGGCACCAGGAAAAGCCCTGGAATGGCTGGGC
AGCATCGATACCGGCGGGAACACAGGGTACAATCCCG
GACTGAAGAGCAGACTGTCCATTACCAAGGACAACTC
TAAAAGTCAGGTGTCACTGAGCGTGAGCTCCGTCACC
ACAGAGGATAGTGCAACTTACTATTGCACCTCTGTGC
ACCAGGAAACTAAGAAATACCAGAGCTGC(7(7(7(7(7r(7(7
CGGAAGCA TCGAA GGTCGTCA CGCTGA GGGAA CA TTCA CTTC
CGA TGTGTCCTCCTA CCTGGA GGGCCA GGCTGCCAAA GAGT
TCA TCGCTTGGCTCGTCAA GGGCA GGGGCGGAGGTGGGAGT
TGCTCTTATACCTACAATTATGAATGGCATGTGGATGT
CTGGGGACAGGGCCTGCTGGTGACAGTCTCTAGTGCT
TCCACAACTGCACCAAAGGTGTACCCCCTGTCAAGCT
GCTGTGGGGACAAATCCTCTAGTACCGTGACACTGGG
ATGCCTGGTCTCAAGCTATATGCCCGAGCCTGTGACT
GTCACCTGGAACTCAGGAGCCCTGAAAAGCGGAGTGC
ACACCTTCCCAGCTGTGCTGCAGTCCTCTGGCCTGTA
TAGCCTGAGTTCAATGGTGACAGTCCCCGGCAGTACT
TCAGGGCAGACCTTCACCTGTAATGTGGCCCATCCTG
CCAGCTCCACCAAAGTGGACAAAGCAGTGGAACCCAA
ATCTTGCGACAAAACT£ACACA
A^CTG^CTCCJGGGGGGACCGTCAGTC
Figure imgf000219_0002
GAGGXCACATGjCGTGGTGGTGGAm
CCTGAGGTCAAGTTCAACTGGTACGTGGACGGCGTGGAG GTGCATAAXGC^AAGACAAAG
AACAGCA^GTACCGTCTGGTCAGCGT
A^CAGGACTGGCTGA^TGGCAAGGACT
TCTCC CAAAGCCCTCCCAGCj ^
TCXCCAAAGCCAAAGGGj^AGj^CC^GA^
A^ACCCTGi:CCCj ATC_CCGGGA
AGGTCAGCCTGACCTGCCTGGXCA^
CGACATCGJ GXGGAGTGGGAGAG^
GAACAACXACAAGACCACGCCTC^CGXGC
CGGCXCCTXCXTCCXCTACAGj AAGCTCA^
AGCAQGTGGCAGCAGGGGAACGXCTXCTCAXG
AXGCA GAGGCXCTGjCACAAa:ACXACACG
CTCTCCCTGTCTCCGGGTAAA
hGLP-1 CAGGTCCAGCTGAGAGAGAGCGGCCCTTCACTGGTCA
AGCCATCCCAGACACTGAGCCTGACATGCACAGCAAG
CGGGTTTTCACTGAGCGACAAGGCAGTGGGATGGGTC
CGACAGGCACCAGGAAAAGCCCTGGAATGGCTGGGC
AGCATCGATACCGGCGGGAACACAGGGTACAATCCCG
GACTGAAGAGCAGACTGTCCATTACCAAGGACAACTC
TAAAAGTCAGGTGTCACTGAGCGTGAGCTCCGTCACC
ACAGAGGATAGTGCAACTTACTATTGCACCTCTGTGC
ACCAGGAAACTAAGAAATACCAGAGCTGC(7(7(7(7(7r(7(7
CGGAAGCA TCGAA GGTCGTCA CGCTGA GGGAA CA TTCA CTTC
CGA TGTGTCCTCCTA CCTGGA GGGCCA GGCTGCCAAA GAGT
TCA TCGCTTGGCTCGTCAA GGGCA GGGGCGGAGGTGGGAGT
TGCTCTTATACCTACAATTATGAATGGCATGTGGATGT
CTGGGGACAGGGCCTGCTGGTGACAGTCTCTAGTGCT
TCCACAACTGCACCAAAGGTGTACCCCCTGTCAAGCT
GCTGTGGGGACAAATCCTCTAGTACCGTGACACTGGG
ATGCCTGGTCTCAAGCTATATGCCCGAGCCTGTGACT
GTCACCTGGAACTCAGGAGCCCTGAAAAGCGGAGTGC
ACACCTTCCCAGCTGTGCTGCAGTCCTCTGGCCTGTA
TAGCCTGAGTTCAATGGTGACAGTCCCCGGCAGTACT
TCAGGGCAGACCTTCACCTGTAATGTGGCCCATCCTG
CCAGCTCCACCAAAGTGGACAAAGCAGTGGAACCCAA
ATCTTGCGACAAAACXCACACAXGC ACC_GTGjCC
ACCTGAACTCCTGGGGGGACCGTCAGTCTTCCTCTTCCCC CjCAAAACCjCAAGC^
GAGGTCACAT^
CCTCAGGTCAAGTTCA^
GTGCATAAXGC^AAGACAAAG
AACAGCA^GTACCGXGTGGTCAGCG
A^CAGGACTGGCTGA^TGGCAAGGACT
TCTCCAACAAAGCCCTCCCAGCj^
TCXCCAAAGCCAAAGGG
A^ACCCTGi:CCCj ATC_CCGGGA
AGGTCAGCCTGACCTGCCTGGXCA^
C_GACATCGJ GXGGAGTGGGAGAG
GAACAACXACAAGACCACGCCTCCICGXGCTC
Figure imgf000221_0001
AGCAGGTGGCAGCAGGGGAACGXCTXQTCA G
AXGCA GAGGCXCTGjCACAAa:ACXACACG
CTCTCCCTGTCTCCGGGTAAA
hEPO 10 CAGGTCCAGCTGAGAGAGAGCGGCCCTTCACTGGTCA
AGCCATCCCAGACACTGAGCCTGACATGCACAGCAAG CGGGTTTTCACTGAGCGACAAGGCAGTGGGATGGGTC CGACAGGCACCAGGAAAAGCCCTGGAATGGCTGGGC AGCATCGATACCGGCGGGAACACAGGGTACAATCCCG GACTGAAGAGCAGACTGTCCATTACCAAGGACAACTC TAAAAGTCAGGTGTCACTGAGCGTGAGCTCCGTCACC ACAGAGGATAGTGCAACTTACTATTGCACCTCTGTGC ACCAGGAAACTAAGAAATACCAGA( -£GGGGTGGCGG AAGCGCCCCA CCA C GCCTCA TCTGTGA CA GCCGA GTCCTGG AGAGGTA CCTCTTGGA GGCCAA GGA GGCCGA GAA TA TCA CG A CGGGCTGTGCTGAA CA CTGCA GCTTGAA TGA GAA TA TCA CT GTCCCA GA CA CCAAA GTTAA TTTCTA TGCCTGGAA GA GGA TG GA GGTCGGGCA GCA GGCCGTA GAA GTCTGGCA GGGCCTGG CCCTGCTGTCGGAA GCTGTCCTGCGGGGCCA GGCCCTGTTG GTCAA CTCTTCCCA GCCGTGGGA GCCC CTGCA GCTGCA TGT GGA TAAA GCCGTCA GTGGCCTTCGCA GCCTCA CCA CTCTGCT TCGGGCTCTGGGA GCCC A GAA GGAA GCCA TCTCCCCTCCA G ATGCGGCCTCAGCTGCTCCACTCCGAACAATCACTGCTGACA CTTTCCGCAAACTCTTCCGAGTCTACTCCAATTTCCTCCGGGG AAA GCTGAA GCTGTA CA CA GGGGA GGCCTGCA GGA CAGGGG A CA GA GGCGGA GGTGGGA 77TCTT AT ACCTACAATTATG
AATGGCATGTGGATGTCTGGGGACAGGGCCTGCTGGT
GACAGTCTCTAGTGCTTCCACAACTGCACCAAAGGTG
TACCCCCTGTCAAGCTGCTGTGGGGACAAATCCTCTA
GTACCGTGACACTGGGATGCCTGGTCTCAAGCTATAT
GCCCGAGCCTGTGACTGTCACCTGGAACTCAGGAGCC
CTGAAAAGCGGAGTGCACACCTTCCCAGCTGTGCTGC
AGTCCTCTGGCCTGTATAGCCTGAGTTCAATGGTGAC
AGTCCCCGGCAGTACTTCAGGGCAGACCTTCACCTGT
AATGTGGCCCATCCTGCCAGCTCCACCAAAGTGGACA
AAGCAGTGGAACCCAAATCTTGCGACAAAAC_TCAj ACA
TGJCCCACCCTGCJ ^
TCAGTCTTCCTCTTCCC
TGATCTCCC(TOACC^
AClGTGAGCjCACGAAGAC CCT
A^GTGGACGG^GTGGAGGTGJCAJA^
CGCGGGAGGAGCAGTACAACAGJ
G£GTCCTCACCGTC
AGGAGTA^AACT
CCJCCCATCGAGAA CCA CTCCAA^
COCGAGAACCACAGGTGT;ACACCCTC
Figure imgf000222_0001
TC_AAAGGCTTCTA^
AGAG^AATGGGCAGCCGGAG
CCTCCCGTGCTGGACT^
Gi^AAGCTCACCGTGGACAAGAG
AACGTCTTCTCAJGCTQCGTGAT^
A(1CACTACACG£AGAAGA
AA
Moka-LO 11 CAGGTCCAGCTGAGAGAGAGCGGCCCTTCACTGGTCA
AGCCATCCCAGACACTGAGCCTGACATGCACAGCAAG
CGGGTTTTCACTGAGCGACAAGGCAGTGGGATGGGTC
CGACAGGCACCAGGAAAAGCCCTGGAATGGCTGGGC
AGCATCGATACCGGCGGGAACACAGGGTACAATCCCG
GACTGAAGAGCAGACTGTCCATTACCAAGGACAACTC
TAAAAGTCAGGTGTCACTGAGCGTGAGCTCCGTCACC
ACAGAGGATAGTGCAACTTACTATTGCACCTCTGTGC ACCAGGAAACTAAGA A AT ACC AG AGCA TCAACGTGAAGT
GCA GCCTGCCCCA GCA GTGCA TCAA GCCCTGCAA GGA CGCC GGCA TGCGGTTCGGCAA GTGCA TGAA CAA GAA GTGCA GGTG CTA CA (7CTCTTATACCTACAATTATGAATGGCATGTGG
ATGTCTGGGGACAGGGCCTGCTGGTGACAGTCTCTAG
TGCTTCCACAACTGCACCAAAGGTGTACCCCCTGTCA
AGCTGCTGTGGGGACAAATCCTCTAGTACCGTGACAC
TGGGATGCCTGGTCTCAAGCTATATGCCCGAGCCTGT
GACTGTCACCTGGAACTCAGGAGCCCTGAAAAGCGGA
GTGCACACCTTCCCAGCTGTGCTGCAGTCCTCTGGCC
TGTATAGCCTGAGTTCAATGGTGACAGTCCCCGGCAG
TACTTCAGGGCAGACCTTCACCTGTAATGTGGCCCAT
CCTGCCAGCTCCACCAAAGTGGACAAAGCAGTGGAAC
CCAAATCTTGCGACAAAACTCACACATGCCCAC
CAQCACCJGAACTCCTG^
CCjCCCCj AAACj
CCCTGAGGTCAC^
AGACC_CTGAGGT;C GTTjCAACT
QGAGGTGCATAAT^C GACAAAGO^
Figure imgf000223_0001
TCCTGCACCAGGACJGGCTG^
Figure imgf000223_0002
AAACC_ATCTCCAAAGCCA GG
AGGTGTACACCCTGCJ CCCl^
AGAACCAGGTCAGCICTGA^
AXCCCAGCGACATCGCCGXGGAGTGGGAG GCCGGAGAACAACTA^
ACTCCGACGGCTCCTJCTTCCTCTA^
GGACAAGAGCAGGTGTC
CJj CGTGAJGCATGAGGCTCTGi:AC
GAAGAGCCTCTCCCTGTCTCCGGGTAAA
Moka-Ll 12 CAGGTCCAGCTGAGAGAGAGCGGCCCTTCACTGGTCA
AGCCATCCCAGACACTGAGCCTGACATGCACAGCAAG
CGGGTTTTCACTGAGCGACAAGGCAGTGGGATGGGTC
CGACAGGCACCAGGAAAAGCCCTGGAATGGCTGGGC
AGCATCGATACCGGCGGGAACACAGGGTACAATCCCG
GACTGAAGAGCAGACTGTCCATTACCAAGGACAACTC TAAAAGTCAGGTGTCACTGAGCGTGAGCTCCGTCACC
ACAGAGGATAGTGCAACTTACTATTGCACCTCTGTGC
ACCAGGAAACTAAGAAATACCAGAGC(7(7R(7(7R(7(7^(7(7^
TCT A TCAA CGTGAA GTGCA GCCTGCCCCA GCA GTGCA TCAA G
CCCTGCAA GGA CGCCGGCATGCGGTTCGGCAA GTGCA TGAA
CAA GAA GTGCA GGTGCTA CA GCGGA GGTGGTGGTTCATCTT
ATACCTACAATTATGAATGGCATGTGGATGTCTGGGG
ACAGGGCCTGCTGGTGACAGTCTCTAGTGCTTCCACA
ACTGCACCAAAGGTGTACCCCCTGTCAAGCTGCTGTG
GGGACAAATCCTCTAGTACCGTGACACTGGGATGCCT
GGTCTCAAGCTATATGCCCGAGCCTGTGACTGTCACC
TGGAACTCAGGAGCCCTGAAAAGCGGAGTGCACACCT
TCCCAGCTGTGCTGCAGTCCTCTGGCCTGTATAGCCT
GAGTTCAATGGTGACAGTCCCCGGCAGTACTTCAGGG
CAGACCTTCACCTGTAATGTGGCCCATCCTGCCAGCT
CCACCAAAGTGGACAAAGCAGTGGAACCCAAATCTTG
CGACAAAACTCACACA^^^
ACTCCTGGGGGGACJ CT
COCAAGGACAC_CCI^
ACATGJCGIGGTGGTGGA^^^
Figure imgf000224_0001
AAIGCCAAGACAAAGCm
CACGJACCGTGXGGJi:AGi:GTCCTCAC
GACTGQCJGAAXGGCA
AACAAAGCCCXCCCAGQ C^^
AAAGj CAAAGGGCAG^CCCGAGA^
CTGCCCXCATCCCGGGATGAGCTGA
AGCCTGACCTG^CTGGTCAAAGGCTTC
TCGCCGTGGAGXGGGAGAGCAAJG^
AACTAjCAAGAC_CACGCCXCCCGT
TCCTTCTTCCXCXACAGCAAGCTCACCGX
GGTGGCAGCAGGGGAACGXQTT
AXGAGGCXQTG^ACAACCACTACAC_G
CCCTGTCTCCGGGTAAA
VM-24-L1 13 CAGGTCCAGCTGAGAGAGAGCGGCCCTTCACTGGTCA
AGCCATCCCAGACACTGAGCCTGACATGCACAGCAAG CGGGTTTTCACTGAGCGACAAGGCAGTGGGATGGGTC CGACAGGCACCAGGAAAAGCCCTGGAATGGCTGGGC
AGCATCGATACCGGCGGGAACACAGGGTACAATCCCG
GACTGAAGAGCAGACTGTCCATTACCAAGGACAACTC
TAAAAGTCAGGTGTCACTGAGCGTGAGCTCCGTCACC
ACAGAGGATAGTGCAACTTACTATTGCACCTCTGTGC
ACCAGGAAACTAAGAAATACCAGAGC(7(7(7(7(77r7(7C(7(7
AAGCGCCGCTGCAATCTCCTGCGTCGGCAGCCCCGAATGTC
CTCCCAA GTGCCGGGCTCA GGGA TGCAA GAA CGGCAA GTGT
A TGAA CCGGAA GTGCAA GTGCTA CTA TTGCGGCGGAGGTGG
7 f 7TCTTATACCTACAATTATGAATGGCATGTGGATG
TCTGGGGACAGGGCCTGCTGGTGACAGTCTCTAGTGC
TTCCACAACTGCACCAAAGGTGTACCCCCTGTCAAGC
TGCTGTGGGGACAAATCCTCTAGTACCGTGACACTGG
GATGCCTGGTCTCAAGCTATATGCCCGAGCCTGTGAC
TGTCACCTGGAACTCAGGAGCCCTGAAAAGCGGAGTG
CACACCTTCCCAGCTGTGCTGCAGTCCTCTGGCCTGT
ATAGCCTGAGTTCAATGGTGACAGTCCCCGGCAGTAC
TTCAGGGCAGACCTTCACCTGTAATGTGGCCCATCCT
GCCAGCTCCACCAAAGTGGACAAAGCAGTGGAACCCA
AATCTTGCGACAAAACTCA^
CACCJGAACTCCTGGGGGGAOC
COCAAAACCC GGACACCCT
TGAGGTCACATGCGXGGJGGTG^
C 1CTGAGGXCAAGTJ AACT
GGTG^ATAATGi^CAAGA^AAAGCj^
Figure imgf000225_0001
GCACCAGGACTGGCTG TGGC
GGTCJC_CAACAAAGi:CCJj CCAG^
CAICTQCAAAGCCAAAGGGCAG^
GTACAjCCCT_GCCj CCATCCC_GGG^
CCAGGTCAGCCTGAC_CT
AGCGACAXCG^CGTGGAGTGGGAGAGC
GAG C CTACAAGAj CAC_GCCTCCC_GTG
GACGGCTCCTTCTTCCJCT
AGAG^AGGTGGCAGCAGGGGA^
TGATGJ ATGAGGCTCT
GC_CTCTjCCCTGTCT_CCGGGTAAA VM-24-L2 14 CAGGTCCAGCTGAGAGAGAGCGGCCCTTCACTGGTCA
AGCCATCCCAGACACTGAGCCTGACATGCACAGCAAG
CGGGTTTTCACTGAGCGACAAGGCAGTGGGATGGGTC
CGACAGGCACCAGGAAAAGCCCTGGAATGGCTGGGC
AGCATCGATACCGGCGGGAACACAGGGTACAATCCCG
GACTGAAGAGCAGACTGTCCATTACCAAGGACAACTC
TAAAAGTCAGGTGTCACTGAGCGTGAGCTCCGTCACC
ACAGAGGATAGTGCAACTTACTATTGCACCTCTGTGC
ACCAGGAAACTAAGA A AT ACC AG AGCGGCGGTGGA TCT
GGGGGTGGCGGA GCGCCGCTGCAATCTCCTGCGTCGGCA
GCCCCGAA TGTCCTCCCAA GTGCCGGGCTCA GGGA TGCAA G
AA CGGCAA GTGTA TGAA CCGGAA GTGCAA GTGCTA CTA TTGC
GGCGGA GGTGGGA GTGGA GGCGGTA 7C7TCTT AT ACCT AC
AATTATGAATGGCATGTGGATGTCTGGGGACAGGGCC
TGCTGGTGACAGTCTCTAGTGCTTCCACAACTGCACC
AAAGGTGTACCCCCTGTCAAGCTGCTGTGGGGACAAA
TCCTCTAGTACCGTGACACTGGGATGCCTGGTCTCAA
GCTATATGCCCGAGCCTGTGACTGTCACCTGGAACTC
AGGAGCCCTGAAAAGCGGAGTGCACACCTTCCCAGCT
GTGCTGCAGTCCTCTGGCCTGTATAGCCTGAGTTCAA
TGGTGACAGTCCCCGGCAGTACTTCAGGGCAGACCTT
CACCTGTAATGTGGCCCATCCTGCCAGCTCCACCAAA
GTGGACAAAGCAGTGGAACCCAAATCTTGCGA£AAAA
CI£ACACATGCCJ AC^^^
GGGA CGXCAG_TCTJ CT
ACJ TCATGATCTC^
TGGTGGACGTGAGC^
ACITGGXACGTGGACGG
CAAAGCCGCGGGAGG
Figure imgf000226_0001
TGGCAAGGAGTACAAGTGCAAGGTC
COCAGjCCQ AXCGAGA^
Figure imgf000226_0002
CCGGGATGAGCTGA^
CCTGGXCAAAGGCTJCTATCCCAG
GXGGGAGAGCAATGGGj AGj CGGAG_^
CCACGCCTCCCGTGCTGGACTCCGACGGCTCCTTCTTCCT CJACAGCAAGCTCA^CGJGGACAAG
Figure imgf000227_0001
CACAACCACTA ACGCA GGTAAA
Protoxin2-Ll 15 CAGGTCCAGCTGAGAGAGAGCGGCCCTTCACTGGTCA
AGCCATCCCAGACACTGAGCCTGACATGCACAGCAAG
CGGGTTTTCACTGAGCGACAAGGCAGTGGGATGGGTC
CGACAGGCACCAGGAAAAGCCCTGGAATGGCTGGGC
AGCATCGATACCGGCGGGAACACAGGGTACAATCCCG
GACTGAAGAGCAGACTGTCCATTACCAAGGACAACTC
TAAAAGTCAGGTGTCACTGAGCGTGAGCTCCGTCACC
ACAGAGGATAGTGCAACTTACTATTGCACCTCTGTGC
ACCAGGAAACTAAGAAATACCAGAGC(7(7(7(7(77R7(7C(7(7
AAGCTA CTGCCA GAAA TGGA TGTGGA CCTGCGA CTCTGAA CG
TAAATGCTGCGAAGGTATGGTTTGCCGTCTGTGGTGCAAAAA
AAAA CTGTGGGGCGGA GGTGGGA 77TCTT AT ACCT AC A AT
TATGAATGGCATGTGGATGTCTGGGGACAGGGCCTGC
TGGTGACAGTCTCTAGTGCTTCCACAACTGCACCAAA
GGTGTACCCCCTGTCAAGCTGCTGTGGGGACAAATCC
TCTAGTACCGTGACACTGGGATGCCTGGTCTCAAGCT
ATATGCCCGAGCCTGTGACTGTCACCTGGAACTCAGG
AGCCCTGAAAAGCGGAGTGCACACCTTCCCAGCTGTG
CTGCAGTCCTCTGGCCTGTATAGCCTGAGTTCAATGG
TGACAGTCCCCGGCAGTACTTCAGGGCAGACCTTCAC
CTGTAATGTGGCCCATCCTGCCAGCTCCACCAAAGTG
GACAAAGCAGTGGAACCCAAATCTTGCGACAAAACTC
A^ACAIGCJ AJ GTGCC^
GACCGTCAGTCTTCCTCT^
CCTCATGAJCTCO GGACCC_C
GXGGACGXGAGCCACGAAGACCCXGAGG
Figure imgf000227_0002
GXCAGjCGXCCTCACCGTCCXGCAjCCA
Gi^AAGGAGTA^AAGTGi^AAGGT
CAGCOCCCATCGAGAA CCATCXCCA^
AGCCCjCGAGAACCACAGGTGXACACCCT
GGGATGAGCTGACCAAGAACCAGGTCAGCCTGACCTGCC TGGTCAAAGGCTTCTATCCCAGCGACATCGCCGTGGAGT
GGGAGAGCAATGGGCAGCCGGAGAACAACTACAAGACC
ACGCCTCCCGTGCTGGACTCCGACGGCTCCTTCTTCCTCT
ACAGCAAGCTCACCGTGGACAAGAGCAGGTGGCAGCAG
GGGAACGTCTTCTCATGCTCCGTGATGCATGAGGCTCTGC
ACAACCACTACACGCAGAAGAGCCTCTCCCTGTCTCCGG
GTAAA
For SEQ ID NOS: 2-15
bovine heavy chain sequence = bold
human heavy chain sequence = dashed underline
non-antibody sequence = italic
Stalk = bold, underline; knob = bold, double underline; linker
Figure imgf000228_0001
Table 20.
Description SEQ ID Sequence
NO:
BLV1H12-IL8 16 CAGGTCCAGCTGAGAGAGAGCGGCCCTTCACTGGTCAA
GCCATCCCAGACACTGAGCCTGACATGCACAGCAAGCG
GGTTTTCACTGAGCGACAAGGCAGTGGGATGGGTCCGAC
AGGCACCAGGAAAAGCCCTGGAATGGCTGGGCAGCATC
GATACCGGCGGGAACACAGGGTACAATCCCGGACTGAA
GAGCAGACTGTCCATTACCAAGGACAACTCTAAAAGTCA
GGTGTCACTGAGCGTGAGCTCCGTCACCACAGAGGATAG
TGCAACTTACTATTGCACCTCTGTGCACCAGGAAACTAA
GAAATACCAGAGCCCAAGGAGTGCTAAAGAACTTAGAT
GTCAGTGCATAAAGACATACTCCAAACCTTTCCACCCCA
AGTTCATCAAGGAGCTGAGAGTGATTGAGAGTGGACCA
CACTGCGCCAACACAGAGATTATTGTAAAGCTTTCTGAT
GGGAGAGAGCTCTGCCTGGACCCCAAGGAAAACTGGGT
GCAGAGGGTCGTGGAGAAGTTCTTGAAGAGGGCTGAGA
ACTCAGGCAGCGGTTCTTATACCTACAATTATGAATGGC
ATGTGGATGTCTGGGGACAGGGCCTGCTGGTGACAGTC
BLV1H12- 17 CAGGTCCAGCTGAGAGAGAGCGGCCCTTCACTGGTCAA Ziconotide GCCATCCCAGACACTGAGCCTGACATGCACAGCAAGCG
GGTTTTCACTGAGCGACAAGGCAGTGGGATGGGTCCGAC
AGGCACCAGGAAAAGCCCTGGAATGGCTGGGCAGCATC
GATACCGGCGGGAACACAGGGTACAATCCCGGACTGAA
GAGCAGACTGTCCATTACCAAGGACAACTCTAAAAGTCA
GGTGTCACTGAGCGTGAGCTCCGTCACCACAGAGGATAG
TGCAACTTACTATTGCACCTCTGTGCACCAGGAAACTAA
GAAATACCAGAGCTGCAAGGGCAAAGGTGCGAAATGCA
GCCGCCTGATGTATGATTGCTGTACCGGGTCCTGCCGCA
GTGGCAAGTGCTCTTATACCTACAATTATGAATGGCATG
TGGATGTCTGGGGACAGGGCCTGCTGGTGACAGTC
BLV1H12- 18 CAGGTCCAGCTGAGAGAGAGCGGCCCTTCACTGGTCAA Somatostatin GCCATCCCAGACACTGAGCCTGACATGCACAGCAAGCG
GGTTTTCACTGAGCGACAAGGCAGTGGGATGGGTCCGAC AGGCACCAGGAAAAGCCCTGGAATGGCTGGGCAGCATC GATACCGGCGGGAACACAGGGTACAATCCCGGACTGAA
GAGCAGACTGTCCATTACCAAGGACAACTCTAAAAGTCA
GGTGTCACTGAGCGTGAGCTCCGTCACCACAGAGGATAG
TGCAACTTACTATTGCACCTCTGTGCACCAGGAAACTAA
GAAATACCAGAGCGCTGGCTGCAAGAATTTCTTCTGGAA
GACTTTCACATCCTGTGGTTCTTATACCTACAATTATGAA
TGGCATGTGGATGTCTGGGGACAGGGCCTGCTGGTGACA
GTC
BLV1H12- 19 CAGGTCCAGCTGAGAGAGAGCGGCCCTTCACTGGTCAA Chlorotoxin GCCATCCCAGACACTGAGCCTGACATGCACAGCAAGCG
GGTTTTCACTGAGCGACAAGGCAGTGGGATGGGTCCGAC
AGGCACCAGGAAAAGCCCTGGAATGGCTGGGCAGCATC
GATACCGGCGGGAACACAGGGTACAATCCCGGACTGAA
GAGCAGACTGTCCATTACCAAGGACAACTCTAAAAGTCA
GGTGTCACTGAGCGTGAGCTCCGTCACCACAGAGGATAG
TGCAACTTACTATTGCACCTCTGTGCACCAGGAAACTAA
GAAATACCAGAGCATGTGTATGCCCTGCTTCACGACCGA
TCACCAGATGGCGCGCAAATGCGATGACTGTTGCGGCGG
TAAAGGTCGCGGAAAGTGCTATGGCCCGCAGTGTCTGTC
TTATACCTACAATTATGAATGGCATGTGGATGTCTGGGG
ACAGGGCCTGCTGGTGACAGTC
