US20230147782A1

US20230147782A1 - Cleavable linker compositions and methods

Info

Publication number: US20230147782A1
Application number: US17/972,348
Authority: US
Inventors: David Campbell; Thomas R. DIRAIMONDO
Original assignee: Janux Therapeutics Inc
Current assignee: Janux Therapeutics Inc
Priority date: 2020-08-11
Filing date: 2022-10-24
Publication date: 2023-05-11
Also published as: AU2021326469A1; WO2022035866A1; MX2023001788A; CN116348597A; US11512113B2; CA3187754A1; US20220048949A1; EP4196488A4; JP2023547978A; EP4196488A1; KR20230080399A

Abstract

Provided herein are cleavable linkers, pharmaceutical compositions thereof, as well as nucleic acids, and methods for making and discovering the same. The cleavable linkers described herein have improved efficacy and safety.

Description

CROSS-REFERENCE

This application is a continuation of U.S. patent application Ser. No. 17/398,500, filed on Aug. 10, 2021, which claims the benefit of U.S. Provisional Application No. 63/064,268, filed Aug. 11, 2020, which application is incorporated herein by reference.

SEQUENCE LISTING

The instant application contains a Sequence Listing which has been submitted electronically in XML format and is hereby incorporated by reference in its entirety. Said XML copy, created on Oct. 18, 2022, is named 52426-720_301 SL.xml and is 42,044 bytes in size.