BLV1H12- 20 CAGGTCCAGCTGAGAGAGAGCGGCCCTTCACTGGTCAA SDF1 (alpha) GCCATCCCAGACACTGAGCCTGACATGCACAGCAAGCG
GGTTTTCACTGAGCGACAAGGCAGTGGGATGGGTCCGAC
AGGCACCAGGAAAAGCCCTGGAATGGCTGGGCAGCATC
GATACCGGCGGGAACACAGGGTACAATCCCGGACTGAA
GAGCAGACTGTCCATTACCAAGGACAACTCTAAAAGTCA
GGTGTCACTGAGCGTGAGCTCCGTCACCACAGAGGATAG
TGCAACTTACTATTGCACCTCTGTGCACCAGGAAACTAA
GAAATACCAGAGCAAGCCCGTCAGCCTGAGCTACAGAT
GCCCATGCCGATTCTTCGAAAGCCATGTTGCCAGAGCCA
ACGTCAAGCATCTCAAAATTCTCAACACTCCAAACTGTG
CCCTTCAGATTGTAGCCCGGCTGAAGAACAACAACAGAC
AAGTGTGCATTGACCCGAAGCTAAAGTGGATTCAGGAGT
ACCTGGAGAAAGCTTTAAACAAGGGCAGCGGTTCTTATA
CCTACAATTATGAATGGCATGTGGATGTCTGGGGACAGG
GCCTGCTGGTGACAGTC
BLV1H12- 21 CAGGTCCAGCTGAGAGAGAGCGGCCCTTCACTGGTCAA IL21 GCCATCCCAGACACTGAGCCTGACATGCACAGCAAGCG
GGTTTTCACTGAGCGACAAGGCAGTGGGATGGGTCCGAC
AGGCACCAGGAAAAGCCCTGGAATGGCTGGGCAGCATC
GATACCGGCGGGAACACAGGGTACAATCCCGGACTGAA
GAGCAGACTGTCCATTACCAAGGACAACTCTAAAAGTCA
GGTGTCACTGAGCGTGAGCTCCGTCACCACAGAGGATAG
TGCAACTTACTATTGCACCTCTGTGCACCAGGAAACTAA
GAAATACCAGAGCCAAGGTCAAGATCGCCACATGATCA
GAATGCGTCAGCTCATAGATATTGTTGATCAGCTGAAGA
ACTACGTGAACGACTTGGTCCCTGAATTTCTGCCAGCTC
CCGAAGATGTAGAGACAAACTGTGAGTGGTCAGCCTTCT
CCTGCTTTCAGAAGGCCCAACTAAAGTCAGCAAATACCG
GCAACAACGAGAGGATAATCAATGTATCAATCAAAAAG
CTGAAGAGGAAGCCACCTTCCACAAATGCAGGGAGACG
GCAGAAACACCGCCTGACATGCCCTTCATGTGATTCTTA
CGAGAAGAAGCCACCCAAAGAGTTCCTAGAGCGGTTCA
AGTCACTTCTCCAAAAGATGATTCATCAGCATCTGTCCT
CTCGCACACACGGAAGTGAAGATTCCTCTTATACCTACA ATTATGAATGGCATGTGGATGTCTGGGGACAGGGCCTGC
TGGTGACAGTC
BLV1H12- 22 CAGGTCCAGCTGAGAGAGAGCGGCCCTTCACTGGTCAA ProTxII GCCATCCCAGACACTGAGCCTGACATGCACAGCAAGCG
GGTTTTCACTGAGCGACAAGGCAGTGGGATGGGTCCGAC
AGGCACCAGGAAAAGCCCTGGAATGGCTGGGCAGCATC
GATACCGGCGGGAACACAGGGTACAATCCCGGACTGAA
GAGCAGACTGTCCATTACCAAGGACAACTCTAAAAGTCA
GGTGTCACTGAGCGTGAGCTCCGTCACCACAGAGGATAG
TGCAACTTACTATTGCACCTCTGTGCACCAGGAAACTAA
GAAATACCAGAGCTATTGCCAGAAGTGGATGTGGACCT
GCGATAGCGAACGGAAATGTTGCGAAGGCATGGTGTGC
CGCCTGTGGTGCAAGAAGAAACTCTGGTCTTATACCTAC
AATTATGAATGGCATGTGGATGTCTGGGGACAGGGCCTG
CTGGTGACAGTC
Table 21.
Figure imgf000230_0001
QKSLSLSPGK
bGCSF- 26 QVQLRESGPSLVKPSQTLSLTCTASGFSLSDKAVGWVRQAPG LO KALEWLGSIDTGGNTGYNPGLKSRLSITKDNSKSQVSLSVSSV
TTEOSATYYCTSYttOETKKYOSTPLGPARSLPOSFLLKCLEOVRKI
QADGAELQERLCAAHKLCHPEELMLLRHSLGIPQAPLSSCSSQSLQLT
SCLNQLHGGLFL YQGLL QALA GISPELAPTLDTL QLD VTDFA TNIWL Q
MEDLGAAPA VQPTQGAMPTFTSAFQRRAGGVLVASQLHRFLELAYRG
LRFL ^ SYTYNYEWHVDVWGOGLLVTVSSASTTAPKVYPLSS
CCGDKSSSTVTLGCLVSSYMPEPVTVTWNSGALKSGVHTFPA
VLQSSGLYSLSSMVTVPGSTSGQTFTCNVAHPASSTKVDKAVE
PKSCDKTHTCPPCPAPELLGGPSVFLFPPKPKDTLMISRTPEVTCV
WDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRWSV
LTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVY
TLPPSRDELTK QVSLTCLVKGFYPSDIAVEWESNGQPEN YKTT
PPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQ
KSLSLSPGK
bGCSF- 27 QVQLRESGPSLVKPSQTLSLTCTASGFSLSDKAVGWVRQAPG Ll KALEWLGSIDTGGNTGYNPGLKSRLSITKDNSKSQVSLSVSSV
TTEOSATYYCTSYttOETKKYOSGGGGSTPLGPARSLPOSFLLKCL
EQVRKIQADGAELQERLCAAHKLCHPEELMLLRHSLGIPQAPLSSCSS
QSLQLTSCLNQLHGGLFL YQGLLQALA GISPELAPTLDTLQLD VTDFA
TNIWLQMEDLGAAPA VQPTQGAMPTFTSAFQRRAGGVL VASQLHRFL
ELAYRGLRYLAEPGGGGSSYTYNYILWHVOYWGOGLLYTYSSAS
TTAPKVYPLSSCCGDKSSSTVTLGCLVSSYMPEPVTVTWNSGA
LKSGVHTFPAVLQSSGLYSLSSMVTVPGSTSGQTFTCNVAHPA
SSTKVDKAVEPKSCDKTHTCPPCPAPELLGGPSVFLFPPKPKDTL
MISRTPEVTCVWDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQ
YNSTYRWSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKA
KGQPREPQVYTLPPSRDELTK QVSLTCLVKGFYPSDIAVEWESN
GQPEN YKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVM HEALHNHYT QKSLSLSPGK
GMCSF 28 QVQLRESGPSLVKPSQTLSLTCTASGFSLSDKAVGWVRQAPG
KALEWLGSIDTGGNTGYNPGLKSRLSITKDNSKSQVSLSVSSV
TTEOSATYYCTSYttOETKKYOSGGGGSAPARSPSPSTOPWEHVN
AIQEARRLLNLSRDTAAEMNETVEVISEMFDLQEPTCLQTRLELYKQG LRGSLTKLKGPLTMMASHYKQHCPPTPETSCATQIITFESFKENLKDF LLVIPFDCWEPVOEGGGGSSYTYNYEWttYOYWGOGLLYTYSSA STTAPKVYPLSSCCGDKSSSTVTLGCLVSSYMPEPVTVTWNSG ALKSGVHTFPAVLQSSGLYSLSSMVTVPGSTSGQTFTCNVAHP
ASSTKVDKAVEPKSCDKTHTCPPCPAPELLGGPSVFLFPPKPKDT LMISRTPEVTCVWDVSHEDPEVKFNWYVDGVEVHNAKTKPREE
QYNSTYRWSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISK AKGQPREPQVYTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWES
NGQPEN YKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSV
MHEALHNHYTQKSLSLSPGK
hFGF21 29 QVQLRESGPSLVKPSQTLSLTCTASGFSLSDKAVGWVRQAPG
KALEWLGSIDTGGNTGYNPGLKSRLSITKDNSKSQVSLSVSSV
TTEOSATYYCTSYttOETKKYOSGGGGSHPIPDSSPLLOFGGOVR QR YL YTDDA QQTEAHLEIREDGTVGGAADQSPESLL QLKALKPG VIQI L G VKTSRFL CQRPDGAL YGSLHFDPEA CSFRELLLEDGYNVYQSEAH GLPLHLPGNKSPHRDPAPRGPARFLPLPGLPPAPPEPPGILAPQPPD VGSSDPLSMVGPSOGRSPSYASGGGGSSYTYNYKWWVOVWGOGL LVTVSSASTTAPKVYPLSSCCGDKSSSTVTLGCLVSSYMPEPVT VTWNSGALKSGVHTFPAVLQSSGLYSLSSMVTVPGSTSGQTFT CNVAHPASSTKVDKAVEPKSCDKTHTCPPCPAPELLGGPSVFLFP
PKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAK
TKPREEQYNSTYRWSVLTVLHQDWLNGKEYKCKVSNKALPAPI
EKTISKAKGQPREPQVYTLPPSRDELTK QVSLTCLVKGFYPSDIA
VEWESNGQPEN YKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNV
FSCSVMHEALHNHYTQKSLSLSPGK
Ex-4 30 QVQLRESGPSLVKPSQTLSLTCTASGFSLSDKAVGWVRQAPG
KALEWLGSIDTGGNTGYNPGLKSRLSITKDNSKSQVSLSVSSV
TTEDSATYYCTSVHOETKKYOSCGGGGSffiGRHG^Gr rS LS^
OMEEEA VRLFIEWLKNGGPSSGAPPPSGGGGSCSYTYNYEWHVOY
WGQGLLVTVSSASTTAPKVYPLSSCCGDKSSSTVTLGCLVSSY
MPEPVTVTWNSGALKSGVHTFPAVLQSSGLYSLSSMVTVPGS
TSGQTFTCNVAHPASSTKVDKAVEPKSCDKTHTCPPCPAPELLG
GPSVFLFPPKPKDTLMISRTPEVTCVWDVSHEDPEVKFNWYVDG
VEVHNAKTKPREEQYNSTYRWSVLTVLHQDWLNGKEYKCKVS
NKALPAPIEKTISKAKGQPREPQVYTLPPSRDELTK QVSLTCLVK
GFYPSDIAVEWESNGQPEN YKTTPPVLDSDGSFFLYSKLTVDKS
RWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK
hGLP-1 31 QVQLRESGPSLVKPSQTLSLTCTASGFSLSDKAVGWVRQAPG
KALEWLGSIDTGGNTGYNPGLKSRLSITKDNSKSQVSLSVSSV TTEDSATYYCTSVHOETKKYOSCGGGGS/£GRH £Gr rS£> VSSY
LEGQAAKEFIA WL F^GRGGGGSCSYTYNYEWHVDVWGOGLLVT
VSSASTTAPKVYPLSSCCGDKSSSTVTLGCLVSSYMPEPVTVT
WNSGALKSGVHTFPAVLQSSGLYSLSSMVTVPGSTSGQTFTCN
VAHPASSTKVDKAVEPKSCDKJOT^
P_™XLMISRXP_EVTCVVYDV
PREEQYNSXYRVVSyLXVLHQPW
TISKAKGQPI EPQ YTLPP_Sj D
.WESNGQPE YK XPPV^
CSVMHEALiWHYXQKSXSLSPGK
hEPO 32 QVQLRESGPSLVKPSQTLSLTCTASGFSLSDKAVGWVRQAPG
KALEWLGSIDTGGNTGYNPGLKSRLSITKDNSKSQVSLSVSSV
TTEDSATYYCTSVHOETKKYOSGGGGS PPRL/C SR VLER YLLE
AKEAENITTGCAEHCSLNENITVPDTKVNFYA WKRMEVGQQA VEVWQ
GLALLSEA VLRGQALL VNSSQPWEPLQLHVDKA VSGLRSLTTLLRALG
A QKEAISPPDAASAAPLR TITADTFRKLFR VYSNFLR GKLKL YTGEA CR
rG RGGGGSSYTYNYEWHVDVWGOGLLVTVSSASTTAPKVYP
LSSCCGDKSSSTVTLGCLVSSYMPEPVTVTWNSGALKSGVHTF
PAVLQSSGLYSLSSMVTVPGSTSGQTFTCNVAHPASSTKVDKA
VEPKSCDKTHTCPPCPAPELLGGPS LF
CVV\X)VSHEPXEVKFNWY DG^
.SYLXyLHQDWLNOT
Y LPPSRDELXiC^^^
TPPVLDSDGSJET^
QKSLSLSPGK
Moka- 33 QVQLRESGPSLVKPSQTLSLTCTASGFSLSDKAVGWVRQAPG L0 KALEWLGSIDTGGNTGYNPGLKSRLSITKDNSKSQVSLSVSSV
TTEDSATYYCTSVHOETKKYOS/NF^CSLfQQC/^C^ GMRF
G^C N CRCFSSYTYNYEWHVDVWGOGLLVTVSSASTTAPK
VYPLSSCCGDKSSSTVTLGCLVSSYMPEPVTVTWNSGALKSGV
HTFPAVLQSSGLYSLSSMVTVPGSTSGQTFTCNVAHPASSTKV
DKAVEPKSCD H CPPCXAPELXGGP_S LFPP
EWC_YV DV_SHEDP
RYVSJVLTVLHQDWLNG]^
EP_QVYTLPP DELX™(iVSLXCLVK^
i-TKTTPPyLJDSPJ SFFL
NHYTQKSXSLSPGK Moka- 34 QVQLRESGPSLVKPSQTLSLTCTASGFSLSDKAVGWVRQAPG Ll KALEWLGSIDTGGNTGYNPGLKSRLSITKDNSKSQVSLSVSSV
TTEOSATYYCTSYttOETKKYOSGGGGSINVKCSLPOOCIKPCKDA
GMRFGKCMNKKCRCYSGGGGSSYTYNYEWttYOYWGOGLLYTY
SSASTTAPKVYPLSSCCGDKSSSTVTLGCLVSSYMPEPVTVTW
NSGALKSGVHTFPAVLQSSGLYSLSSMVTVPGSTSGQTFTCNV
AHPASSTKVDKAVEPKSCDKTHTCPPCPAPELLGGPSVFLFPPKP
KDTLMISRTPEVTCVWDVSHEDPEVKFNWYVDGVEVHNAKTKP
REEQYNSTYRWSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKT
ISKAKGQPREPQVYTLPPSRDELTK QVSLTCLVKGFYPSDIAVE
WESNGQPEN YKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFS
CSVMHEALHNHYTQKSLSLSPGK
VM-24- 35 QVQLRESGPSLVKPSQTLSLTCTASGFSLSDKAVGWVRQAPG Ll KALEWLGSIDTGGNTGYNPGLKSRLSITKDNSKSQVSLSVSSV
TTEOSATYYCTSYtlOETKKYOSGGGGSAAAISCVGSPECPPKCRA OGCKNGKCMNRKCKCYYCGGGGSSYTYNYEW VOYWGOGLLY TVSSASTTAPKVYPLSSCCGDKSSSTVTLGCLVSSYMPEPVTVT WNSGALKSGVHTFPAVLQSSGLYSLSSMVTVPGSTSGQTFTCN VAHPASSTKVDKAVEPKSCDKTHTCPPCPAPELLGGPSVFLFPPK
PKDTLMISRTPEVTCVWDVSHEDPEVKFNWYVDGVEVHNAKTK
PREEQYNSTYRWSVLTVLHQDWLNGKEYKCKVSNKALPAPIEK
TISKAKGQPREPQVYTLPPSRDELTK QVSLTCLVKGFYPSDIAVE
WESNGQPEN YKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFS
CSVMHEALHNHYTQKSLSLSPGK
VM-24- 36 QVQLRESGPSLVKPSQTLSLTCTASGFSLSDKAVGWVRQAPG L2 KALEWLGSIDTGGNTGYNPGLKSRLSITKDNSKSQVSLSVSSV
TTEDSATYYCTSVHOETKKYOSGGGSGGGGS β,CFGS/,£'C/,/,
KCRAOGCKNGKCMNRKCKCYYCGGGGSGGGSSYTYNYEWWVOY
WGQGLLVTVSSASTTAPKVYPLSSCCGDKSSSTVTLGCLVSSY
MPEPVTVTWNSGALKSGVHTFPAVLQSSGLYSLSSMVTVPGS
TSGQTFTCNVAHPASSTKVDKAVEPKSCDKTHTCPPCPAPELLG
GPSVFLFPPKPKDTLMISRTPEVTCVWDVSHEDPEVKFNWYVDG
VEVFTNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVS
NKALPAPIEKTISKAKGQPREPQVYTLPPSRDELTKNQVSLTCLVK
GFYPSDIAVEWESNGQPEN YKTTPPVLDSDGSFFLYSKLTVDKS
RWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK
Protoxin 37 QVQLRESGPSLVKPSQTLSLTCTASGFSLSDKAVGWVRQAPG 2-Ll KALEWLGSIDTGGNTGYNPGLKSRLSITKDNSKSQVSLSVSSV
TTEDSATYYCTSVHOETKKYOSGGGGSFCQ^^ ^rC S^R^CC
EGMVCRL WCKKKL ^GGGGSSYTYNYEWHVDVWGOGLLVTVSS
ASTTAPKVYPLSSCCGDKSSSTVTLGCLVSSYMPEPVTVTWNS
GALKSGVHTFPAVLQSSGLYSLSSMVTVPGSTSGQTFTCNVAH
PASSTKVDKAVEPKSCDKTfflCT^
TLMJSRTPEVTCVyVDyS_HEpre
EQYNSTYRVyS_VLT\^HQD
AKGQPREPQVYTLjiP_SRDE^
SJ^GQPENNYK TPP
MHEALHNHYTQ LSLSP_GK
For SEQ ID NOS: 24-37
bovine heavy chain sequence = bold
human heavy chain sequence = dashed underline
non-antibody sequence = italic
Stalk = bold, underline; knob = bold, double underline
Table 22.
Name SEQ ID SEQUENCE (bold font = non-antibody sequence)
NO
BLV1H 38 QVQLRESGPSLVKPSQTLSLTCTASGFSLSDKAVGWVRQAPGKAL 12-IL8 EWLGSIDTGGNTGYNPGLKSRLSITKDNSKSQVSLSVSSVTTEDSA
TYYCTSVHQETKKYQSPRSAKELRCQCIKTYSKPFHPKFIKELR VIESGPHCANTEIIVKLSDGRELCLDPKENWVQRWEKFLKRA ENSGSGSYTYNYEWHVDVWGQGLLVTV
BLV1H 39 QVQLRESGPSLVKPSQTLSLTCTASGFSLSDKAVGWVRQAPGKAL 12- EWLGSIDTGGNTGYNPGLKSRLSITKDNSKSQVSLSVSSVTTEDSA
Ziconoti TYYCTSVHQETKKYQSCKGKGAKCSRLMYDCCTGSCRSGKCS de YTYNYEWHVDVWGQGLLVTV
BLV1H 40 QVQLRESGPSLVKPSQTLSLTCTASGFSLSDKAVGWVRQAPGKAL 12- EWLGSIDTGGNTGYNPGLKSRLSITKDNSKSQVSLSVSSVTTEDSA
Somatos TYYCTSVHQETKKYQSAGCKNFFWKTFTSCGSYTYNYEWHVD tatin VWGQGLLVTV
BLV1H 41 QVQLRESGPSLVKPSQTLSLTCTASGFSLSDKAVGWVRQAPGKAL 12- EWLGSIDTGGNTGYNPGLKSRLSITKDNSKSQVSLSVSSVTTEDSA
Chlorot TYYCTSVHQETKKYQSMCMPCFTTDHQMARKCDDCCGGKGR oxin GKCYGPQCLSYTYNYEWHVD VWGQGLLVTV
BLV1H 42 QVQLRESGPSLVKPSQTLSLTCTASGFSLSDKAVGWVRQAPGKAL 12- EWLGSIDTGGNTGYNPGLKSRLSITKDNSKSQVSLSVSSVTTEDSA
SDFl(al TYYCTSVHQETKKYQSKPVSLSYRCPCRFFESHVARANVKHLK pha) ILNTPNCALQIVARLKNNNRQVCIDPKLKWIQEYLEKALNKGS
GSYTYNYEWHVD VWGQGLLVTV
BLV1H 43 QVQLRESGPSLVKPSQTLSLTCTASGFSLSDKAVGWVRQAPGKAL 12-IL21 EWLGSIDTGGNTGYNPGLKSRLSITKDNSKSQVSLSVSSVTTEDSA
T YYCT S VHQETKKYQ S QGQDRHMIRMRQLIDIVDQLKNYVND LVPEFLPAPEDVETNCEWSAFSCFQKAQLKSANTGNNERIINV
SIKKLKRKPPSTNAGRRQKHRLTCPSCDSYEKKPPKEFLERFK SLLQKMIHQHLSSRTHGSEDSSYTYNYEWHVDVWGQGLLVTV
BLV1H 44 QVQLRESGPSLVKPSQTLSLTCTASGFSLSDKAVGWVRQAPGKAL 12- EWLGSIDTGGNTGYNPGLKSRLSITKDNSKSQVSLSVSSVTTEDSA
ProTxII TYYCTSVHQETKKYQSYCQKWMWTCDSERKCCEGMVCRLW
CKKKLWSYTYNYEWHVDVWGQGLLVTV
BLV5B 340 QVQLRESGPSLVQPSQTLSLTCTASGFSLSDKAVGWVRQAPGKAL
8 EWLGSIDTGGSTGYNPGLKSRLSITKDNSKSQVSLSVSSVTTEDSA
VHCH1 TYYCTTVHQETRKTCSDGYIAVDSCGRGQSDGCVNDCNSCYYG
WRNCRRQPAIHS YEFHVD AWGRGLLVTVS SASTTAPKVYPLSSC
CGDKS S ST VTLGCLVS S YMPEP VT VTWNS GALKS GVHTFP AVLQ S
SGLYSLSSMVTVPGSTSGQTFTCNVAHPASSTKVDKAVEPKSCDG
S
BLV5B 341 QAVLNQPSSVSGSLGQRVSITCSGSSSNVGNGYVSWYQLIPGSAP 8 VLCL RTLIYGDT SRAS GVPDRF S GSRS GNT ATLTIS SLQAEDE AD YFC AS
AED S S SNAVFGS GTTLT VLGQPKSPP S VTLFPP STEELNGNKATL V CLISDFYPGSVTWWKADGSTITRNVETTRASKQSNSKYAASSYL SLTSSDWKSKGSYSCEVTHEGSTVTKTVKPSECS
Table 23. Exemplary cysteine motifs
Figure imgf000236_0001
Figure imgf000237_0001
Figure imgf000238_0001
Table 24. Exemplary conserved motifs with the stalk domain
SEQ ID NO: Sequence
157 TSVHQETKKYQ
158 VHQETKKYQ
159 TTVHQ
160 TSVHQ
161 SSVTQ
162 STVHQ
163 ATVRQ
164 TTVYQ
165 SPVHQ
166 ATVYQ
167 TAVYQ
168 TNVHQ
169 ATVHQ
170 STVYQ
171 TIVHQ
172 AIVYQ
173 TTVFQ
174 AAVFQ
175 GTVHQ
176 ASVHQ
Figure imgf000239_0001
Figure imgf000240_0001
Figure imgf000241_0001
Table 25. Exemplary Linker Sequences
Figure imgf000241_0002
Table 26. Exemplary non-antibody sequences
Description SEQ ID Sequence
NO:
317 PRSAKELRCQCIKTYSKPFHPKFIKELRVIESGPHCANTEIIVKLS
IL8 DGRELCLDPKENWVQRWEKFLKRAENS
ziconotide 318 CKGKGAKCSRLMYDCCTGSCRSGKC
somatostatin 319 AGCKNFFWKTFTSCG
chlorotoxin 320 MCMPCFTTDHQMARKCDDCCGGKGRGKCYGPQCL
321 KPVSLSYRCPCRFFESHVARANVKHLKILNTPNCALQIVARLK
SDF1 (alpha) NNNRQVCIDPKLKWIQEYLEKALNK
322 QGQDRHMIRMRQLIDIVDQLKNYVNDLVPEFLPAPEDVETNCE
WSAFSCFQKAQLKSANTGNNERIINVSIKKLKRKPPSTNAGRR QKHRLTCPSCDSYEKKPPKEFLERFKSLLQKMIHQHLSSRTHGS
IL21 EDS
Protoxin2 323 YCQKWMWTCDSERKCCEGMVCRLWCKKKLW 324 MSYNLLGFLQRSSNFQCQKLLWQLNGRLEYCLKDRMNFDIPE
EIKQLQQFQKEDAALTIYEMLQNIF AIFRQDS S STGWNETIVEN LLANVYHQINHLKTVLEEKLEKEDFTRGKLMSSLHLKRYYGRI
IFN-beta LHYLKAKEYSHCAWTIVRVEILRNFYFINRLTGYLRN
325 TPLGPARSLPQSFLLKCLEQVRKIQADGAELQERLCAAHKLCH
PEELMLLRHSLGIPQAPLSSCSSQSLQLTSCLNQLHGGLFLYQG LLQALAGISPELAPTLDTLQLDVTDFATNIWLQMEDLGAAPAV QPTQGAMPTFTSAFQRRAGGVLVASQLHRFLELAYRGLRYLA
bGCSF EP
326 APARSPSPSTQPWEHVNAIQEARRLLNLSRDTAAEMNETVEVIS
EMFDLQEPTCLQTRLELYKQGLRGSLTKLKGPLTMMASHYKQ
GMCSF HCPPTPETSCATQIITFESFKENLKDFLLVIPFDCWEPVQE
327 HPIPDSSPLLQFGGQVRQRYLYTDDAQQTEAHLEIREDGTVGG
AADQSPESLLQLKALKPGVIQILGVKTSRFLCQRPDGALYGSLH
FDPEACSFRELLLEDGYNVYQSEAHGLPLHLPGNKSPHRDPAP
RGPARFLPLPGLPPAPPEPPGILAPQPPDVGSSDPLSMVGPSQGR
hFGF21 SPSYAS
Ex-4 328 HGEGTFTSDLSKQMEEEAVRLFIEWLK GGPSSGAPPPS hGLP-1 329 HAEGTFTSDVS S YLEGQ AAKEFIAWLVKGR
330 PPRLICDSRVLERYLLEAKEAENITTGCAEHCSLNENITVPDTK
VNFYAWKRMEVGQQAVEVWQGLALLSEAVLRGQALLVNSSQ PWEPLQLHVDKAVSGLRSLTTLLRALGAQKEAISPPDAASAAP
hEPO LRTITADTFRKLFRVYSNFLRGKLKLYTGEACRTGDR
Moka 331 INVKCSLPQQCIKPCKDAGMRFGKCMNKKCRCYS
VM-24 332 AAAISCVGSPECPPKCRAQGCK GKCMNRKCKCYYC

Claims

What is claimed is:
1. A library of antibodies or binding fragments thereof, wherein the antibodies or binding fragments thereof comprise an ultralong CDR3.
2. A library of polynucleotides encoding for antibodies or binding fragments thereof, wherein the encoded antibodies or binding fragments thereof comprise an ultralong CDR3.
3. The library of claims 1 or 2, wherein the ultralong CDR3 is 35 amino acids in length or longer, 40 amino acids in length or longer, 45 amino acids in length or longer, 50 amino acids in length or longer, 55 amino acids in length or longer, or 60 amino acids in length or longer.
4. The library of claim 3, wherein the ultralong CDR3 is 35 amino acids in length or longer.
5. The library of claims 1 or 2, wherein the ultralong CDR3 comprises 3 or more cysteine residues, 4 or more cysteine residues, 5 or more cysteine residues, 6 or more cysteine residues, 7 or more cysteine residues, 8 or more cysteine residues, 9 or more cysteine residues, 10 or more cysteine residues, 11 or more cysteine residues, or 12 or more cysteine residues.
6. The library of claim 5, wherein the ultralong CDR3 comprises 3 or more cysteine residues.
7. The library of claims 1 or 2, wherein the antibodies or binding fragments thereof comprise a cysteine motif.
8. The library of claim 7, wherein the cysteine motif is any one of SEQ ID NOS: 45-99 or any one of SEQ ID NOS: 100-56.
9. The library of claims 1 or 2, wherein the ultralong CDR3 comprises a non- human DH or a derivative thereof.
10. The library of claims 1 or 2, wherein the ultralong CDR3 comprises a JH sequence or a derivative thereof.
11. The library of claims 1 or 2, wherein the ultralong CDR3 comprises: (a) a non-human VH sequence or a derivative thereof; (b) a non-human DH sequence or a derivative thereof; and/or (c) a JH sequence or derivative thereof.
12. The library of claim 11, wherein the ultralong CDR3 comprises an additional amino acid sequence comprising two to six amino acid residues or more positioned between the VH sequence and the DH sequence.
13. The library of claims 1 or 2, wherein the ultralong CDR3 comprises a non-bovine sequence.
14. The library of claim 13, wherein the non-bovine sequence is a non-antibody or a human sequence.
15. The library of claim 13, wherein the non-bovine sequence replaces at least a portion of the ultralong CDR3.
16. The library of any one of claims 12-14, wherein the non-bovine sequence is a hormone, lymphokine, interleukin, chemokine, cytokine, toxin, or combination thereof.
17. The library of claim 16, wherein the non-bovine sequence is a cytokine.
18. The library of claim 17, wherein the cytokine is granulocyte colony- stimulating factor (G- CSF).
19. The library of claim 13, wherein the ultralong CDR3 comprises an additional sequence that is a linker.
20. The library of claim 19, wherein the linker is linked to a C-terminus, a N-terminus, or both C-terminus and N-terminus of the non-antibody sequence.
21. The library of claim 19, wherein the linker is (GGGGS)„ (SEQ ID NO: 339), where n is an integer between 1 and 5.
22. The library of claims 1 or 2, wherein the ultralong CDR3 comprises a X1X2X3X4X5 motif, wherein X1 is threonine (T), glycine (G), alanine (A), serine (S), or valine (V), wherein X2 is serine (S), threonine (T), proline (P), isoleucine (I), alanine (A), valine (V), or asparagine (N), wherein X3 is valine (V), alanine (A), threonine (T), or aspartic acid (D), wherein X4 is histidine (H), threonine (T), arginine (R), tyrosine (Y), phenylalanine (F), or leucine (L), and wherein X5 is glutamine (Q).
23. The library of claim 21 , wherein the wherein the X1X2X3X4X5 motif is selected from the group comprising SEQ ID NOS: 159-191.
24. The library of claim 22, wherein the ultralong CDR3 further comprises (XaXb)z motif, wherein Xa is any amino acid residue, Xb is an aromatic amino acid selected from the group consisting of: tyrosine (Y), phenylalanine (F), tryptophan (W), and histidine (H), and wherein z is 1 - 4.
25. The library of claim 24, wherein the the (XaXb)z motif is YXYXYX.
26. The library of claims 1 or 2, wherein the ultralong CDR3 comprises a
X1X2X3X4X5Xn(XaXb)z motif, wherein X1 is threonine (T), glycine (G), alanine (A), serine (S), or valine (V), wherein X2 is serine (S), threonine (T), proline (P), isoleucine (I), alanine (A), valine (V), or asparagine (N), wherein X3 is valine (V), alanine (A), threonine (T), or aspartic acid (D), wherein X4 is histidine (H), threonine (T), arginine (R), tyrosine (Y), phenylalanine (F), or leucine (L), and wherein X5 is glutamine (Q), wherein Xa is any amino acid residue, Xb is an aromatic amino acid selected from the group consisting of: tyrosine (Y), phenylalanine (F), tryptophan (W), and histidine (H), wherein n is 27 - 54, and wherein z is 1 - 4.
27. The library of claim 26, wherein the X'X^x motif is TTVHQ (SEQ ID NO. 159) or TSVHQ (SEQ ID NO. 160), and wherein the (XaXb)z motif is YXYXYX.
28. The library of claims 1 or 2, wherein the ultralong CDR3 comprises TSVHQETKKYQ (SEQ ID NO. 157), VHQETKKYQ (SEQ ID NO: 158), CTTVHQXn (SEQ ID NO. 223)m
CTSVHQXn (SEQ ID NO. 224), wherein n is 1-8, TTVHQ (SEQ ID NO. 159), TSVHQ (SEQ ID NO. 160), VHQ, KKQ, VYQ, YTYNYEW (SEQ ID NO: 235), or a combination thereof.
29. The library of claims 1 or 2, wherein the ultralong CDR3 comprises CX1 X2 X3 X4Q, wherein X1 is T, S, A, or G, wherein X2 is T, S, A, P, or I, wherein X3 is V or K, and wherein X4 is H, K, or Y.
30. The library of claims 1 or 2, wherein the ultralong CDR3 comprises CX1 X2VHQ, wherein X1 is T, S, A, or G, and wherein X2 is T, S, A, P, or I.
31. The library of claims 1 or 2, wherein the ultralong CDR3 comprises CX1 X2VX3Q, wherein X1 is T, S, A, or G, wherein X2 is T, S, A, P, or I, and wherein X3 is H, Y, or K.
32. The library of claims 1 or 2, wherein the ultralong CDR3 comprises CX1 X2K Q, wherein X1 is T, S, A, or G, and wherein X2 is T, S, A, P, or I.
33. The library of claims 1 or 2, wherein the ultralong CDR3 comprises YXJYX2, wherein X2 is E or D.
34. The library of claims 1 or 2, wherein the ultralong CDR3 comprises YXJYX2 Y.
35. The library of claims 1 or 2, wherein the ultralong CDR3 comprises Y(E/D)X, wherein X is H, W, N, F, I or Y.
36. The library of claims 1 or 2, wherein the ultralong CDR3 comprises XY(E/D), wherein X is T, S, N or I.
37. The library of claims 1 or 2, wherein the ultralong CDR3 comprises Y(E/D)X1XnW, wherein X1 is H,W, N, F, I or Y, and wherein n is 1-4.
38. The library of claims 1 or 2, wherein the antibodies or binding fragments thereof are chimeric, human engineered, or humanized.
39. The library of claims 1 or 2, wherein the ultralong CDR3 is a ruminant CDR3.
40. The library of claim 39, wherein the ruminant is a cow.
41. A library of vectors comprising the library of polynucleotides of any one of claims 2-40.
42. A library of host cells comprising the library of vectors of claim 41.
43. The library of claim 42, wherein the cell is a bacteria, insect, virus, or bacteriophage.
44. The library of claim 42, wherein the cell is a mammalian cell.
45. The library of claim 42, wherein the antibodies or binding fragments thereof are displayed on the cell surface.
46. The library of claim 42, wherein the antibodies or binding fragments thereof are secreted from the cell.
47. The library of claim 42, wherein the antibodies or binding fragments thereof are present in a spatially addressed format.
48. A recombinant antibody or fragment thereof, wherein at least a portion of the recombinant antibody or fragment thereof is based on or derived from at least a portion of an ultralong CDR3.
49. An antibody or fragment thereof comprising: (a) a first antibody sequence, wherein at least a portion of the first antibody sequence is derived from at least a portion of an ultralong CDR3; (b) a non-antibody sequence; and (c) optionally, a second antibody sequence, wherein at least a portion of the second antibody sequence is derived from at least a portion of an ultralong CDR3.
50. The antibody of claims 48 or 49, wherein the antibody is a chimeric, human engineered, or humanized antibody.
51. The antibody of claims 48 or 49, wherein the antibody is a bovine, bovinized, bovine engineered, or fully bovine antibody.
52. The antibody of claims 48 or 49, wherein the antibody comprises a Fab, a scFv, dsFv, diabody, (dsFv)2, minibody, flex minibody or bi-specific fragment.
53. The antibody of claims 48 or 49, wherein the antibody is an isolated antibody.
54. The antibody of claim 48 further comprising a non-antibody sequence.
55. The antibody of claims 49 or 54, wherein the non-antibody sequence is derived from a mammal.
56. The antibody of claim 55, wherein the mammal is a bovine, human, or non-bovine mammal.
57. The antibody of claims 49 or 54, wherein the non-antibody sequence is derived from a non- bovine animal.
58. The antibody of claim 57, wherein the non-bovine animal is a scorpion, lizard or snail.
59. The antibody of claim 58, wherein the lizard is a gila monster.
60. The antibody of claims 49 or 54, wherein the non-antibody sequence is a derived from a growth factor, cytokine, hormone, or toxin.
61. The antibody of claim 60, wherein the growth factor is a GSCF, GMCSF or FGF21.
62. The antibody of claim 61, wherein the GCSF is a bovine GCSF or human GCSF.
63. The antibody of claim 60, wherein the cytokine is a beta-interferon.
64. The antibody of claim 60, wherein the hormone is an exendin-4, GLP-1, somatostatin, or erythropoietin.
65. The antibody of claim 60, wherein the toxin is a Mokal, VM-24, chlorotoxin, ziconotide or protoxin2.
66. The antibody of claims 49 or 54, wherein the non-antibody sequence is a synthetic sequence.
67. The antibody of claims 49 or 54, wherein the non-antibody sequence is a cytokine sequence, a lymphokine sequence, a chemokine sequence, a growth factor sequence, a hormone sequence, or a toxin sequence.
68. The antibody of claim 49 or 54, wherein the non-antibody sequence is an IL-8 sequence, an IL-21 sequence, an SDF-1 (alpha) sequence, a somatostatin sequence, a chlorotoxin sequence, a protoxin2 sequence, or a ziconotide sequence.
69. The antibody of claims 49 or 54, wherein the non-antibody sequence is selected from the group comprising SEQ ID NOS: 317-332.
70. The antibody of claims 48 or 49, wherein the ultralong CDR3 is based on or derived from a cow ultralong CDR3.
71. The antibody of claim 48, wherein at least a portion of the antibody is from a mammal.
72. The antibody of claim 49, wherein at least a portion of the first antibody sequence and/or at least a portion of the second antibody sequence is from a mammal.
73. The antibody of any of claims 71-72, wherein the mammal is a bovine, human or non- bovine mammal.
74. The antibody of claim 48, wherein the antibody is 3 or more amino acids in length.
75. The antibody of claim 48, wherein the portion of the antibody based on or derived from at least a portion of the ultralong CDR3 is 20 or fewer amino acids in length
76. The antibody of claim 48, wherein the portion of the antibody based on or derived from at least a portion of the ultralong CDR3 is 3 or more amino acids in length
77. The antibody of claim 48, wherein the antibody comprises one or more amino acid residues based on or derived from a stalk domain of the ultralong CDR3, a knob domain of the ultralong CDR3, or a combination thereof.
78. The antibody of claim 48, wherein the antibody comprises comprise one or more conserved motifs derived from a stalk domain of the ultralong CDR3.
79. The antibody of claim 54, wherein the non-antibody sequence replaces at least a portion of the ultralong CDR3.
80. The antibody of claim 48 or 49, wherein the portion of the ultralong CDR3 comprises at least a portion of a stalk domain of the ultralong CDR3, at least a portion of the knob domain of the ultralong CDR3, or a combination thereof.
81. The antibody of claim 48, wherein the antibody comprises a sequence selected from any one of SEQ ID NOS: 157-307 and SEQ ID NOS: 333-336.
82. The antibody of claim 48, wherein the antibody comprises a sequence that is 50% or more homologous to a sequence selected from any one of SEQ ID NOS: 157-224 and 235-295.
83. The antibody of claim 48, wherein the antibody comprises a first sequence selected from SEQ ID NOS: 157-234 and a second sequence selected from SEQ ID NOS: 235-307 and SEQ ID NOS: 333-336.
84. The antibody of claim 48, wherein the portion of the recombinant antibody or fragment thereof is based on or derived from at least a portion of a single ultralong CDR3 sequence.
85. The antibody of claim 48, wherein the portion of the recombinant antibody or fragment thereof is based on or derived from at least a portion of two or more different ultralong CDR3 sequences.
86. The antibody of claim 48, wherein the portion of the ultralong CDR3 is based on or derived from a BLV1H12 ultralong CDR3 sequence.
87. The antibody of claim 48, wherein the portion of the ultralong CDR3 is based on or derived from a sequence that is 50% or more homologous to a BLV1H12 ultralong CDR3 sequence.
88. The antibody of claim 48, wherein the portion of the ultralong CDR3 is based on or derived from a BLV5B8, BLVCVl, BLV5D3, BLV8C11, BF1H1, or F18 ultralong CDR3 sequence.
89. The antibody of claim 48, wherein the portion of the ultralong CDR3 is based on or derived from a sequence that is 50% or more homologous to a BLV5B8, BLVCVl, BLV5D3, BLV8C11, BF1H1, or F18 ultralong CDR3 sequence.
90. The antibody of claim 49, wherein the first and second antibody sequences are 3 or more amino acids in length.
91. The antibody of claim 49, wherein the portion of the first antibody sequence derived from at least a portion of the ultralong CDR3 and/or the portion of the second antibody sequence derived from at least a portion of the ultralong CDR3 is 20 or fewer amino acids in length.
92. The antibody of claim 49, wherein the portion of the first antibody sequence derived from at least a portion of the ultralong CDR3 and/or the portion of the second antibody sequence derived from at least a portion of the ultralong CDR3 is 3 or more amino acids in length.
93. The antibody of claim 49, wherein the first and/or second antibody sequences comprise one or more amino acid residues based on or derived from a stalk domain of the ultralong CDR3, a knob domain of the ultralong CDR3, or a combination thereof.
94. The antibody of claims 77 or 93, wherein the one or more amino acid residues derived from the knob domain of the ultralong CDR3 is a serine and/or cysteine residue.
95. The antibody of claim 49, wherein the first and/or second antibody sequences comprise one or more conserved motifs derived from a stalk domain of the ultralong CDR3.
96. The antibody of claims 78 or 95 wherein the one or more conserved motifs derived from the stalk domain of the ultralong CDR3 comprises a sequence selected from any one of SEQ ID NOS: 157-307 and SEQ ID NOS: 333-336.
97. The antibody of claim 49, wherein the portion of the first antibody sequence derived from at least a portion of the ultralong CDR3 and/or the portion of the second antibody sequence derived from at least a portion of the ultralong CDR3 comprises a sequence selected from any one of SEQ ID NOS: 157-307 and SEQ ID NOS: 333-336.
98. The antibody of claim 49, wherein the portion of the first antibody sequence derived from at least a portion of the ultralong CDR3 and/or the portion of the second antibody sequence derived from at least a portion of the ultralong CDR3 comprises a sequence that is 50% or more
homologous to a sequence selected from any one of SEQ ID NOS: 157-224 and 235-295.
99. The antibody of claim 49, wherein the portion of the first antibody sequence derived from at least a portion of the ultralong CDR3 comprises a sequence selected from any one of SEQ ID NOS: 157-234.
100. The antibody of claim 49, wherein the portion of the first antibody sequence derived from at least a portion of the ultralong CDR3 comprises a sequence that is 50% or more homologous to a sequence selected from any one of SEQ ID NOS: 157-224.
101. The antibody of claim 49, wherein the portion of the second antibody sequence derived from at least a portion of the ultralong CDR3 comprises a sequence selected from any one of SEQ ID NOS: 235-307 and SEQ ID NOS: 333-336.
102. The antibody of claim 49, wherein the portion of the second antibody sequence derived from at least a portion of the ultralong CDR3 comprises a sequence that is 50% or more
homologous to a sequence selected from any one of SEQ ID NOS: 235-295.
103. The antibody of claim 49, wherein the portion of the first antibody sequence derived from at least a portion of the ultralong CDR3 and the portion of the second antibody sequence derived from at least a portion of the ultralong CDR3 are derived from the same ultralong CDR3 sequence.
104. The antibody of claim 49, wherein the portion of the first antibody sequence derived from at least a portion of the ultralong CDR3 and the portion of the second antibody sequence derived from at least a portion of the ultralong CDR3 are derived from two or more different ultralong CDR3 sequences.
105. The antibody of claim 49, wherein the portions of the ultralong CDR3 of the first and/or second antibody sequences are based on or derived from a BLV1H12 ultralong CDR3 sequence.
106. The antibody of claim 49, wherein the portions of the ultralong CDR3 of the first and/or second antibody sequences are based on or derived from a sequence that is 50% or more homologous to a BLV1H12 ultralong CDR3 sequence.
107. The antibody of claim 49, wherein the portions of the ultralong CDR3 of the first and/or second antibody sequences are based on or derived from a BLV5B8, BLVCV1, BLV5D3,
BLV8C11, BF1H1, or F18 ultralong CDR3 sequence.
108. The antibody of claim 49, wherein the portions of the ultralong CDR3 of the first and/or second antibody sequences are based on or derived from a sequence that is 50% or more homologous to a BLV5B8, BLVCV1, BLV5D3, BLV8C11, BF1H1, or F18 ultralong CDR3 sequence.
109. The antibodies of any of claims 48-49, wherein the ultralong CDR3 is based on or derived from an ultralong CDR3 that is 35 or more amino acids in length.
110. The antibodies of any of claims 48-49, wherein the ultralong CDR3 is based on or derived from an ultralong CDR3 comprising 3 or more cysteine residues.
111. The antibodies of any of claims 48-49, wherein the ultralong CDR3 is based on or derived from an ultralong CDR3 comprises one or more cysteine motifs.