SUMMARY

Disclosed herein, in certain embodiments, are isolated polypeptides comprising a cleavable linker according to the amino acid sequence of SEQ ID NO: 1 (LSGRSDAG). In some embodiments, the cleavable linker comprises the amino acid sequence of SEQ ID NO: 3 (ISSGLLSGRSDAG). In some embodiments, the cleavable linker comprises the amino acid sequence of SEQ ID NO: 26 (AGLLAPPGGLSGRSDAG). In some embodiments, the cleavable linker comprises the amino acid sequence of SEQ ID NO: 4 (AAGLLAPPGGLSGRSDAG). In some embodiments, the cleavable linker comprises the amino acid sequence of SEQ ID NO: 5 (SPLGLSGRSDAG). In some embodiments, the cleavable linker comprises the amino acid sequence of SEQ ID NO: 6 (LSGRSDAGSPLGLAG). In some embodiments, the cleavable linker is cleavable by a protease. In some embodiments, the protease comprises a tumor specific protease. In some embodiments, the protease comprises a matrix metalloprotease (MMP) or a serine protease. In some embodiments, the matrix metalloprotease comprises MMP2, MMP7, MMP9, MMP13, or MMP14. In some embodiments, the serine protease comprises matriptase, urokinase, or hepsin. In some embodiments, the isolated polypeptide further comprises an antigen binding domain that binds to a target antigen. In some embodiments, the antigen binding domain is C-terminal to the cleavable linker. In some embodiments, the isolated polypeptide further comprises a cytokine or cytokine fragment that binds to a cytokine receptor. In some embodiments, the cytokine or cytokine fragment is C-terminal to the cleavable linker. In some embodiments, the cleavable linker connects a peptide to an antigen binding domain that binds to a target antigen or to a cytokine or cytokine fragment that binds to a cytokine receptor in a configuration according to Formula I: A₁-L₁-P₁wherein A₁comprises the antigen binding domain that binds to the target antigen or the cytokine or cytokine fragment that binds to the cytokine receptor; L₁comprises the cleavable linker; P₁comprises a peptide that impairs binding of the antigen binding domain to the target antigen or impairs binding of the cytokine to the cytokine receptor. In some embodiments, P₁is connected N-terminal to the cleavable linker and A₁is connected C-terminal to the cleavable linker. In some embodiments, P₁is connected C-terminal to the cleavable linker and A₁is connected N-terminal to the cleavable linker. In some embodiments, P₁is bound to A₁through ionic interactions, electrostatic interactions, hydrophobic interactions, Pi-stacking interactions, and H-bonding interactions, or a combination thereof. In some embodiments, P₁has less than 70% sequence homology to the target antigen or the cytokine receptor. In some embodiments, P₁comprises a peptide sequence of at least 10 amino acids in length. In some embodiments, P₁comprises a peptide sequence of at least 10 amino acids in length and no more than 20 amino acids in length. In some embodiments, P₁comprises a peptide sequence of at least 16 amino acids in length. In some embodiments, P₁comprises a peptide sequence of no more than 40 amino acids in length. In some embodiments, P₁comprises a cyclic peptide or a linear peptide. In some embodiments, P₁comprises a cyclic peptide. In some embodiments, P₁is further linked to a half-life extending moiety. In some embodiments, the half-life extending moiety is a single-domain antibody. In some embodiments, the single domain antibody comprises 10G. In some embodiments, A₁comprises an antibody, a single chain variable fragment (scFv), a heavy chain variable domain (VH domain), a light chain variable domain (VL domain), a variable domain (VHH) of a camelid derived single domain antibody, a Fab, a Fab′, a Fab light chain polypeptide, or a Fab heavy chain polypeptide. In some embodiments, the target antigen comprises a tumor antigen. In some embodiments, A₁comprises the Fab light chain polypeptide or the Fab heavy chain polypeptide. In some embodiments, A₁comprises an epidermal growth factor receptor (EGFR) binding domain. In some embodiments, the target antigen comprises an effector cell antigen. In some embodiments, A₁comprises the scFv. In some embodiments, the scFv comprises an anti-CD3e single chain variable fragment. In some embodiments, A₁comprises the cytokine. In some embodiments, the cytokine or cytokine fragment is a wild-type cytokine. In some embodiments, the cytokine or cytokine fragment is a mutein of the cytokine. In some embodiments, the cytokine receptor is an interferon receptor or an interleukin receptor. In some embodiments, the cytokine receptor comprises an interferon receptor, GM-CSF receptor, IL-2 receptor, IL-4 receptor, IL-6 receptor, IL-7 receptor, IL-10 receptor, IL-12 receptor, IL-15 receptor, IL-21 receptor, or TGF-β receptor. In some embodiments, the cytokine or cytokine fragment comprises an interferon, GM-CSF, IL-2, IL-7, IL-12, IL-15, or IL-21. In some embodiments, the cytokine or cytokine fragment comprises an IL-2, IL-12, IL-6, IL-4, IL-10, or TGFβ. In some embodiments, the isolated polypeptide is complexed with a second isolated polypeptide comprising a second antigen binding domain or a second cytokine or second cytokine fragment. In some embodiments, the second isolated polypeptide is in a configuration according to Formula II: A₂-L₂-P₂wherein A₂comprises the second antigen binding domain or the second cytokine; L₂comprises a second cleavable linker; P₂comprises a second peptide that impairs binding of the second antigen binding domain to a second target antigen or impairs binding of the second cytokine or second cytokine fragment to a second cytokine receptor. In some embodiments, the second cleavable linker comprises the amino acid sequence of SEQ ID NO: 1 (LSGRSDAG). In some embodiments, the second cleavable linker comprises the amino acid sequence of SEQ ID NO: 3 (ISSGLLSGRSDAG). In some embodiments, the second cleavable linker comprises the amino acid sequence of SEQ ID NO: 26 (AGLLAPPGGLSGRSDAG). In some embodiments, the second cleavable linker comprises the amino acid sequence of SEQ ID NO: 4 (AAGLLAPPGGLSGRSDAG). In some embodiments, the second cleavable linker comprises the amino acid sequence of SEQ ID NO: 5 (SPLGLSGRSDAG). In some embodiments, the second cleavable linker comprises the amino acid sequence of SEQ ID NO: 6 (LSGRSDAGSPLGLAG). In some embodiments, P₂is connected N-terminal to the second cleavable linker and A₂is connected C-terminal to the second cleavable linker. In some embodiments, P₂is connected C-terminal to the second cleavable linker and A₂is connected N-terminal to the second cleavable linker. In some embodiments, P₂is bound to A₂through ionic interactions, electrostatic interactions, hydrophobic interactions, Pi-stacking interactions, and H-bonding interactions, or a combination thereof. In some embodiments, P₂has less than 70% sequence homology to the second target antigen or the second cytokine receptor. In some embodiments, P₂comprises a peptide sequence of at least 10 amino acids in length. In some embodiments, P₂comprises a peptide sequence of at least 10 amino acids in length and no more than 20 amino acids in length. In some embodiments, P₂comprises a peptide sequence of at least 16 amino acids in length. In some embodiments, P₂comprises a peptide sequence of no more than 40 amino acids in length. In some embodiments, P₂comprises a cyclic peptide or a linear peptide. In some embodiments, P₂comprises a cyclic peptide. In some embodiments, A₂comprises an antibody, a single chain variable fragment (scFv), a heavy chain variable domain (VH domain), a light chain variable domain (VL domain), a variable domain (VHH) of a camelid derived single domain antibody, a Fab, a Fab′, a Fab light chain polypeptide, or a Fab heavy chain polypeptide. In some embodiments, the second target antigen comprises a tumor antigen. In some embodiments, A₂comprises the Fab light chain polypeptide or the Fab heavy chain polypeptide. In some embodiments, A₂comprises an epidermal growth factor receptor (EGFR) binding domain. In some embodiments, the second target antigen comprises an effector cell antigen. In some embodiments, A₂comprises the scFv. In some embodiments, the scFv comprises an anti-CD3e single chain variable fragment. In some embodiments, A₂comprises the second cytokine. In some embodiments, the second cytokine or second cytokine fragment is a wild-type cytokine. In some embodiments, the second cytokine or second cytokine fragment is a mutein of the cytokine. In some embodiments, the second cytokine receptor is an interferon receptor or an interleukin receptor. In some embodiments, the second cytokine receptor comprises an interferon receptor, GM-CSF receptor, IL-2 receptor, IL-4 receptor, IL-6 receptor, IL-7 receptor, IL-10 receptor, IL-12 receptor, IL-15 receptor, IL-21 receptor, or TGF-β receptor. In some embodiments, the second cytokine or second cytokine fragment comprises an interferon, GM-CSF, IL-2, IL-7, IL-12, IL-15, or IL-21. In some embodiments, the second cytokine or second cytokine fragment comprises an IL-2, IL-12, IL-6, IL-4, IL-10, or TGFβ.
Disclosed herein are pharmaceutical compositions comprising: the isolated polypeptide comprising a cleavable linker according to any of the above embodiments; and a pharmaceutically acceptable excipient.
Disclosed herein are isolated recombinant nucleic acid molecule encoding the isolated polypeptide comprising a cleavable linker according to any of the above embodiments.
Disclosed herein are vectors comprising the recombinant nucleic acid molecule according to the above embodiment.
Disclosed herein are methods of producing an isolated polypeptide comprising a cleavable linker comprising culturing a cell under conditions that lead to expression of the polypeptide, wherein the cell comprises the vector of the above embodiment.
Disclosed herein are methods of manufacturing an isolated polypeptide comprising a cleavable linker, the method comprising: (a) culturing a cell comprising the recombinant nucleic acid molecule of the above embodiments under conditions that lead to expression of the polypeptide, and (b) isolating the polypeptide.