112. The antibody of claim 111, wherein the one or more cysteine motifs are selected from the group comprising SEQ ID NOS: 45-99.
113. The antibody of claim 112, wherein the one or more cysteine motifs are selected from the group comprising SEQ ID NOS: 100-156.
114. The antibodies of any of claims 48-49, wherein the antibody is based on or derived from an ultralong CDR3 that is 35 or more amino acids in length.
115. The antibodies of any of claims 48-49, wherein the antibody is based on or derived from an ultralong CDR3 comprising 3 or more cysteine residues.
116. The antibodies of any of claims 48-49, wherein the antibody is based on or derived from an ultralong CDR3 comprises 1 or more cysteine motifs.
117. The antibodies of any of claims 48-49, wherein the antibody comprises an ultralong CDR3 that is 35 or more amino acids in length.
118. The antibodies of any of claims 48-49, wherein the antibody comprises an ultralong CDR3 comprising 3 or more cysteine residues.
119. The antibodies of any of claims 48-49, wherein the antibody comprises an ultralong CDR3 comprises 1 or more cysteine motifs.
120. The antibodies of any of claims 48-49, wherein the ultralong CDR3 is a heavy chain CDR3.
121. The antibodies of any of claims 48-49, wherein the ultralong CDR3 comprises an amino acid sequence derived from or based on a non-human DH sequence.
122. The antibodies of any of claims 48-49, wherein the ultralong CDR3 comprises an amino acid sequence derived from or based on a JH sequence.
123. The antibodies of any of claims 48-49, wherein the ultralong CDR3 comprises:
a. an amino acid sequence derived from or based on a non-human VH sequence;
b. an amino acid sequence derived from or based on a non-human DH sequence; and/or c. an amino acid sequence derived from or based on a JH sequence.
124. The antibodies of any of claims 48-49, wherein the ultralong CDR3 comprises an additional amino acid sequence comprising at least about two amino acid residues positioned between the VH derived amino acid sequence and the DH derived amino acid sequence.
125. The antibody of claim 48, wherein the antibody or binding fragment thereof comprises a sequence selected from SEQ ID NOS: 24-44, the antibody or binding fragment thereof encoded by the DNA of SEQ ID NOS: 2-22.
126. The antibody of claim 48, wherein the antibody or binding fragment thereof comprises a sequence selected from SEQ ID NO: 23, the antibody or binding fragment thereof encoded by the DNA of SEQ ID NO: 1.
127. The antibody of claim 48, wherein the ultralong CDR3 comprises a sequence selected from SEQ ID NOS: 24-44.
128. The antibody of claim 48, wherein the ultralong CDR3 comprises a sequence selected from SEQ ID NO: 23.
129. The antibody of claim 48, wherein the ultralong CDR3 is encoded by a DNA sequence that is derived from or based on SEQ ID NOS: 2-22.
130. The antibody of claim 48, wherein the ultralong CDR3 is encoded by a DNA sequence that is derived from or based on SEQ ID NO: 1.
131. The antibody of claims 48, 49 or 54 further comprising a first linker sequence.
132. The antibody of claim 131 further comprising a second linker sequence.
133. The antibody of claim 132, wherein the first and second linker sequences comprise the same sequence.
134. The antibody of claim 132, wherein the first and second linker sequences comprise different sequences.
135. The antibody of any of claims 131-132, wherein the first and/or second linker sequence attach the non-antibody sequence to the portion based on or derived from the portion of the ultralong CDR3.
136. The antibody of claim 132, wherein the first and/or second linker sequences attach the non- antibody sequence to the first antibody sequence.
137. The antibody of claim 132, wherein the first and/or second linker sequences attach the non- antibody sequence to the second antibody sequence.
138. The antibody of claim 132, wherein the first and/or second linker sequences comprise the sequence GGGGS.
139. The antibody of claim 132, wherein the first and/or second linker sequences comprise (a) the sequence (GGGGS)n and wherein n = 1 to 5; (b) the sequence GGGSGGGGS; (c) the sequence GGGGSGGGS; or (d) a combination of (a) - (c).
140. The antibody of claim 132, wherein the first and/or second linker sequences are the same length.
141. The antibody of claim 132, wherein the first and/or second linker sequences are different lengths.
142. The antibody of claim 132, wherein the first and/or second linker sequences are 3 or more amino acids in length.
143. The antibody of claim 132, wherein the first and/or second linker sequences comprise 1 or more glycine residues.
144. The antibody of claim 132, wherein the first and/or second linker sequences comprise 2 or more consecutive glycine residues.
145. The antibody of claim 132, wherein the first and/or second linker sequences comprise 1 or more serine residues.
146. The antibody of claim 132, wherein the first and/or second linker sequence comprise 1 or more polar amino acid residues.
147. The antibody of claim 146, wherein the 1 or more polar amino acid residues are selected from serine, threonine, asparagine, or glutamine.
148. The antibody of claim 146, wherein the polar amino acid residues comprise uncharged side chains.
149. The antibody of claim 48 further comprising one or more cleavage sites.
150. The antibody of claim 149, wherein the one or more cleavage sites comprise a recognition site for a protease.
151. The antibody of claim 149, wherein the protease is a Factor Xa.
152. The antibody of claim 149, wherein the one or more cleavage sites comprise an amino acid sequence of IEGR.
153. The antibody of claim 149, wherein the one or more cleavage site are between the first antibody sequence and the non-antibody sequence.
154. The antibody of claim 149, wherein the one or more cleavage sites are between the second antibody sequence and the non-antibody sequence.
155. The antibody of claim 49, further comprising one or more cleavage sites and one or more linkers.
156. The antibody of claim 155, wherein the one or more cleavage sites are between the one or more linkers and the non-antibody sequence.
157. The antibody of claim 155, wherein the one or more cleavage sites are between the first antibody sequence and the one or more linkers.
158. The antibody of claim 155, wherein the one or more cleavage sites are between the second antibody sequence and the one or more linkers.
159. A library of antibodies or binding fragments thereof, wherein the antibodies or binding fragments thereof comprise an ultralong CDR3.
160. A library of antibodies or binding fragments thereof, wherein the antibodies or binding fragments thereof comprise the antibody or binding fragment of any of claims 48-158.
161. A nucleic acid library comprising a plurality of polynucleotides comprising sequences coding for antibodies or binding fragments thereof, wherein the antibodies or binding fragments thereof comprise an ultralong CDR3.
162. A nucleic acid library comprising a plurality of polynucleotides comprising sequences coding for antibodies or binding fragments thereof, wherein the antibodies or binding fragments thereof comprise the antibody or binding fragment of any of claims 48-158.
163. A polynucleotide comprising a nucleic acid sequence that encodes a variable region, wherein the variable region comprises an ultralong CDR3.
164. A vector comprising a polynucleotide, wherein the polynucleotide comprises a nucleic acid sequence that encodes a variable region, wherein the variable region comprises an ultralong CDR3.
165. A host cell comprising a polynucleotide, wherein the polynucleotide comprises a nucleic acid sequence that encodes a variable region, wherein the variable region comprises an ultralong CDR3.
166. A polynucleotide comprising a nucleic acid sequence that encodes the antibody or binding fragment thereof of any of claims 48-158.
167. A vector comprising a polynucleotide, wherein the polynucleotide comprises a nucleic acid sequence that encodes the antibody or binding fragment thereof of any of claims [00144]-[00173].
168. A host cell comprising a polynucleotide, wherein the polynucleotide comprises a nucleic acid sequence that encodes the antibody or binding fragment thereof of any of claims 48-158.
169. A method of producing an antibody or binding fragment thereof comprising an ultralong CDR3 or fragment thereof comprising culturing the host cell of claim 168 under conditions wherein the polynucleotide sequence is expressed and the antibody or binding fragment thereof comprising an ultralong CDR3 or fragment thereof is produced.
170. The method of claim 169 further comprising recovering the antibody or binding fragment thereof comprising an ultralong CDR3 or fragment thereof from the host cell culture.
171. A pharmaceutical composition comprising an antibody or fragment thereof of any of claims 48-158.
172. A pharmaceutical composition comprising (a) an antibody or fragment thereof comprising sequence based on or derived from at least a portion of an ultralong CDR3; and (b) a
pharmaceutically acceptable excipient.
173. The pharmaceutical composition of claims 172 or 173, further comprising a therapeutic agent.
174. The pharmaceutical composition of claim 172 or 173, wherein the therapeutic agent is an antibody, small molecule, organic compound, peptide, protein.
175. A method of treating a disease or condition in a subject in need thereof comprising administering to the mammal a therapeutically effective amount of the antibody of any of claims 48-158.
176. The method of claim 175, wherein the antibody comprises an ultralong CDR3 sequence and a non-antibody sequence.
177. The method of claim 176, wherein the non-antibody sequence is selected from the group comprising Mokal, Vm24, GLP-1, Exendin-4, beta- interferon, human EPO, human FGF21, human GMCSF, human interferon-beta, bovine GCSF, human GCSF, IL8, ziconotide, somatostatin, chlorotoxin, SDF1 (alpha), IL21, protoxin2 and a derivative or variant thereof.
178. The method of claim 175, wherein the disease or condition is selected from the group comprising autoimmune disease, heteroimmune disease or condition, inflammatory disease, pathogenic infection, thromboembolic disorder, respiratory disease or condition, metabolic disease, central nervous system (CNS) disorder, bone disease, cancer, blood disorder, obesity, diabetes, osteoporosis, anemia, or pain.
179. The method of claim 175, wherein the disease or condition would benefit from the modulation of an ion channel.
180. The method of claim 179, wherein the ion channel is selected from the group comprising a potassium ion channel, sodium ion channel, or acid sensing ion channel.
181. The method of claim 175 , wherein the ion channel is selected from the group comprising Kvl .3 ion channel, Navl .7 ion channel and acid sensing ion channel (ASIC).
182. The method of claim 175, wherein the disease or condition would benefit from the modulation of a receptor.
183. The method of claim 182, wherein the receptor is selected from the group comprising GLPIR, GCGR, EPO receptor, FGFR, FGF21R, CSFR, GMCSFR, IL8R, IL21R, and GCSFR.
184. The method of claim 175, wherein the disease or condition is mastitis.
185. The method of claim 175, wherein the subject is a mammal.
186. The method of claim 185, wherein the mammal is a bovine or human.
187. An isolated crystal comprising a bovine antibody Fab fragment comprising SEQ ID NO: 24 and SEQ ID NO: 23, wherein the crystal has a space group P212121 and unit cell dimensions of a=71.4 angstroms, b=127.6 angstroms and c=127.9 angstroms.
188. An isolated crystal comprising a bovine antibody Fab fragment comprising SEQ ID NO: 340 and SEQ ID NO: 341, wherein the crystal has a space group P212121 and unit cell dimensions of a=54.6 angstroms, b=53.7 angstroms and c=330.5 angstroms.
PCT/US2013/020903 2012-01-09 2013-01-09 Ultralong complementarity determining regions and uses thereof WO2013106485A2 (en)

Priority Applications (6)

Application Number Priority Date Filing Date Title
JP2014552273A JP6684490B2 (en) 2012-01-09 2013-01-09 Ultralong complementarity determining regions and uses thereof
EP13735853.7A EP2802603A4 (en) 2012-01-09 2013-01-09 Ultralong complementarity determining regions and uses thereof
AU2013208003A AU2013208003B2 (en) 2012-01-09 2013-01-09 Ultralong complementarity determining regions and uses thereof
CA2863224A CA2863224A1 (en) 2012-01-09 2013-01-09 Ultralong complementarity determining regions and uses thereof
CN201380013323.8A CN104520321A (en) 2012-01-09 2013-01-09 Ultralong complementarity determining regions and uses thereof
AU2018201832A AU2018201832A1 (en) 2012-01-09 2018-03-14 Ultralong complementarity determining regions and uses thereof

Applications Claiming Priority (4)

Application Number Priority Date Filing Date Title
US201261584680P 2012-01-09 2012-01-09
US61/584,680 2012-01-09
US201261671629P 2012-07-13 2012-07-13
US61/671,629 2012-07-13

Publications (2)

Publication Number Publication Date
WO2013106485A2 true WO2013106485A2 (en) 2013-07-18
WO2013106485A3 WO2013106485A3 (en) 2014-03-06

Family

ID=48782074

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2013/020903 WO2013106485A2 (en) 2012-01-09 2013-01-09 Ultralong complementarity determining regions and uses thereof

Country Status (7)

Country Link
US (3) US20140050720A1 (en)
EP (1) EP2802603A4 (en)
JP (2) JP6684490B2 (en)
CN (1) CN104520321A (en)
AU (2) AU2013208003B2 (en)
CA (1) CA2863224A1 (en)
WO (1) WO2013106485A2 (en)

Cited By (23)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2014110368A1 (en) * 2013-01-11 2014-07-17 The California Institute For Biomedical Research Bovine fusion antibodies
WO2015010100A3 (en) * 2013-07-18 2015-06-25 Fabrus, Inc. Humanized antibodies with ultralong complementarity determining regions
EP3019531A4 (en) * 2013-07-11 2017-03-15 The California Institute for Biomedical Research Immunoglobulin fusion proteins and compositions thereof
WO2017093947A1 (en) * 2015-12-04 2017-06-08 Novartis Ag Antibody cytokine engrafted compositions and methods of use for immunoregulation
CN107208315A (en) * 2014-12-01 2017-09-26 斯克利普斯研究院 It is related to the method and composition of the functional polypeptide in embedded heterologous protein support
WO2018215938A1 (en) * 2017-05-24 2018-11-29 Novartis Ag Antibody-cytokine engrafted proteins and methods of use
WO2018215935A1 (en) * 2017-05-24 2018-11-29 Novartis Ag Antibody-cytokine engrafted proteins and methods of use for immune related disorders
WO2018215937A1 (en) * 2017-05-24 2018-11-29 Novartis Ag Interleukin-7 antibody cytokine engrafted proteins and methods of use in the treatment of cancer
WO2018215936A1 (en) * 2017-05-24 2018-11-29 Novartis Ag Antibody-cytokine engrafted proteins and methods of use in the treatment of cancer
WO2019140150A1 (en) 2018-01-12 2019-07-18 Bristol-Myers Squibb Company Combination therapy with anti-il-8 antibodies and anti-pd-1 antibodies for treating cancer
US10562980B2 (en) 2012-01-09 2020-02-18 The Scripps Research Institute Humanized antibodies
US10774132B2 (en) 2012-01-09 2020-09-15 The Scripps Research Instittue Ultralong complementarity determining regions and uses thereof
US10975166B2 (en) 2016-10-03 2021-04-13 The Regents Of The University Of California Inhibitory antibodies against MMP-14
WO2021081440A3 (en) * 2019-10-24 2021-05-27 Minotaur Therapeutics, Inc. Chimeric cytokine modified antibodies and methods of use thereof
WO2021191424A1 (en) 2020-03-27 2021-09-30 UCB Biopharma SRL Autonomous knob domain peptides
US11332546B2 (en) 2019-05-21 2022-05-17 The Regents Of The University Of California Protease inhibitory antibodies and methods of use thereof
GB2562933B (en) * 2016-01-08 2022-06-29 Maxion Therapeutics Ltd Binding members with altered diversity scaffold domains
WO2022232321A1 (en) * 2021-04-28 2022-11-03 Minotaur Therapeutics, Inc. Humanized chimeric bovine antibodies and methods of use
WO2022241057A1 (en) * 2021-05-12 2022-11-17 Applied Biomedical Science Institute Binding polypeptides against sars cov-2 and uses thereof
WO2022241058A1 (en) * 2021-05-12 2022-11-17 Applied Biomedical Science Institute Methods of screening and expression of disulfide-bonded binding polypeptides
RU2786730C2 (en) * 2017-05-24 2022-12-26 Новартис Аг Proteins based on antibody with grafted cytokine and methods for their use in immune disorders
WO2023192478A1 (en) 2022-04-01 2023-10-05 Bristol-Myers Squibb Company Combination therapy with anti-il-8 antibodies and anti-pd-1 antibodies for treating cancer
US11932673B2 (en) 2017-07-12 2024-03-19 Maxion Therapeutics Limited Sodium channel inhibitors

Families Citing this family (13)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US9718865B2 (en) * 2012-07-27 2017-08-01 Purdue Pharma L.P. Sodium channel blocking peptides and the use thereof
SG11201510011VA (en) 2013-06-07 2016-01-28 California Inst Biomedical Res Small molecule inhibitors of fibrosis
US20170210818A1 (en) * 2014-06-06 2017-07-27 The California Institute For Biomedical Research Constant region antibody fusion proteins and compositions thereof
US10336735B2 (en) 2014-12-10 2019-07-02 The Scripps Research Institute Small molecule inhibitors of fibrosis
WO2016115218A1 (en) * 2015-01-14 2016-07-21 The California Institute For Biomedical Research Antibody drug conjugates for the treatment of immune conditions
TW201704263A (en) * 2015-05-01 2017-02-01 梅迪繆思有限公司 Novel phage display library, members thereof and uses of the same
US11161891B2 (en) 2015-12-09 2021-11-02 The Scripps Research Institute Relaxin immunoglobulin fusion proteins and methods of use
KR102136742B1 (en) 2016-10-20 2020-07-23 아이-맵 바이오파마 유에스 리미티드 New CD47 monoclonal antibodies and uses
CN108079300B (en) * 2016-11-22 2021-03-30 上海交通大学医学院 Use of acid-sensitive ion channel regulator
CA3102125A1 (en) * 2018-06-13 2019-12-19 Crystal Bioscience Inc. Transgenic chicken that makes antibodies with long cdr-h3s stabilized by multiple disulfide bridges and diversified by gene conversion
CA3097443A1 (en) * 2018-11-12 2020-05-22 I-Mab Biopharma Us Limited Fusion proteins containing cd47 antibodies and cytokines
CN112034169A (en) * 2020-08-27 2020-12-04 华威特（江苏）生物制药有限公司 Direct immunofluorescence reagent for detecting bovine viral diarrhea virus type 1 and kit thereof
WO2024155604A1 (en) 2023-01-18 2024-07-25 Gilead Sciences, Inc. Chimeric transgenic immunoglobulin mice with an altered heavy chain locus and methods of making and using same

Citations (177)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US30985A (en) 1860-12-18 Thomas l
US3773919A (en) 1969-10-23 1973-11-20 Du Pont Polylactide-drug mixtures
US3854480A (en) 1969-04-01 1974-12-17 Alza Corp Drug-delivery system
US3887699A (en) 1969-03-24 1975-06-03 Seymour Yolles Biodegradable polymeric article for dispensing drugs
US3896111A (en) 1973-02-20 1975-07-22 Research Corp Ansa macrolides
US4137230A (en) 1977-11-14 1979-01-30 Takeda Chemical Industries, Ltd. Method for the production of maytansinoids
US4151042A (en) 1977-03-31 1979-04-24 Takeda Chemical Industries, Ltd. Method for producing maytansinol and its derivatives
EP0003089A1 (en) 1978-01-06 1979-07-25 Bernard David Drier for silkscreen printed sheets
US4248870A (en) 1978-10-27 1981-02-03 Takeda Chemical Industries, Ltd. Maytansinoids and use
US4256746A (en) 1978-11-14 1981-03-17 Takeda Chemical Industries Dechloromaytansinoids, their pharmaceutical compositions and method of use
US4260608A (en) 1978-11-14 1981-04-07 Takeda Chemical Industries, Ltd. Maytansinoids, pharmaceutical compositions thereof and methods of use thereof
US4265814A (en) 1978-03-24 1981-05-05 Takeda Chemical Industries Matansinol 3-n-hexadecanoate
EP0036676A1 (en) 1978-03-24 1981-09-30 The Regents Of The University Of California Method of making uniformly sized liposomes and liposomes so made
US4294757A (en) 1979-01-31 1981-10-13 Takeda Chemical Industries, Ltd 20-O-Acylmaytansinoids
US4307016A (en) 1978-03-24 1981-12-22 Takeda Chemical Industries, Ltd. Demethyl maytansinoids
US4308268A (en) 1979-06-11 1981-12-29 Takeda Chemical Industries, Ltd. Maytansinoids, pharmaceutical compositions thereof and method of use thereof
US4308269A (en) 1979-06-11 1981-12-29 Takeda Chemical Industries, Ltd. Maytansinoids, pharmaceutical compositions thereof and method of use thereof
US4309428A (en) 1979-07-30 1982-01-05 Takeda Chemical Industries, Ltd. Maytansinoids
US4313946A (en) 1981-01-27 1982-02-02 The United States Of America As Represented By The Secretary Of Agriculture Chemotherapeutically active maytansinoids from Trewia nudiflora
US4315929A (en) 1981-01-27 1982-02-16 The United States Of America As Represented By The Secretary Of Agriculture Method of controlling the European corn borer with trewiasine
US4317821A (en) 1979-06-08 1982-03-02 Takeda Chemical Industries, Ltd. Maytansinoids, their use and pharmaceutical compositions thereof
US4322348A (en) 1979-06-05 1982-03-30 Takeda Chemical Industries, Ltd. Maytansinoids
US4331598A (en) 1979-09-19 1982-05-25 Takeda Chemical Industries, Ltd. Maytansinoids
EP0052322A2 (en) 1980-11-10 1982-05-26 Gersonde, Klaus, Prof. Dr. Method of preparing lipid vesicles by ultrasonic treatment, the use of this method and apparatus for its application
EP0058481A1 (en) 1981-02-16 1982-08-25 Zeneca Limited Continuous release pharmaceutical compositions
US4362663A (en) 1979-09-21 1982-12-07 Takeda Chemical Industries, Ltd. Maytansinoid compound
US4364866A (en) 1979-09-21 1982-12-21 Takeda Chemical Industries, Ltd. Maytansinoids
US4371533A (en) 1980-10-08 1983-02-01 Takeda Chemical Industries, Ltd. 4,5-Deoxymaytansinoids, their use and pharmaceutical compositions thereof
EP0088046A2 (en) 1982-02-17 1983-09-07 Ciba-Geigy Ag Lipids in the aqueous phase
DE3218121A1 (en) 1982-05-14 1983-11-17 Leskovar, Peter, Dr.-Ing., 8000 München Pharmaceutical compositions for tumour treatment
US4419446A (en) 1980-12-31 1983-12-06 The United States Of America As Represented By The Department Of Health And Human Services Recombinant DNA process utilizing a papilloma virus DNA as a vector
US4424219A (en) 1981-05-20 1984-01-03 Takeda Chemical Industries, Ltd. 9-Thiomaytansinoids and their pharmaceutical compositions and use
EP0102324A2 (en) 1982-07-29 1984-03-07 Ciba-Geigy Ag Lipids and surfactants in an aqueous medium
US4450254A (en) 1980-11-03 1984-05-22 Standard Oil Company Impact improvement of high nitrile resins
US4452775A (en) 1982-12-03 1984-06-05 Syntex (U.S.A.) Inc. Cholesterol matrix delivery system for sustained release of macromolecules
CA1176565A (en) 1980-11-18 1984-10-23 John S. Kent Microencapsulation of water soluble polypeptides
US4485045A (en) 1981-07-06 1984-11-27 Research Corporation Synthetic phosphatidyl cholines useful in forming liposomes
EP0133988A2 (en) 1983-08-02 1985-03-13 Hoechst Aktiengesellschaft Regulating peptide-containing pharmaceutical preparations with retarded release, and process for their preparation
EP0142641A2 (en) 1983-09-26 1985-05-29 Udo Dr. Ehrenfeld Means and product for the diagnosis and therapy of tumours and for the treatment of weaknesses of the cellular and humoral immune system
EP0143949A1 (en) 1983-11-01 1985-06-12 TERUMO KABUSHIKI KAISHA trading as TERUMO CORPORATION Pharmaceutical composition containing urokinase
US4544545A (en) 1983-06-20 1985-10-01 Trustees University Of Massachusetts Liposomes containing modified cholesterol for organ targeting
EP0158277A2 (en) 1984-04-11 1985-10-16 Hoechst Aktiengesellschaft Implantable controlled-release preparations of regulatory peptides, and process for their preparation
US4560655A (en) 1982-12-16 1985-12-24 Immunex Corporation Serum-free cell culture medium and process for making same
US4601978A (en) 1982-11-24 1986-07-22 The Regents Of The University Of California Mammalian metallothionein promoter system
WO1987000195A1 (en) 1985-06-28 1987-01-15 Celltech Limited Animal cell culture
US4657866A (en) 1982-12-21 1987-04-14 Sudhir Kumar Serum-free, synthetic, completely chemically defined tissue culture media
US4675189A (en) 1980-11-18 1987-06-23 Syntex (U.S.A.) Inc. Microencapsulation of water soluble active polypeptides
US4676980A (en) 1985-09-23 1987-06-30 The United States Of America As Represented By The Secretary Of The Department Of Health And Human Services Target specific cross-linked heteroantibodies
US4767704A (en) 1983-10-07 1988-08-30 Columbia University In The City Of New York Protein-free culture medium
US4816567A (en) 1983-04-08 1989-03-28 Genentech, Inc. Recombinant immunoglobin preparations
WO1990003430A1 (en) 1988-09-23 1990-04-05 Cetus Corporation Cell culture medium for enhanced cell growth, culture longevity and product expression
US4927762A (en) 1986-04-01 1990-05-22 Cell Enterprises, Inc. Cell culture medium with antioxidant
US4965199A (en) 1984-04-20 1990-10-23 Genentech, Inc. Preparation of functional human factor VIII in mammalian cells using methotrexate based selection
US4970198A (en) 1985-10-17 1990-11-13 American Cyanamid Company Antitumor antibiotics (LL-E33288 complex)
US4975278A (en) 1988-02-26 1990-12-04 Bristol-Myers Company Antibody-enzyme conjugates in combination with prodrugs for the delivery of cytotoxic agents to tumor cells
US4980286A (en) 1985-07-05 1990-12-25 Whitehead Institute For Biomedical Research In vivo introduction and expression of foreign genetic material in epithelial cells
EP0404097A2 (en) 1989-06-22 1990-12-27 BEHRINGWERKE Aktiengesellschaft Bispecific and oligospecific, mono- and oligovalent receptors, production and applications thereof
WO1991000360A1 (en) 1989-06-29 1991-01-10 Medarex, Inc. Bispecific reagents for aids therapy
EP0425235A2 (en) 1989-10-25 1991-05-02 Immunogen Inc Cytotoxic agents comprising maytansinoids and their therapeutic use
WO1991010741A1 (en) 1990-01-12 1991-07-25 Cell Genesys, Inc. Generation of xenogeneic antibodies
US5053394A (en) 1988-09-21 1991-10-01 American Cyanamid Company Targeted forms of methyltrithio antitumor agents
US5079233A (en) 1987-01-30 1992-01-07 American Cyanamid Company N-acyl derivatives of the LL-E33288 antitumor antibiotics, composition and methods for using the same
WO1992000373A1 (en) 1990-06-29 1992-01-09 Biosource Genetics Corporation Melanin production by transformed microorganisms
WO1992009690A2 (en) 1990-12-03 1992-06-11 Genentech, Inc. Enrichment method for variant proteins with altered binding properties
US5122469A (en) 1990-10-03 1992-06-16 Genentech, Inc. Method for culturing Chinese hamster ovary cells to improve production of recombinant proteins
US5133974A (en) 1989-05-05 1992-07-28 Kv Pharmaceutical Company Extended release pharmaceutical formulations
EP0517565A2 (en) 1991-05-31 1992-12-09 FIDIA S.p.A. Process for the preparation of microspheres containing biologically active components
WO1993001161A1 (en) 1991-07-11 1993-01-21 Pfizer Limited Process for preparing sertraline intermediates
US5208020A (en) 1989-10-25 1993-05-04 Immunogen Inc. Cytotoxic agents comprising maytansinoids and their therapeutic use
WO1993008829A1 (en) 1991-11-04 1993-05-13 The Regents Of The University Of California Compositions that mediate killing of hiv-infected cells
WO1993011161A1 (en) 1991-11-25 1993-06-10 Enzon, Inc. Multivalent antigen-binding proteins
WO1993015722A1 (en) 1992-02-07 1993-08-19 Syntex (Usa) Inc. Controlled delivery of pharmaceuticals from preformed porous microparticles
WO1993016185A2 (en) 1992-02-06 1993-08-19 Creative Biomolecules, Inc. Biosynthetic binding protein for cancer marker
WO1993021232A1 (en) 1992-04-10 1993-10-28 Research Development Foundation IMMUNOTOXINS DIRECTED AGAINST c-erbB-2 (HER-2/neu) RELATED SURFACE ANTIGENS
US5264365A (en) 1990-11-09 1993-11-23 Board Of Regents, The University Of Texas System Protease-deficient bacterial strains for production of proteolytically sensitive polypeptides
WO1994004690A1 (en) 1992-08-17 1994-03-03 Genentech, Inc. Bispecific immunoadhesins
WO1994011026A2 (en) 1992-11-13 1994-05-26 Idec Pharmaceuticals Corporation Therapeutic application of chimeric and radiolabeled antibodies to human b lymphocyte restricted differentiation antigen for treatment of b cell lymphoma
WO1994018221A1 (en) 1993-02-02 1994-08-18 The Scripps Research Institute Methods for producing polypeptide binding sites
WO1994020069A1 (en) 1993-03-08 1994-09-15 Amgen Inc. Pulmonary administration of granulocyte colony stimulating factor
US5362852A (en) 1991-09-27 1994-11-08 Pfizer Inc. Modified peptide derivatives conjugated at 2-hydroxyethylamine moieties
WO1994029351A2 (en) 1993-06-16 1994-12-22 Celltech Limited Antibodies
US5407686A (en) 1991-11-27 1995-04-18 Sidmak Laboratories, Inc. Sustained release composition for oral administration of active ingredient
WO1996007754A1 (en) 1994-09-02 1996-03-14 The Scripps Research Institute Methods for producing antibody libraries using universal or randomized immunoglobulin light chains
WO1996007399A1 (en) 1994-09-09 1996-03-14 Takeda Chemical Industries, Ltd. Sustained release preparation containing metal salt of a peptide
US5500362A (en) 1987-01-08 1996-03-19 Xoma Corporation Chimeric antibody with specificity to human B cell surface antigen
US5508192A (en) 1990-11-09 1996-04-16 Board Of Regents, The University Of Texas System Bacterial host strains for producing proteolytically sensitive polypeptides
US5545806A (en) 1990-08-29 1996-08-13 Genpharm International, Inc. Ransgenic non-human animals for producing heterologous antibodies
US5545807A (en) 1988-10-12 1996-08-13 The Babraham Institute Production of antibodies from transgenic animals
WO1996029998A1 (en) 1995-03-28 1996-10-03 Fidia Advanced Biopolymers S.R.L. Nanospheres comprising a biocompatible polysaccharide
WO1996032478A1 (en) 1995-04-14 1996-10-17 Genentech, Inc. Altered polypeptides with increased half-life
US5569825A (en) 1990-08-29 1996-10-29 Genpharm International Transgenic non-human animals capable of producing heterologous antibodies of various isotypes
WO1996033735A1 (en) 1995-04-27 1996-10-31 Abgenix, Inc. Human antibodies derived from immunized xenomice
WO1996034096A1 (en) 1995-04-28 1996-10-31 Abgenix, Inc. Human antibodies derived from immunized xenomice
US5571894A (en) 1991-02-05 1996-11-05 Ciba-Geigy Corporation Recombinant antibodies specific for a growth factor receptor
US5585089A (en) 1988-12-28 1996-12-17 Protein Design Labs, Inc. Humanized immunoglobulins
WO1996040072A2 (en) 1995-06-07 1996-12-19 Alkermes Controlled Therapeutics, Inc. Composition for sustained release of human growth hormone
US5587458A (en) 1991-10-07 1996-12-24 Aronex Pharmaceuticals, Inc. Anti-erbB-2 antibodies, combinations thereof, and therapeutic and diagnostic uses thereof
US5591669A (en) 1988-12-05 1997-01-07 Genpharm International, Inc. Transgenic mice depleted in a mature lymphocytic cell-type
WO1997003692A1 (en) 1995-07-14 1997-02-06 Novo Nordisk A/S A stabilized pharmaceutical formulation comprising a growth hormone pre-treated with zinc and optionally lysine or calcium ions
US5606040A (en) 1987-10-30 1997-02-25 American Cyanamid Company Antitumor and antibacterial substituted disulfide derivatives prepared from compounds possessing a methyl-trithio group
US5625126A (en) 1990-08-29 1997-04-29 Genpharm International, Inc. Transgenic non-human animals for producing heterologous antibodies
US5624821A (en) 1987-03-18 1997-04-29 Scotgen Biopharmaceuticals Incorporated Antibodies with altered effector functions
WO1997017852A1 (en) 1995-11-15 1997-05-22 Hoechst Schering Agrevo Gmbh Synergetic herbicidal mixtures
US5633425A (en) 1990-08-29 1997-05-27 Genpharm International, Inc. Transgenic non-human animals capable of producing heterologous antibodies
US5635483A (en) 1992-12-03 1997-06-03 Arizona Board Of Regents Acting On Behalf Of Arizona State University Tumor inhibiting tetrapeptide bearing modified phenethyl amides
US5641870A (en) 1995-04-20 1997-06-24 Genentech, Inc. Low pH hydrophobic interaction chromatography for antibody purification
US5648237A (en) 1991-09-19 1997-07-15 Genentech, Inc. Expression of functional antibody fragments
US5654010A (en) 1992-12-02 1997-08-05 Alkermes, Inc. Composition for sustained release of human growth hormone
WO1997030087A1 (en) 1996-02-16 1997-08-21 Glaxo Group Limited Preparation of glycosylated antibodies
US5661016A (en) 1990-08-29 1997-08-26 Genpharm International Inc. Transgenic non-human animals capable of producing heterologous antibodies of various isotypes
US5663149A (en) 1994-12-13 1997-09-02 Arizona Board Of Regents Acting On Behalf Of Arizona State University Human cancer inhibitory pentapeptide heterocyclic and halophenyl amides
WO1997034631A1 (en) 1996-03-18 1997-09-25 Board Of Regents, The University Of Texas System Immunoglobin-like domains with increased half lives
US5712374A (en) 1995-06-07 1998-01-27 American Cyanamid Company Method for the preparation of substantiallly monomeric calicheamicin derivative/carrier conjugates
US5714586A (en) 1995-06-07 1998-02-03 American Cyanamid Company Methods for the preparation of monomeric calicheamicin derivative/carrier conjugates
US5736152A (en) 1995-10-27 1998-04-07 Atrix Laboratories, Inc. Non-polymeric sustained release delivery system
US5739116A (en) 1994-06-03 1998-04-14 American Cyanamid Company Enediyne derivatives useful for the synthesis of conjugates of methyltrithio antitumor agents
WO1998024893A2 (en) 1996-12-03 1998-06-11 Abgenix, Inc. TRANSGENIC MAMMALS HAVING HUMAN IG LOCI INCLUDING PLURAL VH AND Vλ REGIONS AND ANTIBODIES PRODUCED THEREFROM
US5766886A (en) 1991-12-13 1998-06-16 Xoma Corporation Modified antibody variable domains
US5770701A (en) 1987-10-30 1998-06-23 American Cyanamid Company Process for preparing targeted forms of methyltrithio antitumor agents
US5780588A (en) 1993-01-26 1998-07-14 Arizona Board Of Regents Elucidation and synthesis of selected pentapeptides
US5789199A (en) 1994-11-03 1998-08-04 Genentech, Inc. Process for bacterial production of polypeptides
US5821337A (en) 1991-06-14 1998-10-13 Genentech, Inc. Immunoglobulin variants
US5840523A (en) 1995-03-01 1998-11-24 Genetech, Inc. Methods and compositions for secretion of heterologous polypeptides
WO1998058964A1 (en) 1997-06-24 1998-12-30 Genentech, Inc. Methods and compositions for galactosylated glycoproteins
US5869046A (en) 1995-04-14 1999-02-09 Genentech, Inc. Altered polypeptides with increased half-life
WO1999022764A1 (en) 1997-10-31 1999-05-14 Genentech, Inc. Methods and compositions comprising glycoprotein glycoforms
US5959177A (en) 1989-10-27 1999-09-28 The Scripps Research Institute Transgenic plants expressing assembled secretory antibodies
WO1999051642A1 (en) 1998-04-02 1999-10-14 Genentech, Inc. Antibody variants and fragments thereof
WO1999054342A1 (en) 1998-04-20 1999-10-28 Pablo Umana Glycosylation engineering of antibodies for improving antibody-dependent cellular cytotoxicity
US6027888A (en) 1996-04-05 2000-02-22 Board Of Regents, The University Of Texas System Methods for producing soluble, biologically-active disulfide-bond containing eukaryotic proteins in bacterial cells
US6040498A (en) 1998-08-11 2000-03-21 North Caroline State University Genetically engineered duckweed
US6083715A (en) 1997-06-09 2000-07-04 Board Of Regents, The University Of Texas System Methods for producing heterologous disulfide bond-containing polypeptides in bacterial cells
WO2000042072A2 (en) 1999-01-15 2000-07-20 Genentech, Inc. Polypeptide variants with altered effector function
WO2000061739A1 (en) 1999-04-09 2000-10-19 Kyowa Hakko Kogyo Co., Ltd. Method for controlling the activity of immunologically functional molecule
US6194551B1 (en) 1998-04-02 2001-02-27 Genentech, Inc. Polypeptide variants
US6204023B1 (en) 1985-11-01 2001-03-20 Xoma Ltd. Modular assembly of antibody genes, antibodies prepared thereby and use
WO2001029246A1 (en) 1999-10-19 2001-04-26 Kyowa Hakko Kogyo Co., Ltd. Process for producing polypeptide
US6248516B1 (en) 1988-11-11 2001-06-19 Medical Research Council Single domain ligands, receptors comprising said ligands methods for their production, and use of said ligands and receptors
US6372716B1 (en) 1994-04-26 2002-04-16 Genetics Institute, Inc. Formulations for factor IX
US6420548B1 (en) 1999-10-04 2002-07-16 Medicago Inc. Method for regulating transcription of foreign genes
US6441163B1 (en) 2001-05-31 2002-08-27 Immunogen, Inc. Methods for preparation of cytotoxic conjugates of maytansinoids and cell binding agents
US20020164328A1 (en) 2000-10-06 2002-11-07 Toyohide Shinkawa Process for purifying antibody
WO2002088172A2 (en) 2001-04-30 2002-11-07 Seattle Genetics, Inc. Pentapeptide compounds and uses related thereto
WO2003011878A2 (en) 2001-08-03 2003-02-13 Glycart Biotechnology Ag Antibody glycosylation variants having increased antibody-dependent cellular cytotoxicity
US6566329B1 (en) 1999-06-28 2003-05-20 Novo Nordisk A/S Freeze-dried preparation of human growth hormone
US20030115614A1 (en) 2000-10-06 2003-06-19 Yutaka Kanda Antibody composition-producing cell
US20030157108A1 (en) 2001-10-25 2003-08-21 Genentech, Inc. Glycoprotein compositions
US20030170646A1 (en) 2001-04-20 2003-09-11 Azad Kaushik I. BF1H1 Cassette
WO2003084570A1 (en) 2002-04-09 2003-10-16 Kyowa Hakko Kogyo Co., Ltd. DRUG CONTAINING ANTIBODY COMPOSITION APPROPRIATE FOR PATIENT SUFFERING FROM FcϜRIIIa POLYMORPHISM
WO2003085119A1 (en) 2002-04-09 2003-10-16 Kyowa Hakko Kogyo Co., Ltd. METHOD OF ENHANCING ACTIVITY OF ANTIBODY COMPOSITION OF BINDING TO FcϜ RECEPTOR IIIa
WO2004009664A2 (en) 2002-07-19 2004-01-29 Omeros Corporation Biodegradable triblock copolymers, synthesis methods therefor, and hydrogels and biomaterials made there from
US6685940B2 (en) 1995-07-27 2004-02-03 Genentech, Inc. Protein formulation
EP1391213A1 (en) 2002-08-21 2004-02-25 Boehringer Ingelheim International GmbH Compositions and methods for treating cancer using maytansinoid CD44 antibody immunoconjugates and chemotherapeutic agents
US20040093621A1 (en) 2001-12-25 2004-05-13 Kyowa Hakko Kogyo Co., Ltd Antibody composition which specifically binds to CD20
US6737056B1 (en) 1999-01-15 2004-05-18 Genentech, Inc. Polypeptide variants with altered effector function
US20040110704A1 (en) 2002-04-09 2004-06-10 Kyowa Hakko Kogyo Co., Ltd. Cells of which genome is modified
US20040110282A1 (en) 2002-04-09 2004-06-10 Kyowa Hakko Kogyo Co., Ltd. Cells in which activity of the protein involved in transportation of GDP-fucose is reduced or lost
US20040109865A1 (en) 2002-04-09 2004-06-10 Kyowa Hakko Kogyo Co., Ltd. Antibody composition-containing medicament
WO2004056312A2 (en) 2002-12-16 2004-07-08 Genentech, Inc. Immunoglobulin variants and uses thereof
US20040132140A1 (en) 2002-04-09 2004-07-08 Kyowa Hakko Kogyo Co., Ltd. Production process for antibody composition
US20050014934A1 (en) 2002-10-15 2005-01-20 Hinton Paul R. Alteration of FcRn binding affinities or serum half-lives of antibodies by mutagenesis
WO2005035778A1 (en) 2003-10-09 2005-04-21 Kyowa Hakko Kogyo Co., Ltd. PROCESS FOR PRODUCING ANTIBODY COMPOSITION BY USING RNA INHIBITING THE FUNCTION OF α1,6-FUCOSYLTRANSFERASE
WO2005035586A1 (en) 2003-10-08 2005-04-21 Kyowa Hakko Kogyo Co., Ltd. Fused protein composition
WO2005053742A1 (en) 2003-12-04 2005-06-16 Kyowa Hakko Kogyo Co., Ltd. Medicine containing antibody composition
WO2005087201A1 (en) 2004-03-18 2005-09-22 Octoplus Technologies B.V. Hydrogel microspheres with improved release profile
WO2005100402A1 (en) 2004-04-13 2005-10-27 F.Hoffmann-La Roche Ag Anti-p-selectin antibodies
US6982321B2 (en) 1986-03-27 2006-01-03 Medical Research Council Altered antibodies
US6998253B1 (en) 1995-04-14 2006-02-14 Genentech, Inc. Altered polypeptides with increased half-life
WO2006029879A2 (en) 2004-09-17 2006-03-23 F.Hoffmann-La Roche Ag Anti-ox40l antibodies
US7087409B2 (en) 1997-12-05 2006-08-08 The Scripps Research Institute Humanization of murine antibody
US7125978B1 (en) 1999-10-04 2006-10-24 Medicago Inc. Promoter for regulating expression of foreign genes
US7196185B2 (en) 2001-04-20 2007-03-27 Azad Kumar Kaushik Bovine germline D-genes and their application
JP2008118008A (en) 2006-11-07 2008-05-22 Nippon Telegr & Teleph Corp <Ntt> Method for depositing silicon compound thin film
US7498289B2 (en) 1999-02-22 2009-03-03 Celanese International Corporation Ni catalysts and methods for alkane dehydrogenation
US7498298B2 (en) 2003-11-06 2009-03-03 Seattle Genetics, Inc. Monomethylvaline compounds capable of conjugation to ligands
US7527791B2 (en) 2004-03-31 2009-05-05 Genentech, Inc. Humanized anti-TGF-beta antibodies
WO2010054007A1 (en) 2008-11-07 2010-05-14 Fabrus Llc Combinatorial antibody libraries and uses thereof