BRIEF DESCRIPTION OF THE DRAWINGS

The novel features of the disclosure are set forth with particularity in the appended claims. A better understanding of the features and advantages of the present disclosure will be obtained by reference to the following detailed description that sets forth illustrative embodiments, in which the principles of the disclosure are utilized, and the accompanying drawings of which:

FIGS. 1A-1B illustrate binding of polypeptide complexes PC-1, PC-2, PC-3, PC-4, and PC-5 comprising EGFR masking (FIG. 1A) and followed by cleavage by the tumor protease MTSP1 (FIG. 1B).

FIGS. 2A-2B illustrate of polypeptide complexes PC-1, PC-2, PC-3, PC-4, and PC-5 comprising CD3ε masking (FIG. 2A) and followed by cleavage by the tumor protease MTSP1 (FIG. 2B).

FIGS. 3A-3B illustrate binding of polypeptide complexes PC-2, PC-3, PC-4, PC-5, PC-1, and PC-6 to EGFR-biotin (FIG. 3A) and CD3ε-biotin (FIG. 3B) measured by ELISA.

FIGS. 4A-4E illustrate cytotoxicity against tumor target cells HCT116 for polypeptide complexes PC-2, PC-3, PC-4, PC-5, PC-1, and PC-6.

FIGS. 5A-5D illustrate pharmacokinetics of polypeptide PC-1, PC-2, PC-3, PC-7, PC-4, and PC-5 in cynomolgus monkey.

FIGS. 6A-6D illustrate cytokine release of polypeptide complexes PC-1, PC-2, PC-3, PC-7, PC-4, and PC-5 molecules in cynomolgus monkey.

FIG. 7A-7B illustrates graphs of AST and ALT levels of polypeptide complexes PC-1, PC-2, PC-3, PC-4, and PC-5 in cynomolgus monkey.

DETAILED DESCRIPTION

Protein-based therapies such as antibodies, T cell receptors (TCR), and cytokine therapies have proven effective for a variety diseases and disorders. As with any therapy, there is a need to minimize off-target effects of the protein-based therapy in healthy tissue while maintaining activity of the protein-based therapy in disease tissue. One such strategy is to create an inactive form of the protein-based therapy in which a necessary binding site on the protein-based therapy is blocked with a peptide linked to the protein-based therapy, thereby preventing the protein-based therapy from binding or interacting with its cognate receptor or target antigen when in healthy tissue. For activating the protein-based therapy in the desired disease-state microenvironment, the peptide is linked to the protein-based therapy with a linker that is cleavable by a protease that is specific to the disease-state microenvironment. The peptide is then released from the protein-based therapy when in the disease-state microenvironment.
Accordingly, disclosed herein, are cleavable linkers which can be applied to a variety of protein-based therapy formats, for use in reducing off-target effects of the protein-based therapy in healthy tissue, while maintaining activity of the protein-based therapy in disease tissue. The cleavable linkers, as disclosed herein, have desirable properties, which include, for example but are not limited to, increased rates of proteolysis by tumor proteases or cleavable by an expanded panel of tumor proteases while also having comparable safety profiles relative to control linkers.