Family Cites Families (58)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
JP3095168B2 (en) 1988-02-05 2000-10-03 エル． モリソン，シェリー Antibodies with domain-denaturing constants
US6146850A (en) * 1991-11-04 2000-11-14 Xoma Corporation Proteins encoding gelonin sequences
GB9207479D0 (en) * 1992-04-06 1992-05-20 Scotgen Ltd Novel antibodies for treatment and prevention of respiratory syncytial virus infection in animals and man
US20080152586A1 (en) 1992-09-25 2008-06-26 Avipep Pty Limited High avidity polyvalent and polyspecific reagents
GB9501079D0 (en) 1995-01-19 1995-03-08 Bioinvent Int Ab Activation of T-cells
EP0739981A1 (en) * 1995-04-25 1996-10-30 Vrije Universiteit Brussel Variable fragments of immunoglobulins - use for therapeutic or veterinary purposes
GB9714680D0 (en) 1997-07-11 1997-09-17 Medical Res Council Recombinant production of proteins
AUPP221098A0 (en) 1998-03-06 1998-04-02 Diatech Pty Ltd V-like domain binding molecules
GB9912350D0 (en) * 1999-05-26 1999-07-28 European Molecular Biology Lab Embl Modified cytokine
AU782496B2 (en) 1999-07-13 2005-08-04 Bolder Biotechnology, Inc. Immunoglobulin fusion proteins
JP4439808B2 (en) 2000-06-05 2010-03-24 アルター・バイオサイエンス・コーポレーション T cell receptor fusions and conjugates and methods for their use
DK1366077T3 (en) 2000-09-15 2011-09-12 Coley Pharm Gmbh Method for screening in large quantities of CpG-based immunoagonists / antagonists
FI117667B (en) * 2001-07-05 2007-01-15 Univ Zuerich A pharmaceutical composition suitable for use in orthopedics and dentistry
WO2003030821A2 (en) 2001-10-05 2003-04-17 Human Genome Sciences, Inc. Albumin fusion proteins
EP2261250B1 (en) 2001-12-21 2015-07-01 Human Genome Sciences, Inc. GCSF-Albumin fusion proteins
US8491896B2 (en) 2002-06-14 2013-07-23 Immunomedics, Inc. Anti-pancreatic cancer antibodies
US7736652B2 (en) 2002-03-21 2010-06-15 The Regents Of The University Of California Antibody fusion proteins: effective adjuvants of protein vaccination
US7939641B2 (en) 2002-04-09 2011-05-10 The Scripps Research Institute Motif-grafted hybrid polypeptides and uses thereof
ATE386810T1 (en) 2002-06-14 2008-03-15 Dyax Corp RECOMBINATION OF NUCLEIC ACID LIBRARY MEMBERS
US7575893B2 (en) 2003-01-23 2009-08-18 Genentech, Inc. Methods for producing humanized antibodies and improving yield of antibodies or antigen binding fragments in cell culture
JP2007501021A (en) 2003-05-30 2007-01-25 アレクシオン ファーマシューティカルズ， インコーポレイテッド Antibodies and fusion proteins containing genetically engineered constant regions
WO2005000891A2 (en) 2003-06-26 2005-01-06 Merck Patent Gmbh Thrombopoietin proteins with improved properties
JP4870569B2 (en) 2003-11-13 2012-02-08 ハンミ ホールディングス カンパニー リミテッド Protein conjugate using immunoglobulin fragment and method for producing the same
TWI329649B (en) * 2003-12-22 2010-09-01 Glaxo Group Ltd Immunoglobulins
WO2005082353A2 (en) 2004-02-20 2005-09-09 Arqule, Inc. Use of beta-lapachone for treating or preventing cancer
JP2008511286A (en) 2004-06-02 2008-04-17 ダイアテック・ピーティワイ・リミテッド Binding components based on the IgNAR domain of sharks
CA2580796C (en) 2004-09-24 2013-03-26 Amgen Inc. Modified fc molecules having peptides inserted in internal loop regions
US7947839B2 (en) 2004-12-01 2011-05-24 Genentech, Inc. Heterocyclic-substituted bis-1,8 naphthalimide compounds, antibody drug conjugates, and methods of use
PT1877090E (en) 2005-05-06 2014-04-15 Providence Health System Trimeric ox40-immunoglobulin fusion protein and methods of use
CN103127523A (en) 2005-06-20 2013-06-05 Psma开发有限公司 Psma antibody-drug conjugates
BRPI0811562A2 (en) 2007-05-07 2014-12-09 Novartis Ag ORGANIC COMPOUNDS
JP2010533004A (en) * 2007-07-13 2010-10-21 バク アイピー ベスローテン フェンノートシャップ Single domain antigen binding protein that binds to mammalian IgG
MX2010001307A (en) 2007-08-02 2010-07-30 Novimmune Sa Anti-rantes antibodies and methods of use thereof.
SG193868A1 (en) 2007-09-26 2013-10-30 Chugai Pharmaceutical Co Ltd Modified antibody constant region
CA2968164C (en) 2008-04-24 2019-08-20 Dyax Corp. Libraries of genetic packages comprising novel hc cdr1, cdr2, and cdr3 and novel lc cdr1, cdr2, and cdr3 designs
EP2113255A1 (en) 2008-05-02 2009-11-04 f-star Biotechnologische Forschungs- und Entwicklungsges.m.b.H. Cytotoxic immunoglobulin
JP5346507B2 (en) * 2008-06-30 2013-11-20 公益財団法人東京都医学総合研究所 Antibody complex, antigen detection method, and antibody complex production method
US8586543B2 (en) * 2008-08-19 2013-11-19 Merck Sharp & Dohme Corp. IL-8 biomarker for monitoring cancer treatment with certain ERK inhibitors
EP2331570B1 (en) * 2008-09-10 2014-08-27 Philochem AG Display library for antibody selection
US8524863B2 (en) 2008-10-06 2013-09-03 Commonwealth Scientific And Industrial Research Organisation Amyloid-beta peptide crystal structure
AU2010203698B2 (en) * 2009-01-06 2016-07-21 C3 Jian, Inc. Targeted antimicrobial moieties
LT3912643T (en) 2009-02-13 2023-02-10 Immunomedics Inc. Immunoconjugates with an intracellularly-cleavable linkage
JP5873003B2 (en) 2009-03-18 2016-03-01 アーメイゲン・テクノロジーズ・インコーポレイテッドＡｒｍａｇｅｎ Ｔｅｃｈｎｏｌｏｇｉｅｓ， Ｉｎｃ． Compositions and methods for blood brain barrier delivery of IgG decoy receptor fusion proteins
WO2010119249A1 (en) * 2009-04-14 2010-10-21 Trojan Technologies Ltd. Therapeutic antennapedia-antibody molecules and methods of use thereof
RU2573915C2 (en) 2009-09-16 2016-01-27 Дженентек, Инк. Protein complexes containing superhelix and/or banding, and their use
DK2485761T3 (en) 2009-10-09 2019-05-06 Armagen Inc Methods and compositions for increasing iduronate-2-sulfatase activity in the CNS
EA027502B1 (en) * 2009-12-23 2017-08-31 Зиниммуне Гмбх Anti-flt3 antibodies and methods of using the same
EP2407487A1 (en) 2010-07-14 2012-01-18 F-Star Biotechnologische Forschungs - und Entwicklungsges. M.B.H. Multispecific modular antibody
US8481038B2 (en) 2010-11-15 2013-07-09 Five Prime Therapeutics, Inc. Treatment of cancer with elevated dosages of soluble FGFR1 fusion proteins
US20140303078A1 (en) 2011-06-10 2014-10-09 President And Fellows Of Harvard College Modulation of pancreatic beta cell proliferation
WO2012169822A2 (en) 2011-06-10 2012-12-13 강원대학교산학협력단 Fusion protein for suppressing cancer cell growth and suppressing vasculogenesis, and anticancer composition comprising same
AU2013208007A1 (en) 2012-01-09 2014-07-31 The Scripps Research Institute Humanized antibodies with ultralong CDR3
CA2863224A1 (en) 2012-01-09 2013-07-18 The Scripps Research Institute Ultralong complementarity determining regions and uses thereof
US8956000B2 (en) 2012-07-20 2015-02-17 Stephane Martinez System and method for illumination of a rain gutter
US9644021B2 (en) 2013-01-11 2017-05-09 The California Institute For Biomedical Research Bovine fusion antibodies
CN105593242B (en) 2013-07-11 2020-11-06 斯克利普斯研究所 Coiled coil immunoglobulin fusion proteins and compositions thereof
EP3022224A2 (en) 2013-07-18 2016-05-25 Fabrus, Inc. Antibodies with ultralong complementarity determining regions
KR20160106637A (en) 2014-01-08 2016-09-12 탱고 테크 아이엔씨 High power portable device and docking system

Patent Citations (197)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US30985A (en) 1860-12-18 Thomas l
US3887699A (en) 1969-03-24 1975-06-03 Seymour Yolles Biodegradable polymeric article for dispensing drugs
US3854480A (en) 1969-04-01 1974-12-17 Alza Corp Drug-delivery system
US3773919A (en) 1969-10-23 1973-11-20 Du Pont Polylactide-drug mixtures
US3896111A (en) 1973-02-20 1975-07-22 Research Corp Ansa macrolides
US4151042A (en) 1977-03-31 1979-04-24 Takeda Chemical Industries, Ltd. Method for producing maytansinol and its derivatives
US4137230A (en) 1977-11-14 1979-01-30 Takeda Chemical Industries, Ltd. Method for the production of maytansinoids
EP0003089A1 (en) 1978-01-06 1979-07-25 Bernard David Drier for silkscreen printed sheets
US4307016A (en) 1978-03-24 1981-12-22 Takeda Chemical Industries, Ltd. Demethyl maytansinoids
US4361650A (en) 1978-03-24 1982-11-30 Takeda Chemical Industries, Ltd. Fermentation process of preparing demethyl maytansinoids
US4265814A (en) 1978-03-24 1981-05-05 Takeda Chemical Industries Matansinol 3-n-hexadecanoate
EP0036676A1 (en) 1978-03-24 1981-09-30 The Regents Of The University Of California Method of making uniformly sized liposomes and liposomes so made
US4248870A (en) 1978-10-27 1981-02-03 Takeda Chemical Industries, Ltd. Maytansinoids and use
US4260608A (en) 1978-11-14 1981-04-07 Takeda Chemical Industries, Ltd. Maytansinoids, pharmaceutical compositions thereof and methods of use thereof
US4256746A (en) 1978-11-14 1981-03-17 Takeda Chemical Industries Dechloromaytansinoids, their pharmaceutical compositions and method of use
US4294757A (en) 1979-01-31 1981-10-13 Takeda Chemical Industries, Ltd 20-O-Acylmaytansinoids
US4322348A (en) 1979-06-05 1982-03-30 Takeda Chemical Industries, Ltd. Maytansinoids
US4317821A (en) 1979-06-08 1982-03-02 Takeda Chemical Industries, Ltd. Maytansinoids, their use and pharmaceutical compositions thereof
US4308268A (en) 1979-06-11 1981-12-29 Takeda Chemical Industries, Ltd. Maytansinoids, pharmaceutical compositions thereof and method of use thereof
US4308269A (en) 1979-06-11 1981-12-29 Takeda Chemical Industries, Ltd. Maytansinoids, pharmaceutical compositions thereof and method of use thereof
US4309428A (en) 1979-07-30 1982-01-05 Takeda Chemical Industries, Ltd. Maytansinoids
US4331598A (en) 1979-09-19 1982-05-25 Takeda Chemical Industries, Ltd. Maytansinoids
US4362663A (en) 1979-09-21 1982-12-07 Takeda Chemical Industries, Ltd. Maytansinoid compound
US4364866A (en) 1979-09-21 1982-12-21 Takeda Chemical Industries, Ltd. Maytansinoids
US4371533A (en) 1980-10-08 1983-02-01 Takeda Chemical Industries, Ltd. 4,5-Deoxymaytansinoids, their use and pharmaceutical compositions thereof
US4450254A (en) 1980-11-03 1984-05-22 Standard Oil Company Impact improvement of high nitrile resins
EP0052322A2 (en) 1980-11-10 1982-05-26 Gersonde, Klaus, Prof. Dr. Method of preparing lipid vesicles by ultrasonic treatment, the use of this method and apparatus for its application
CA1176565A (en) 1980-11-18 1984-10-23 John S. Kent Microencapsulation of water soluble polypeptides
US4675189A (en) 1980-11-18 1987-06-23 Syntex (U.S.A.) Inc. Microencapsulation of water soluble active polypeptides
US4419446A (en) 1980-12-31 1983-12-06 The United States Of America As Represented By The Department Of Health And Human Services Recombinant DNA process utilizing a papilloma virus DNA as a vector
US4313946A (en) 1981-01-27 1982-02-02 The United States Of America As Represented By The Secretary Of Agriculture Chemotherapeutically active maytansinoids from Trewia nudiflora
US4315929A (en) 1981-01-27 1982-02-16 The United States Of America As Represented By The Secretary Of Agriculture Method of controlling the European corn borer with trewiasine
EP0058481A1 (en) 1981-02-16 1982-08-25 Zeneca Limited Continuous release pharmaceutical compositions
US4424219A (en) 1981-05-20 1984-01-03 Takeda Chemical Industries, Ltd. 9-Thiomaytansinoids and their pharmaceutical compositions and use
US4485045A (en) 1981-07-06 1984-11-27 Research Corporation Synthetic phosphatidyl cholines useful in forming liposomes
EP0088046A2 (en) 1982-02-17 1983-09-07 Ciba-Geigy Ag Lipids in the aqueous phase
DE3218121A1 (en) 1982-05-14 1983-11-17 Leskovar, Peter, Dr.-Ing., 8000 München Pharmaceutical compositions for tumour treatment
EP0102324A2 (en) 1982-07-29 1984-03-07 Ciba-Geigy Ag Lipids and surfactants in an aqueous medium
US4601978A (en) 1982-11-24 1986-07-22 The Regents Of The University Of California Mammalian metallothionein promoter system
US4452775A (en) 1982-12-03 1984-06-05 Syntex (U.S.A.) Inc. Cholesterol matrix delivery system for sustained release of macromolecules
US4560655A (en) 1982-12-16 1985-12-24 Immunex Corporation Serum-free cell culture medium and process for making same
US4657866A (en) 1982-12-21 1987-04-14 Sudhir Kumar Serum-free, synthetic, completely chemically defined tissue culture media
US4816567A (en) 1983-04-08 1989-03-28 Genentech, Inc. Recombinant immunoglobin preparations
US4544545A (en) 1983-06-20 1985-10-01 Trustees University Of Massachusetts Liposomes containing modified cholesterol for organ targeting
EP0133988A2 (en) 1983-08-02 1985-03-13 Hoechst Aktiengesellschaft Regulating peptide-containing pharmaceutical preparations with retarded release, and process for their preparation
EP0142641A2 (en) 1983-09-26 1985-05-29 Udo Dr. Ehrenfeld Means and product for the diagnosis and therapy of tumours and for the treatment of weaknesses of the cellular and humoral immune system
US4767704A (en) 1983-10-07 1988-08-30 Columbia University In The City Of New York Protein-free culture medium
EP0143949A1 (en) 1983-11-01 1985-06-12 TERUMO KABUSHIKI KAISHA trading as TERUMO CORPORATION Pharmaceutical composition containing urokinase
EP0158277A2 (en) 1984-04-11 1985-10-16 Hoechst Aktiengesellschaft Implantable controlled-release preparations of regulatory peptides, and process for their preparation
US4965199A (en) 1984-04-20 1990-10-23 Genentech, Inc. Preparation of functional human factor VIII in mammalian cells using methotrexate based selection
WO1987000195A1 (en) 1985-06-28 1987-01-15 Celltech Limited Animal cell culture
US4980286A (en) 1985-07-05 1990-12-25 Whitehead Institute For Biomedical Research In vivo introduction and expression of foreign genetic material in epithelial cells
US4676980A (en) 1985-09-23 1987-06-30 The United States Of America As Represented By The Secretary Of The Department Of Health And Human Services Target specific cross-linked heteroantibodies
US4970198A (en) 1985-10-17 1990-11-13 American Cyanamid Company Antitumor antibiotics (LL-E33288 complex)
US6204023B1 (en) 1985-11-01 2001-03-20 Xoma Ltd. Modular assembly of antibody genes, antibodies prepared thereby and use
US6982321B2 (en) 1986-03-27 2006-01-03 Medical Research Council Altered antibodies
US4927762A (en) 1986-04-01 1990-05-22 Cell Enterprises, Inc. Cell culture medium with antioxidant
US5500362A (en) 1987-01-08 1996-03-19 Xoma Corporation Chimeric antibody with specificity to human B cell surface antigen
US5079233A (en) 1987-01-30 1992-01-07 American Cyanamid Company N-acyl derivatives of the LL-E33288 antitumor antibiotics, composition and methods for using the same
US5648260A (en) 1987-03-18 1997-07-15 Scotgen Biopharmaceuticals Incorporated DNA encoding antibodies with altered effector functions
US5624821A (en) 1987-03-18 1997-04-29 Scotgen Biopharmaceuticals Incorporated Antibodies with altered effector functions
US5606040A (en) 1987-10-30 1997-02-25 American Cyanamid Company Antitumor and antibacterial substituted disulfide derivatives prepared from compounds possessing a methyl-trithio group
US5770701A (en) 1987-10-30 1998-06-23 American Cyanamid Company Process for preparing targeted forms of methyltrithio antitumor agents
US5770710A (en) 1987-10-30 1998-06-23 American Cyanamid Company Antitumor and antibacterial substituted disulfide derivatives prepared from compounds possessing a methlytrithio group
US4975278A (en) 1988-02-26 1990-12-04 Bristol-Myers Company Antibody-enzyme conjugates in combination with prodrugs for the delivery of cytotoxic agents to tumor cells
US5053394A (en) 1988-09-21 1991-10-01 American Cyanamid Company Targeted forms of methyltrithio antitumor agents
WO1990003430A1 (en) 1988-09-23 1990-04-05 Cetus Corporation Cell culture medium for enhanced cell growth, culture longevity and product expression
US5545807A (en) 1988-10-12 1996-08-13 The Babraham Institute Production of antibodies from transgenic animals
US6248516B1 (en) 1988-11-11 2001-06-19 Medical Research Council Single domain ligands, receptors comprising said ligands methods for their production, and use of said ligands and receptors
US5591669A (en) 1988-12-05 1997-01-07 Genpharm International, Inc. Transgenic mice depleted in a mature lymphocytic cell-type
US5585089A (en) 1988-12-28 1996-12-17 Protein Design Labs, Inc. Humanized immunoglobulins
US5693762A (en) 1988-12-28 1997-12-02 Protein Design Labs, Inc. Humanized immunoglobulins
US5133974A (en) 1989-05-05 1992-07-28 Kv Pharmaceutical Company Extended release pharmaceutical formulations
EP0404097A2 (en) 1989-06-22 1990-12-27 BEHRINGWERKE Aktiengesellschaft Bispecific and oligospecific, mono- and oligovalent receptors, production and applications thereof
WO1991000360A1 (en) 1989-06-29 1991-01-10 Medarex, Inc. Bispecific reagents for aids therapy
EP0425235A2 (en) 1989-10-25 1991-05-02 Immunogen Inc Cytotoxic agents comprising maytansinoids and their therapeutic use
US5208020A (en) 1989-10-25 1993-05-04 Immunogen Inc. Cytotoxic agents comprising maytansinoids and their therapeutic use
US5416064A (en) 1989-10-25 1995-05-16 Immunogen, Inc. Cytotoxic agents comprising maytansinoids and their therapeutic use
US5959177A (en) 1989-10-27 1999-09-28 The Scripps Research Institute Transgenic plants expressing assembled secretory antibodies
US6417429B1 (en) 1989-10-27 2002-07-09 The Scripps Research Institute Transgenic plants expressing assembled secretory antibodies
WO1991010741A1 (en) 1990-01-12 1991-07-25 Cell Genesys, Inc. Generation of xenogeneic antibodies
WO1992000373A1 (en) 1990-06-29 1992-01-09 Biosource Genetics Corporation Melanin production by transformed microorganisms
US5625126A (en) 1990-08-29 1997-04-29 Genpharm International, Inc. Transgenic non-human animals for producing heterologous antibodies
US5569825A (en) 1990-08-29 1996-10-29 Genpharm International Transgenic non-human animals capable of producing heterologous antibodies of various isotypes
US5633425A (en) 1990-08-29 1997-05-27 Genpharm International, Inc. Transgenic non-human animals capable of producing heterologous antibodies
US5545806A (en) 1990-08-29 1996-08-13 Genpharm International, Inc. Ransgenic non-human animals for producing heterologous antibodies
US5661016A (en) 1990-08-29 1997-08-26 Genpharm International Inc. Transgenic non-human animals capable of producing heterologous antibodies of various isotypes
US5122469A (en) 1990-10-03 1992-06-16 Genentech, Inc. Method for culturing Chinese hamster ovary cells to improve production of recombinant proteins
US5264365A (en) 1990-11-09 1993-11-23 Board Of Regents, The University Of Texas System Protease-deficient bacterial strains for production of proteolytically sensitive polypeptides
US5508192A (en) 1990-11-09 1996-04-16 Board Of Regents, The University Of Texas System Bacterial host strains for producing proteolytically sensitive polypeptides
WO1992009690A2 (en) 1990-12-03 1992-06-11 Genentech, Inc. Enrichment method for variant proteins with altered binding properties
US5571894A (en) 1991-02-05 1996-11-05 Ciba-Geigy Corporation Recombinant antibodies specific for a growth factor receptor
EP0517565A2 (en) 1991-05-31 1992-12-09 FIDIA S.p.A. Process for the preparation of microspheres containing biologically active components
US5821337A (en) 1991-06-14 1998-10-13 Genentech, Inc. Immunoglobulin variants
WO1993001161A1 (en) 1991-07-11 1993-01-21 Pfizer Limited Process for preparing sertraline intermediates
US5648237A (en) 1991-09-19 1997-07-15 Genentech, Inc. Expression of functional antibody fragments
US5362852A (en) 1991-09-27 1994-11-08 Pfizer Inc. Modified peptide derivatives conjugated at 2-hydroxyethylamine moieties
US5587458A (en) 1991-10-07 1996-12-24 Aronex Pharmaceuticals, Inc. Anti-erbB-2 antibodies, combinations thereof, and therapeutic and diagnostic uses thereof
WO1993008829A1 (en) 1991-11-04 1993-05-13 The Regents Of The University Of California Compositions that mediate killing of hiv-infected cells
WO1993011161A1 (en) 1991-11-25 1993-06-10 Enzon, Inc. Multivalent antigen-binding proteins
US5407686A (en) 1991-11-27 1995-04-18 Sidmak Laboratories, Inc. Sustained release composition for oral administration of active ingredient
US5766886A (en) 1991-12-13 1998-06-16 Xoma Corporation Modified antibody variable domains
WO1993016185A2 (en) 1992-02-06 1993-08-19 Creative Biomolecules, Inc. Biosynthetic binding protein for cancer marker
WO1993015722A1 (en) 1992-02-07 1993-08-19 Syntex (Usa) Inc. Controlled delivery of pharmaceuticals from preformed porous microparticles
WO1993021232A1 (en) 1992-04-10 1993-10-28 Research Development Foundation IMMUNOTOXINS DIRECTED AGAINST c-erbB-2 (HER-2/neu) RELATED SURFACE ANTIGENS
WO1994004690A1 (en) 1992-08-17 1994-03-03 Genentech, Inc. Bispecific immunoadhesins
WO1994011026A2 (en) 1992-11-13 1994-05-26 Idec Pharmaceuticals Corporation Therapeutic application of chimeric and radiolabeled antibodies to human b lymphocyte restricted differentiation antigen for treatment of b cell lymphoma
US5654010A (en) 1992-12-02 1997-08-05 Alkermes, Inc. Composition for sustained release of human growth hormone
US5635483A (en) 1992-12-03 1997-06-03 Arizona Board Of Regents Acting On Behalf Of Arizona State University Tumor inhibiting tetrapeptide bearing modified phenethyl amides
US5780588A (en) 1993-01-26 1998-07-14 Arizona Board Of Regents Elucidation and synthesis of selected pentapeptides
WO1994018221A1 (en) 1993-02-02 1994-08-18 The Scripps Research Institute Methods for producing polypeptide binding sites
WO1994020069A1 (en) 1993-03-08 1994-09-15 Amgen Inc. Pulmonary administration of granulocyte colony stimulating factor
WO1994029351A2 (en) 1993-06-16 1994-12-22 Celltech Limited Antibodies
US6372716B1 (en) 1994-04-26 2002-04-16 Genetics Institute, Inc. Formulations for factor IX
US5739116A (en) 1994-06-03 1998-04-14 American Cyanamid Company Enediyne derivatives useful for the synthesis of conjugates of methyltrithio antitumor agents
US5877296A (en) 1994-06-03 1999-03-02 American Cyanamid Company Process for preparing conjugates of methyltrithio antitumor agents
US5773001A (en) 1994-06-03 1998-06-30 American Cyanamid Company Conjugates of methyltrithio antitumor agents and intermediates for their synthesis
US5767285A (en) 1994-06-03 1998-06-16 American Cyanamid Company Linkers useful for the synthesis of conjugates of methyltrithio antitumor agents
WO1996007754A1 (en) 1994-09-02 1996-03-14 The Scripps Research Institute Methods for producing antibody libraries using universal or randomized immunoglobulin light chains
WO1996007399A1 (en) 1994-09-09 1996-03-14 Takeda Chemical Industries, Ltd. Sustained release preparation containing metal salt of a peptide
US5789199A (en) 1994-11-03 1998-08-04 Genentech, Inc. Process for bacterial production of polypeptides
US5663149A (en) 1994-12-13 1997-09-02 Arizona Board Of Regents Acting On Behalf Of Arizona State University Human cancer inhibitory pentapeptide heterocyclic and halophenyl amides
US5840523A (en) 1995-03-01 1998-11-24 Genetech, Inc. Methods and compositions for secretion of heterologous polypeptides
WO1996029998A1 (en) 1995-03-28 1996-10-03 Fidia Advanced Biopolymers S.R.L. Nanospheres comprising a biocompatible polysaccharide
WO1996032478A1 (en) 1995-04-14 1996-10-17 Genentech, Inc. Altered polypeptides with increased half-life
US6998253B1 (en) 1995-04-14 2006-02-14 Genentech, Inc. Altered polypeptides with increased half-life
US5869046A (en) 1995-04-14 1999-02-09 Genentech, Inc. Altered polypeptides with increased half-life
US5641870A (en) 1995-04-20 1997-06-24 Genentech, Inc. Low pH hydrophobic interaction chromatography for antibody purification
WO1996033735A1 (en) 1995-04-27 1996-10-31 Abgenix, Inc. Human antibodies derived from immunized xenomice
WO1996034096A1 (en) 1995-04-28 1996-10-31 Abgenix, Inc. Human antibodies derived from immunized xenomice
US5712374A (en) 1995-06-07 1998-01-27 American Cyanamid Company Method for the preparation of substantiallly monomeric calicheamicin derivative/carrier conjugates
WO1996040072A2 (en) 1995-06-07 1996-12-19 Alkermes Controlled Therapeutics, Inc. Composition for sustained release of human growth hormone
US5714586A (en) 1995-06-07 1998-02-03 American Cyanamid Company Methods for the preparation of monomeric calicheamicin derivative/carrier conjugates
WO1997003692A1 (en) 1995-07-14 1997-02-06 Novo Nordisk A/S A stabilized pharmaceutical formulation comprising a growth hormone pre-treated with zinc and optionally lysine or calcium ions
US6685940B2 (en) 1995-07-27 2004-02-03 Genentech, Inc. Protein formulation
US5736152A (en) 1995-10-27 1998-04-07 Atrix Laboratories, Inc. Non-polymeric sustained release delivery system
WO1997017852A1 (en) 1995-11-15 1997-05-22 Hoechst Schering Agrevo Gmbh Synergetic herbicidal mixtures
WO1997030087A1 (en) 1996-02-16 1997-08-21 Glaxo Group Limited Preparation of glycosylated antibodies
WO1997034631A1 (en) 1996-03-18 1997-09-25 Board Of Regents, The University Of Texas System Immunoglobin-like domains with increased half lives
US6027888A (en) 1996-04-05 2000-02-22 Board Of Regents, The University Of Texas System Methods for producing soluble, biologically-active disulfide-bond containing eukaryotic proteins in bacterial cells
WO1998024893A2 (en) 1996-12-03 1998-06-11 Abgenix, Inc. TRANSGENIC MAMMALS HAVING HUMAN IG LOCI INCLUDING PLURAL VH AND Vλ REGIONS AND ANTIBODIES PRODUCED THEREFROM
US6083715A (en) 1997-06-09 2000-07-04 Board Of Regents, The University Of Texas System Methods for producing heterologous disulfide bond-containing polypeptides in bacterial cells
WO1998058964A1 (en) 1997-06-24 1998-12-30 Genentech, Inc. Methods and compositions for galactosylated glycoproteins
WO1999022764A1 (en) 1997-10-31 1999-05-14 Genentech, Inc. Methods and compositions comprising glycoprotein glycoforms
US7087409B2 (en) 1997-12-05 2006-08-08 The Scripps Research Institute Humanization of murine antibody
WO1999051642A1 (en) 1998-04-02 1999-10-14 Genentech, Inc. Antibody variants and fragments thereof
US6194551B1 (en) 1998-04-02 2001-02-27 Genentech, Inc. Polypeptide variants
WO1999054342A1 (en) 1998-04-20 1999-10-28 Pablo Umana Glycosylation engineering of antibodies for improving antibody-dependent cellular cytotoxicity
US6602684B1 (en) 1998-04-20 2003-08-05 Glycart Biotechnology Ag Glycosylation engineering of antibodies for improving antibody-dependent cellular cytotoxicity
US20040072290A1 (en) 1998-04-20 2004-04-15 Glycart Biotechnology Ag Glycosylation engineering of antibodies for improving antibody-dependent cellular cytotoxicity
US7517670B2 (en) 1998-04-20 2009-04-14 Glycart Biotechnology Ag Glycosylation engineering of antibodies for improving antibody-dependent cellular cytotoxicity
US6040498A (en) 1998-08-11 2000-03-21 North Caroline State University Genetically engineered duckweed
US7332581B2 (en) 1999-01-15 2008-02-19 Genentech, Inc. Polypeptide variants with altered effector function
US7371826B2 (en) 1999-01-15 2008-05-13 Genentech, Inc. Polypeptide variants with altered effector function
WO2000042072A2 (en) 1999-01-15 2000-07-20 Genentech, Inc. Polypeptide variants with altered effector function
US6737056B1 (en) 1999-01-15 2004-05-18 Genentech, Inc. Polypeptide variants with altered effector function
US7498289B2 (en) 1999-02-22 2009-03-03 Celanese International Corporation Ni catalysts and methods for alkane dehydrogenation
US7214775B2 (en) 1999-04-09 2007-05-08 Kyowa Hakko Kogyo Co., Ltd. Method of modulating the activity of functional immune molecules
WO2000061739A1 (en) 1999-04-09 2000-10-19 Kyowa Hakko Kogyo Co., Ltd. Method for controlling the activity of immunologically functional molecule
US7682610B2 (en) 1999-04-09 2010-03-23 Kyowa Hakko Kirin Co., Ltd Method of modulating the activity of functional immune molecules
US6566329B1 (en) 1999-06-28 2003-05-20 Novo Nordisk A/S Freeze-dried preparation of human growth hormone
US6420548B1 (en) 1999-10-04 2002-07-16 Medicago Inc. Method for regulating transcription of foreign genes
US7125978B1 (en) 1999-10-04 2006-10-24 Medicago Inc. Promoter for regulating expression of foreign genes
WO2001029246A1 (en) 1999-10-19 2001-04-26 Kyowa Hakko Kogyo Co., Ltd. Process for producing polypeptide
US20030115614A1 (en) 2000-10-06 2003-06-19 Yutaka Kanda Antibody composition-producing cell
US6946292B2 (en) 2000-10-06 2005-09-20 Kyowa Hakko Kogyo Co., Ltd. Cells producing antibody compositions with increased antibody dependent cytotoxic activity
US20020164328A1 (en) 2000-10-06 2002-11-07 Toyohide Shinkawa Process for purifying antibody
US7064191B2 (en) 2000-10-06 2006-06-20 Kyowa Hakko Kogyo Co., Ltd. Process for purifying antibody
US20030170646A1 (en) 2001-04-20 2003-09-11 Azad Kaushik I. BF1H1 Cassette
US6740747B2 (en) 2001-04-20 2004-05-25 Azad Kaushik Bovine VDJ cassette, BF1H1, suitable for antigenization
US7196185B2 (en) 2001-04-20 2007-03-27 Azad Kumar Kaushik Bovine germline D-genes and their application
WO2002088172A2 (en) 2001-04-30 2002-11-07 Seattle Genetics, Inc. Pentapeptide compounds and uses related thereto
US6441163B1 (en) 2001-05-31 2002-08-27 Immunogen, Inc. Methods for preparation of cytotoxic conjugates of maytansinoids and cell binding agents
WO2003011878A2 (en) 2001-08-03 2003-02-13 Glycart Biotechnology Ag Antibody glycosylation variants having increased antibody-dependent cellular cytotoxicity
US20030157108A1 (en) 2001-10-25 2003-08-21 Genentech, Inc. Glycoprotein compositions
US20040093621A1 (en) 2001-12-25 2004-05-13 Kyowa Hakko Kogyo Co., Ltd Antibody composition which specifically binds to CD20
US20040132140A1 (en) 2002-04-09 2004-07-08 Kyowa Hakko Kogyo Co., Ltd. Production process for antibody composition
US7749753B2 (en) 2002-04-09 2010-07-06 Kyowa Hakko Kirin Co., Ltd Cells in which activity of the protein involved in transportation of GDP-fucose is reduced or lost
WO2003084570A1 (en) 2002-04-09 2003-10-16 Kyowa Hakko Kogyo Co., Ltd. DRUG CONTAINING ANTIBODY COMPOSITION APPROPRIATE FOR PATIENT SUFFERING FROM FcϜRIIIa POLYMORPHISM
US20040110282A1 (en) 2002-04-09 2004-06-10 Kyowa Hakko Kogyo Co., Ltd. Cells in which activity of the protein involved in transportation of GDP-fucose is reduced or lost
WO2003085119A1 (en) 2002-04-09 2003-10-16 Kyowa Hakko Kogyo Co., Ltd. METHOD OF ENHANCING ACTIVITY OF ANTIBODY COMPOSITION OF BINDING TO FcϜ RECEPTOR IIIa
US20040109865A1 (en) 2002-04-09 2004-06-10 Kyowa Hakko Kogyo Co., Ltd. Antibody composition-containing medicament
US20040110704A1 (en) 2002-04-09 2004-06-10 Kyowa Hakko Kogyo Co., Ltd. Cells of which genome is modified
WO2004009664A2 (en) 2002-07-19 2004-01-29 Omeros Corporation Biodegradable triblock copolymers, synthesis methods therefor, and hydrogels and biomaterials made there from
EP1391213A1 (en) 2002-08-21 2004-02-25 Boehringer Ingelheim International GmbH Compositions and methods for treating cancer using maytansinoid CD44 antibody immunoconjugates and chemotherapeutic agents
US20050014934A1 (en) 2002-10-15 2005-01-20 Hinton Paul R. Alteration of FcRn binding affinities or serum half-lives of antibodies by mutagenesis
WO2004056312A2 (en) 2002-12-16 2004-07-08 Genentech, Inc. Immunoglobulin variants and uses thereof
WO2005035586A1 (en) 2003-10-08 2005-04-21 Kyowa Hakko Kogyo Co., Ltd. Fused protein composition
WO2005035778A1 (en) 2003-10-09 2005-04-21 Kyowa Hakko Kogyo Co., Ltd. PROCESS FOR PRODUCING ANTIBODY COMPOSITION BY USING RNA INHIBITING THE FUNCTION OF α1,6-FUCOSYLTRANSFERASE
US7498298B2 (en) 2003-11-06 2009-03-03 Seattle Genetics, Inc. Monomethylvaline compounds capable of conjugation to ligands
WO2005053742A1 (en) 2003-12-04 2005-06-16 Kyowa Hakko Kogyo Co., Ltd. Medicine containing antibody composition
WO2005087201A1 (en) 2004-03-18 2005-09-22 Octoplus Technologies B.V. Hydrogel microspheres with improved release profile
US7527791B2 (en) 2004-03-31 2009-05-05 Genentech, Inc. Humanized anti-TGF-beta antibodies
WO2005100402A1 (en) 2004-04-13 2005-10-27 F.Hoffmann-La Roche Ag Anti-p-selectin antibodies
WO2006029879A2 (en) 2004-09-17 2006-03-23 F.Hoffmann-La Roche Ag Anti-ox40l antibodies
JP2008118008A (en) 2006-11-07 2008-05-22 Nippon Telegr & Teleph Corp <Ntt> Method for depositing silicon compound thin film
WO2010054007A1 (en) 2008-11-07 2010-05-14 Fabrus Llc Combinatorial antibody libraries and uses thereof

Non-Patent Citations (212)

* Cited by examiner, † Cited by third party
Title
"Medical Applications of Controlled Release", 1974, CRC PRES.
"Molecular Biology--Hybridization with Nucleic Probes", 1993, article "Overview of principles of hybridization and the strategy of nucleic acid assays"
ADAMS ET AL., ACTA CRYSTALLOGR D BIOL CRYSTALLOGR, vol. 66, 2010, pages 213 - 221
ALMAGROFRANSSON, FRONT. BIOSCI., vol. 13, 2008, pages 1619 - 1633
ANGAL ET AL., MOL. IMMUNOL., vol. 30, 1993, pages 105 - 8
ARIE ET AL., MOL. MICROBIOL., vol. 39, 2001, pages 199 - 210
ARNDT ET AL., J MOL BIOL., vol. 7, no. 312, 2001, pages 221 - 228
BACA ET AL., BIOL. CHEM., vol. 272, 1997, pages 10678 - 10684
BAKER MJONES TD: "The identification and removal of immunogenicity in therapeutic proteins", CURR. OPIN. DRUG DISCOVERY DEV., vol. 10, no. 2, 2007, pages 219 - 227, XP009109828
BALDWIN ET AL., LANCET, 15 March 1986 (1986-03-15), pages 603 - 05
BARBAS ET AL., PROC NAT. ACAD. SCI. USA, vol. 113, 1994, pages 3809 - 3813
BARBAS ET AL., PROC. NATL. ACAD. SCI. USA, vol. 89, 1992, pages 3576 - 3580
BARNES ET AL., ANAL. BIOCHEM., vol. 102, 1980, pages 255
BASS ET AL., PROTEINS, vol. 8, 1990, pages 309 - 314
BEAUCAGECARUTHERS, TETRAHEDRON LETTERS, vol. 22, 1981, pages 1859 - 1862
BERENS ET AL., INT. IMMUNOL., vol. 9, 1997, pages 189 - 199
BIOCHEM., vol. 11, 1972, pages 1726
BOTHMANNPLUCKTHUN, J. BIOL. CHEM., vol. 275, 2000, pages 17106 - 17113
BRADLEY ET AL., NATURE, vol. 309, 1984, pages 255 - 258
BRENNAN ET AL., SCIENCE, vol. 228, 1985, pages 190
BRUGGEMANN ET AL., YEAR IN IMMUNO., vol. 7, 1993, pages 33
BRUGGEMANN, M. ET AL., EXP. MED., vol. 166, 1987, pages 1351 - 1361
BUCHWALD ET AL., SURGERY, vol. 88, 1980, pages 507
CAPECCHI ET AL., TRENDS GENET., vol. 5, 1989, pages 70 - 76
CAPEL ET AL., IMMUNOMETHODS, vol. 4, 1994, pages 25 - 34
CARLSSON ET AL., BIOCHEM. J., vol. 173, 1978, pages 723 - 737
CARTER ET AL., BIO/TECHNOLOGY, vol. 10, 1992, pages 163 - 167
CHARI ET AL., CANCER RESEARCH, vol. 52, 1992, pages 127 - 131
CHEN ET AL., J BIO CHEM, vol. 274, 1999, pages 19601 - 19605
CHEUNG ET AL., VIROLOGY, vol. 176, 1990, pages 546 - 552
CHOTHIA, C. ET AL., J. MOL. BIOL., vol. 196, 1987, pages 901 - 917
CLACKSON ET AL., NATURE, vol. 352, 1991, pages 624 - 628
CLELAND: "Vaccine Design: The Subunit and Adjuvant Approach", 1995, PLENUM PRESS, article "Design and Production of Single Immunization Vaccines Using Polylactide Polyglycolide Microsphere Systems", pages: 439 - 462
CLYNES ET AL., PROC. NAT'L ACAD. SCI. USA, vol. 95, 1998, pages 652 - 656
CLYNES ET AL., PROC. NATL. ACAD. SCI. USA, vol. 95, 1998, pages 652 - 656
CORTIVO ET AL., BIOMATERIALS, vol. 12, 1991, pages 727 - 730
CRAGG, M. S. ET AL., BLOOD, vol. 101, 2003, pages 1045 - 1052
CRAGG, M. SM. J. GLENNIE, BLOOD, vol. 103, 2004, pages 27382743
CREIGHTON, PROTEINS, 1984
CUNNINGHAMWELLS, SCIENCE, vol. 244, 1989, pages 1288 - 1292
DAI ET AL., COLLOIDS SURF B BIOINTERFACES, vol. 41, 2005, pages 117
DALL'ACQUA ET AL., METHODS, vol. 36, 2005, pages 61 - 68
DORONINA ET AL., NATURE BIOTECHNOLOGY, vol. 21, no. 7, 2003, pages 778 - 784
DORONINA, NAT BIOTECHNOL, vol. 21, no. 7, 2003, pages 778 - 784
DP SIMMONS ET AL., PROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, vol. 71, 2008, pages 119 - 130
DRUGS OF THE FUTURE, vol. 25, no. 7, 2000, pages 686
DURING ET AL., ANN. NEUROL., vol. 25, 1989, pages 351
E. SCHRODERK. LUBKE: "The Peptides", vol. 1, 1965, ACADEMIC PRESS, pages: 76 - 136
EDGAR, NUCLEIC ACIDS RESEARCH, vol. 32, 2004, pages 1792 - 1797
EMBLETON ET AL., NUCL. ACIDS RES., vol. 227, 1992, pages 3831 - 3837
EPPSTEIN ET AL., PROC. NATL. ACAD. SCI. USA, vol. 82, 1985, pages 3688 - 3692
EVANS, NATURE, vol. 292, 1981, pages 154 - 156
FELLOUSE, PROC. NAT. ACAD. SCI. USA, vol. 101, no. 34, 2004, pages 12467 - 12472
FELLOUSE, PROC. NATL. ACAD. SCI. USA, vol. 101, no. 34, 2004, pages 12467 - 12472
FISHWILD ET AL., NATURE BIOTECHNOLOGY, vol. 14, 1996, pages 826 - 851
FRAKER ET AL., BIOCHEM. BIOPHYS. RES. COMMUN., vol. 80, 1978, pages 49 - 57
FROHMAN ET AL., CELL, vol. 56, 1989, pages 145 - 147
GAZZANO-SANTORO ET AL., IMMUNOL. METHODS, vol. 202, 1996, pages 163
GAZZANO-SANTORO ET AL., J. IMMUNOL. METHODS, vol. 202, 1996, pages 163
GEMGROSS, NAT. BIOTECH., vol. 22, 2004, pages 1409 - 1414
GEOGHEGANSTROH, BIOCONJUGATE CHEM., vol. 3, 1992, pages 138 - 146
GOODSON, MEDICAL APPLICATIONS OF CONTROLLED RELEASE, vol. 2, 1984, pages 115 - 138
GOSSLER ET AL., PROC. NATL. ACAD. SCI. USA, vol. 83, 1986, pages 9065 - 9069
GRAHAM ET AL., GEN VLI'OL., vol. 36, 1977, pages 59
GRAHAM ET AL., J. GEN VIROL., vol. 36, 1977, pages 59
GRIFFITHS ET AL., EMBO J., vol. 12, 1993, pages 725 - 734
GRUBER ET AL., J. IMMUNOL., vol. 152, 1994, pages 5368
GUSS ET AL., EMBO J., vol. 5, 1986, pages 15671575
GUYER ET AL., J. IMMUNOL., vol. 117, 1976, pages 587
GUYER, IMMUNOL., vol. 117, 1976, pages 587
HAAS ET AL., J. LAB. CLIN. MED., vol. 126, 1995, pages 330 - 41
HAM ET AL., METH. ENZ., vol. 58, 1979, pages 44
HAMMER ET AL., J. ANIMAL. SCI., vol. 63, 1986, pages 269
HAMMER ET AL., NATURE, vol. 315, 1985, pages 680
HARA ET AL., MICROBIAL DRUG RESISTANCE, vol. 2, 1996, pages 63 - 72
HARRIS, BIOCHEM. SOC. TRANSACTIONS, vol. 23, 1995, pages 1035 - 1038
HELLSTROM, I ET AL., PROC. NAT'L ACAD. SCI. USA, vol. 82, 1985, pages 1499 - 1502
HELLSTROM, I. ET AL., PROC. NAT'! ACAD. SCI. USA, vol. 83, 1986, pages 7059 - 7063
HINMAN ET AL., CANCER RES., vol. 53, 1993, pages 3336 - 3342
HINMAN ET AL., CANCER RESEARCH, 1993, pages 3336 - 3342
HOGREFE ET AL., GENE, vol. 128, 1993, pages 119 - 126
HOOGENBOOM ET AL., NUCL. ACIDS RES., vol. 19, 1991, pages 4133 - 4137
HOOGENBOOM ET AL.: "Methods in Molecular Biology", vol. 248, 2003, HUMANA PRESS, article "Recombinant Antibodies for Cancer Therapy Methods and Protocols", pages: 255 - 268
HORA ET AL., BIO/TECHNOLOGY, vol. 8, 1990, pages 755 - 758
HOSSEINI ET AL., INT. IMMUNOL., vol. 16, 2004, pages 843 - 852
HOWARD ET AL., J. NEUROSURG., vol. 71, 1989, pages 105
HUDSON ET AL., NAT. MED., vol. 9, 2003, pages 129134 - 134
HURLEGROSS, CURR. OP. BIOTECH., vol. 5, 1994, pages 428 - 433
HUST ET AL., BMC BIOTECHNOLOGY, vol. 7, 2007, pages 14
IDUSOGIE ET AL., IMMUNOL., vol. 164, 2000, pages 41784184
IDUSOGIE ET AL., J. IMMUNOL., vol. 164, 2000, pages 4178 - 4184
ILIUM ET AL., J. CONTROLLED REL., vol. 29, 1994, pages 133 - 141
J. BIOL. CHEM., vol. 243, 1969, pages 3552 - 3559
JACKSON ET AL., J. IMMUNOL., vol. 154, no. 7, 1995, pages 3310 - 2004
JAKOBOVITS ET AL., NATURE, vol. 362, 1993, pages 255 - 258
JAKOBOVITS ET AL., PROC. NATL. ACAD. SCI. USA, vol. 90, 1993, pages 6444 - 6448
JOHNSON ET AL., NAT. MED., vol. 2, 1996, pages 795 - 799
JOLIOT ET AL., PROC. NATL. ACAD. SCI. USA, vol. 88, 1991, pages 1864 - 1868
JONES ET AL., BIOTECHNOL., vol. 9, 1991, pages 88 - 89
JONES TDCROMPTON LJCARR FJBAKER MP, METHODS MOL BIOL., vol. 525, 2009, pages 405 - 23
KIM ET AL., IMMUNOL., vol. 24, 1994, pages 249
KIRKLAND ET AL., J. IMMUNOL., vol. 137, 1986, pages 3614 - 3619
KLIMKA ET AL., BR. J. CANCER, vol. 83, 2000, pages 252 - 260
KOHLER ET AL., NATURE, vol. 256, 1975, pages 495
KOSTELNY ET AL., J. IMMUNOL., vol. 148, no. 5, 1992, pages 1547 - 1553
KOTI ET AL., MOL. IMMUNOL., vol. 47, 2010, pages 2119 - 2128
KOZBOR, J. IMMUNOL., vol. 133, 1984, pages 3001
LANGER ET AL., J. BIOMED. MATER. RES., vol. 15, 1981, pages 167 - 277
LANGER, SCIENCE, vol. 249, 1990, pages 1527 - 1533
LEE ET AL., J. IMMUNOL. METHODS, vol. 284, no. 1-2, 2004, pages 1 19 - 132
LEFRACE ET AL., NUCL. ACIDS, RES., vol. 37, 2009, pages D1006 - D1012
LEFRANC ET AL., BRIEFINGS IN BIOINFORMATICS, vol. 9, 2008, pages 263 - 275
LEFRANC, NUCLEIC ACIDS RES., vol. 31, 2003, pages 307 - 310
LEUNG ET AL., TECHNIQUE, vol. 1, 1989, pages 11 - 15
LEWIS: "Biodegradable Polymers as Drug Delivery Systems", 1990, MARCEL DEKKER, article "Controlled release of bioactive agents from lactide/glycolide polyme", pages: 1 - 41
LI ET AL., NAT. BIOTECH., vol. 24, 2006, pages 210 - 215
LINDMARK ET AL., J. IMMUNOL. METH., vol. 62, 1983, pages 1 - 13
LIU ET AL., PROC. NATL. ACAD. SCI. USA, vol. 93, 1996, pages 8618 - 8623
LODE ET AL., CANCER RES., vol. 58, 1998, pages 2928
LODE ET AL., CANCER RESEARCH, vol. 58, 1998, pages 2925 - 2928
LONBERG ET AL., NATURE, vol. 368, 1994, pages 812 - 813
LONBERGHUSZAR, INTERN. REV. IMMUNOL., vol. 13, 1995, pages 65 - 93
M. IN DAERON, ANNU. REV. IMMUNOL., vol. 15, 1997, pages 203 - 234
MANDLER ET AL., BIOCONJUGATE CHEM., vol. 13, 2002, pages 786 - 791
MANDLER ET AL., BIOORGANIC & MED. CHEM. LETTERS, vol. 10, 2000, pages 1025 - 1028
MANDLER ET AL., JOUR. OF THE NAT. CANCER INST., vol. 92, no. 19, 2000, pages 1573 - 1581
MAO ET AL., NAT BIOTECH, vol. 28, 2010, pages 1195 - 1202
MARKS ET AL., BIOTECHNOL., vol. 10, 1992, pages 779 - 783
MARKS ET AL., J. MOL. BIOL., vol. 222, 1991, pages 581 - 597
MARSTON ET AL., METH. ENZ., vol. 182, 1990, pages 264 - 275
MATHER ET AL., ANNALS N.Y. ACAD. SCI., vol. 383, 1982, pages 44 - 68
MATHER ET AL., ANNALS NI'. ACAD. SCI., vol. 383, 1982, pages 44 - 68
MATHER, BIOL. REPROD., vol. 23, 1980, pages 243 - 251
MATSUDA ET AL., NATURE GENET., vol. 3, 1993, pages 88 - 94
MCCAFFERTY ET AL., NATURE, vol. 341, 1989, pages 544 - 546
MOLDENHAUER ET AL., SCAND. J. IMMUNOL., vol. 32, 1990, pages 77 - 82
MOREL ET AL., MOLEC. IMMUNOL., vol. 25, no. 1, 1988, pages 7 - 15
MORIMOTO ET AL., JOURNAL OF BIOCHEMICAL AND BIOPHYSICAL METHODS, vol. 24, 1992, pages 107 - 117
MORRISON ET AL., PROC. NATL. ACAD. SCI. USA, vol. 81, 1984, pages 6851 - 6855
MOSBACH ET AL., NATURE, vol. 302, 1983, pages 543 - 545
NICULESCU-DUVAZSPRINGER, ADV. DRG DEL. REV., vol. 26, 1997, pages 151 - 172
NJONGMETA ET AL., VACCINE, vol. 30, 2012, pages 1624 - 1635
OKAZAKI ET AL., J. MOL. BIOL., vol. 336, no. 5, 2004, pages 1239 - 1249
ORLANDI ET AL., PROC. NATL. ACAD. SCI. (USA, vol. 86, 1989, pages 5728 - 5732
ORUM ET AL., NUCLEIC ACIDS RES., vol. 21, 1993, pages 4491 - 4498
PADLAN, MOL. IMMUNOL., vol. 1-3, 1991, pages 489 - 498
PALVA ET AL., GENE, vol. 22, 1983, pages 229 - 235
PEARSONREANIER, J. CHROM., vol. 255, 1983, pages 137 - 149
PETKOVA, S. B. ET AL., INT'L IMMUNOL., vol. 18, no. 12, 2006, pages 1759 - 1769
PETTIT ET AL., ANTICANCER DRUG DESIGN, vol. 13, 1998, pages 243 - 277
PETTIT ET AL., ANTIMICROB. AGENTS CHEMOTHER., vol. 42, 1998, pages 2961 - 2965
PETTIT ET AL., J. AM. CHEM. SOC., vol. 111, 1989, pages 5463 - 5465
PETTIT ET AL., J. CHEM. SOC. PERKIN TRANS., vol. 1, no. 5, 1996, pages 859 - 863
PETTIT, G. R. ET AL., SYNTHESIS, 1996, pages 719 - 725
PLUCKTHUN, IMMUNOL. REVS, vol. 130, 1992, pages 151
PRESTA ET AL., J. IMMUNOL., vol. 151, 1993, pages 2623
PRESTA, CURR. OP. STRUCT. BIOL., vol. 2, 1992, pages 593 - 596
PROBAPLUCKTHUN, GENE, vol. 159, 1995, pages 203 - 155
QUEEN ET AL., PROC. NAT'L ACAD. SCI. USA, vol. 86, 1989, pages 10029 - 10033
R. LANGER ET AL., CHEM. TECH., vol. 12, 1982, pages 98 - 105
RANGERPEPPAS, J., MACROMOL. SCI. REV. MACROMOL. CHEM., vol. 23, 1983, pages 61
RAVETCHKINET, ANNU. REV. IMMUNOL, vol. 9, 1991, pages 457 - 92
RAVETCHKINET, ANNU. REV. IMMUNOL., vol. 9, 1991, pages 457 - 492
RIECHMANN ET AL., NATURE, vol. 336, 1988, pages 348 - 352
RIPKA ET AL., ARCH. BIOCHEM. BIOPHYS., vol. 249, 1986, pages 533 - 545
ROBERTSON ET AL., NATURE, vol. 322, 1986, pages 445 - 448
ROSOK ET AL., J. BIOL. CHEM., vol. 271, 1996, pages 22611 - 22618
ROWLAND ET AL., CANCER IMMUNOL. IMMUNOTHER., vol. 21, 1986, pages 183 - 506
SAINI ET AL., EUR.J.IMMUNOL., vol. 29, 1999, pages 2420 - 2426
SAINIKAUSHIK, SCAND. J. IMMUNOL., vol. 55, 2002, pages 140 - 148
SAUDEK ET AL., N. ENGL. J. MED., vol. 321, 1989, pages 574 - 365
SAWHNEY ET AL., MACROMOLECULES, vol. 26, 1993, pages 581 - 587
SD NUTTALL ET AL., PROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, vol. 55, 2004, pages 187 - 197
SEFTON, CRC CRIT. REF. BIOMED. ENG., vol. 14, 1987, pages 201
SHALABY ET AL., J. EXP. MED., vol. 175, 1992, pages 217 - 225
SHIELDS ET AL., BIOL. CHEM., vol. 9, no. 2, 2001, pages 6591 - 6604
SHIELDS ET AL., J. BIOL. CHEM., vol. 9, no. 2, 2001, pages 6591 - 6604
SIEBENLIST ET AL., CELL, vol. 20, 1980, pages 269
SIEDEL, G. E., JR.: "Fertilization and Embryonic Development in Vitro", 1981, PLENUM PRESS, article "Critical review of embryo transfer procedures with cattle", pages: 323
SINHA ET AL., J. CONTROL. RELEASE, vol. 90, 2003, pages 261 - 498
SKERRA ET AL., CURR. OPINION IN IMMUNOL., vol. 5, 1993, pages 256
STAHLI ET AL., METHODS IN ENZYMOLOGY, vol. 9, 1983, pages 242 - 253
STUDNICKA ET AL., PROTEIN ENG., vol. 7, no. 6, 1994, pages 805 - 814
SURESH ET AL., METHODS IN ENZYMOLOGY, vol. 121, 1986, pages 210 - 103
SYRIGOSEPENETOS, ANTICANCER RESEARCH, vol. 19, 1999, pages 605 - 614
THORPE: "Antibody Carriers Of Cytotoxic Agents In Cancer Therapy: A Review", MONOCLONAL ANTIBODIES, 1985, pages 84
TOMLINSON ET AL., J. MOL. BIOL., vol. 227, 1992, pages 776 - 798
TRAUNECKER ET AL., EMBO J., vol. 10, 1991, pages 3655
TUTT ET AL., J. IMMUNOL., vol. 147, 1991, pages 60
U. SIDMAN ET AL., BIOPOLYMERS, vol. 22, 1983, pages 547 - 556
URLAUB ET AL., PROC. NATL. ACAD. SCI. USA, vol. 77, 1980, pages 4030 - 4034
VA STRELTSOV ET AL., J. NEUROSCIENCE, vol. 31, 2011, pages 1419 - 1426
VAN DEVANTER ET AL., NUCLEIC ACIDS RES., vol. 12, 1984, pages 6159 - 6168
VASWANIHAMILTON, ANN. ALLERGY, ASTHMA & IMMUNOL., vol. 1, 1998, pages 105 - 115
VERHOEYEN ET AL., SCIENCE, vol. 240, 1988, pages 1468 - 1474
VITETTA ET AL., SCIENCE, vol. 238, 1987, pages 1098
WAGNER ET AL., THERIOGENOLOGY, vol. 21, 1984, pages 29
WALLACE ET AL., GENE, vol. 16, 1981, pages 21 - 26
WATERHOUSE ET AL., NUCL. ACIDS RES., vol. 21, 1993, pages 2265 - 2266
WILLIAMSWINTER, EUR. J. IMMUNOL., vol. 23, 1993, pages 1456 - 1461
WINTER ET AL., ANN. REV. IMMUNOL., vol. 12, 1994, pages 433 - 455
WISEMAN ET AL., BLOOD, vol. 99, no. 12, 2002, pages 4336 - 42
WISEMAN ET AL., EUR. JOUR. NUCL. MED., vol. 27, no. 7, 2000, pages 766 - 77
WITZIG ET AL., J. CLIN. ONCOL., vol. 20, no. 15, 2002, pages 3262 - 69
WOYKE ET AL., ANTIMICROB. AGENTS AND CHEMOTHER., vol. 45, no. 12, 2001, pages 3580 - 3584
WUWU, J. BIOL. CHEM., vol. 262, 1987, pages 4429 - 4432
YAMANE-OHNUKI ET AL., BIOTECH. BIOENG., vol. 87, 2004, pages 614
YANIV, NATURE, vol. 297, 1982, pages 17 - 18
YASUDA, BIOMED. THER., vol. 27, 1993, pages 1221 - 1223
YONG ZHANG ET AL., ACS CHEMICAL BIOLOGY, vol. 8, 2013, pages 2117 - 2121
YONG ZHANG ET AL., ANGEWANDTE CHEMIE INTERNATIONAL EDITION, vol. 52, 2013, pages 8295 - 8298
ZHU ET AL., NAT. BIOTECHNOL., vol. 18, 2000, pages 24

Cited By (46)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US10774132B2 (en) 2012-01-09 2020-09-15 The Scripps Research Instittue Ultralong complementarity determining regions and uses thereof
US10562980B2 (en) 2012-01-09 2020-02-18 The Scripps Research Institute Humanized antibodies
US11390665B2 (en) 2012-01-09 2022-07-19 The Scripps Research Institute Ultralong complementarity determining regions and uses thereof
EP2943512A4 (en) * 2013-01-11 2016-06-01 California Inst Biomedical Res Bovine fusion antibodies
US9644021B2 (en) 2013-01-11 2017-05-09 The California Institute For Biomedical Research Bovine fusion antibodies
WO2014110368A1 (en) * 2013-01-11 2014-07-17 The California Institute For Biomedical Research Bovine fusion antibodies
US10259863B2 (en) 2013-01-11 2019-04-16 The California Institute For Biomedical Research Bovine fusion antibodies
EP3019531A4 (en) * 2013-07-11 2017-03-15 The California Institute for Biomedical Research Immunoglobulin fusion proteins and compositions thereof
US11530493B2 (en) 2013-07-18 2022-12-20 Taurus Biosciences, Llc Humanized antibodies with ultralong complementary determining regions
WO2015010100A3 (en) * 2013-07-18 2015-06-25 Fabrus, Inc. Humanized antibodies with ultralong complementarity determining regions
US10640574B2 (en) 2013-07-18 2020-05-05 Taurus Biosciences, Llc Humanized antibodies with ultralong complementary determining regions
CN107208315A (en) * 2014-12-01 2017-09-26 斯克利普斯研究院 It is related to the method and composition of the functional polypeptide in embedded heterologous protein support
US20180298051A1 (en) * 2014-12-01 2018-10-18 The Scripps Research Institute Methods and compositions related to functional polypeptides embedded in heterologous protein scaffolds
US10941188B2 (en) * 2014-12-01 2021-03-09 The Scripps Research Institute Methods and compositions related to functional polypeptides embedded in heterologous protein scaffolds
JP2017536833A (en) * 2014-12-01 2017-12-14 ザ スクリプス リサーチ インスティテュート Methods and compositions related to functional polypeptides incorporated into heterologous protein scaffolds
US11136366B2 (en) 2015-12-04 2021-10-05 Novartis Ag Methods of treating immune related disorders using antibody-cytokine engrafted compositions
US10144768B2 (en) 2015-12-04 2018-12-04 Novartis Ag Antibody cytokine engrafted compositions and methods of use for immunoregulation
CN108602870A (en) * 2015-12-04 2018-09-28 诺华股份有限公司 Antibody cytokine grafts composition and is used for immunoregulatory method
AU2016362777B2 (en) * 2015-12-04 2020-01-30 Novartis Ag Antibody cytokine engrafted compositions and methods of use for immunoregulation
KR20180081622A (en) * 2015-12-04 2018-07-16 노파르티스 아게 Antibody cytokine-grafted compositions and methods of use for immunomodulation
KR102213790B1 (en) * 2015-12-04 2021-02-09 노파르티스 아게 Antibody cytokine grafted composition and method of use for immunomodulation
WO2017093947A1 (en) * 2015-12-04 2017-06-08 Novartis Ag Antibody cytokine engrafted compositions and methods of use for immunoregulation
GB2562933B (en) * 2016-01-08 2022-06-29 Maxion Therapeutics Ltd Binding members with altered diversity scaffold domains
US10975166B2 (en) 2016-10-03 2021-04-13 The Regents Of The University Of California Inhibitory antibodies against MMP-14
CN111107868A (en) * 2017-05-24 2020-05-05 诺华股份有限公司 Antibody cytokine transplantation proteins and methods of use
WO2018215935A1 (en) * 2017-05-24 2018-11-29 Novartis Ag Antibody-cytokine engrafted proteins and methods of use for immune related disorders
US12006354B2 (en) 2017-05-24 2024-06-11 Novartis Ag Antibody-IL2 engrafted proteins and methods of use in the treatment of cancer
US11930837B2 (en) 2017-05-24 2024-03-19 Novartis Ag Antibody-cytokine engrafted proteins and methods of use for immune related disorders
US11122825B2 (en) 2017-05-24 2021-09-21 Novartis Ag Antibody-cytokine engrafted proteins and methods of use for immune related disorders
RU2815389C2 (en) * 2017-05-24 2024-03-14 Новартис Аг Antibody-based proteins with cytokine grafts and methods of their use in cancer treatment
WO2018215936A1 (en) * 2017-05-24 2018-11-29 Novartis Ag Antibody-cytokine engrafted proteins and methods of use in the treatment of cancer
AU2018274215B2 (en) * 2017-05-24 2021-10-28 Novartis Ag Antibody-cytokine engrafted proteins and methods of use for immune related disorders
KR102381237B1 (en) * 2017-05-24 2022-04-01 노파르티스 아게 Antibody-cytokine engrafted proteins and methods of use for immune-related disorders
RU2786730C2 (en) * 2017-05-24 2022-12-26 Новартис Аг Proteins based on antibody with grafted cytokine and methods for their use in immune disorders
WO2018215937A1 (en) * 2017-05-24 2018-11-29 Novartis Ag Interleukin-7 antibody cytokine engrafted proteins and methods of use in the treatment of cancer
KR20200008614A (en) * 2017-05-24 2020-01-28 노파르티스 아게 Antibody-Cytokine Implanted Proteins and Methods of Use for Immune-Related Disorders
WO2018215938A1 (en) * 2017-05-24 2018-11-29 Novartis Ag Antibody-cytokine engrafted proteins and methods of use
US11932673B2 (en) 2017-07-12 2024-03-19 Maxion Therapeutics Limited Sodium channel inhibitors
WO2019140150A1 (en) 2018-01-12 2019-07-18 Bristol-Myers Squibb Company Combination therapy with anti-il-8 antibodies and anti-pd-1 antibodies for treating cancer
US11332546B2 (en) 2019-05-21 2022-05-17 The Regents Of The University Of California Protease inhibitory antibodies and methods of use thereof
WO2021081440A3 (en) * 2019-10-24 2021-05-27 Minotaur Therapeutics, Inc. Chimeric cytokine modified antibodies and methods of use thereof
WO2021191424A1 (en) 2020-03-27 2021-09-30 UCB Biopharma SRL Autonomous knob domain peptides
WO2022232321A1 (en) * 2021-04-28 2022-11-03 Minotaur Therapeutics, Inc. Humanized chimeric bovine antibodies and methods of use
WO2022241057A1 (en) * 2021-05-12 2022-11-17 Applied Biomedical Science Institute Binding polypeptides against sars cov-2 and uses thereof
WO2022241058A1 (en) * 2021-05-12 2022-11-17 Applied Biomedical Science Institute Methods of screening and expression of disulfide-bonded binding polypeptides
WO2023192478A1 (en) 2022-04-01 2023-10-05 Bristol-Myers Squibb Company Combination therapy with anti-il-8 antibodies and anti-pd-1 antibodies for treating cancer

Also Published As

Publication number Publication date
US20140086871A1 (en) 2014-03-27
AU2013208003A1 (en) 2014-08-07
JP2018140992A (en) 2018-09-13
JP2015504896A (en) 2015-02-16
US11390665B2 (en) 2022-07-19
AU2013208003B2 (en) 2017-12-14
CN104520321A (en) 2015-04-15
WO2013106485A3 (en) 2014-03-06
EP2802603A4 (en) 2015-11-04
CA2863224A1 (en) 2013-07-18
US20200181241A1 (en) 2020-06-11
US10774132B2 (en) 2020-09-15
EP2802603A2 (en) 2014-11-19
AU2018201832A1 (en) 2018-04-12
JP6684490B2 (en) 2020-04-22
US20140050720A1 (en) 2014-02-20

Similar Documents

Publication Publication Date Title
US11390665B2 (en) Ultralong complementarity determining regions and uses thereof
US11530493B2 (en) Humanized antibodies with ultralong complementary determining regions
US20200223944A1 (en) Humanized antibodies
US9644021B2 (en) Bovine fusion antibodies
US20160168231A1 (en) Antibodies with ultralong complementarity determining regions

Legal Events

Date Code Title Description
121 Ep: the epo has been informed by wipo that ep was designated in this application

Ref document number: 13735853

Country of ref document: EP

Kind code of ref document: A2

ENP Entry into the national phase

Ref document number: 2863224

Country of ref document: CA

Ref document number: 2014552273

Country of ref document: JP

Kind code of ref document: A

WWE Wipo information: entry into national phase

Ref document number: 2013735853

Country of ref document: EP

ENP Entry into the national phase

Ref document number: 2013208003

Country of ref document: AU

Date of ref document: 20130109

Kind code of ref document: A