Certain Definitions

The terminology used herein is for the purpose of describing particular cases only and is not intended to be limiting. As used herein, the singular forms “a”, “an” and “the” are intended to include the plural forms as well, unless the context clearly indicates otherwise. Furthermore, to the extent that the terms “including”, “includes”, “having”, “has”, “with”, or variants thereof are used in either the detailed description and/or the claims, such terms are intended to be inclusive in a manner similar to the term “comprising.”
The term “about” or “approximately” means within an acceptable error range for the particular value as determined by one of ordinary skill in the art, which will depend in part on how the value is measured or determined, e.g., the limitations of the measurement system. For example, “about” can mean within 1 or more than 1 standard deviation, per the practice in the given value. Where particular values are described in the application and claims, unless otherwise stated the term “about” should be assumed to mean an acceptable error range for the particular value.
“Fragment” as used herein refers to a peptide or a polypeptide that comprises less than the full length amino acid sequence.
“Peptide”, “P₁”, or “P₂” as used herein refers to an amino acid sequence of less than 50 amino acids and specifically excludes a cytokine ligand binding domain, fragments, or muteins thereof, a cytokine receptor, fragments, or muteins thereof, and any antibody or antibody binding fragments (for example, a single domain antibody, Fab, or scFv) that binds to a cytokine, or binds to a cognate cytokine receptor.
As disclosed herein, in some embodiments, are isolated polypeptides comprising a cleavable linker according to the amino acid sequence of SEQ ID NO: 1 (LSGRSDAG)
In some embodiments, the cleavable linker comprises the amino acid sequence of SEQ ID NO: 3 (ISSGLLSGRSDAG). In some embodiments, the cleavable linker comprises the amino acid sequence of SEQ ID NO: 26 (AGLLAPPGGLSGRSDAG). In some embodiments, the cleavable linker comprises the amino acid sequence of SEQ ID NO: 4 (AAGLLAPPGGLSGRSDAG). In some embodiments, the cleavable linker comprises the amino acid sequence of SEQ ID NO: 5 (SPLGLSGRSDAG). In some embodiments, the cleavable linker comprises the amino acid sequence of SEQ ID NO: 6 (LSGRSDAGSPLGLAG).
In some embodiments, the cleavable linker consists of the amino acid sequence of SEQ ID NO: 1 (LSGRSDAG). In some embodiments, the cleavable linker consists of the amino acid sequence of SEQ ID NO: 3 (ISSGLLSGRSDAG). In some embodiments, the cleavable linker consists of the amino acid sequence of SEQ ID NO: 26 (AGLLAPPGGLSGRSDAG). In some embodiments, the cleavable linker consists of the amino acid sequence of SEQ ID NO: 4 (AAGLLAPPGGLSGRSDAG). In some embodiments, the cleavable linker consists of the amino acid sequence of SEQ ID NO: 5 (SPLGLSGRSDAG). In some embodiments, the cleavable linker consists of the amino acid sequence of SEQ ID NO: 6 (LSGRSDAGSPLGLAG).
In some embodiments, the cleavable linker comprises the amino acid sequence selected from the group consisting of SEQ ID NO: 3, 4, 5, and 6.
In some embodiments, are isolated polypeptides comprising a cleavable linker according to the amino acid sequence of Linker 1 (ISSGLLSGRSDAG) SEQ ID NO: 3, Linker 2 (AAGLLAPPGGLSGRSDAG) SEQ ID NO:4, Linker 3 (SPLGLSGRSDAG) SEQ ID NO: 5, or Linker 4 (LSGRSDAGSPLGLAG) SEQ ID NO: 6 or an isolated polypeptide comprising a cleavable linker that has 1, 2, or 3 amino acid substitutions, additions, or deletions relative to the amino acid sequence of Linker 1, Linker 2, Linker 3, or Linker 4.
In some embodiments, the cleavable linker comprises the amino acid sequence of Linker 1. In some embodiments, the cleavable linker consists of the amino acid sequence of Linker 1. In some embodiments, the cleavable linker has 1 amino acid substitution, addition, or deletion relative to the amino acid sequence of Linker 1. In some embodiments, the cleavable linker has 2 amino acid substitutions, additions, or deletions relative to the amino acid sequence of Linker 1. In some embodiments, the cleavable linker has 3 amino acid substitutions, additions, or deletions relative to the amino acid sequence of Linker 1.
In some embodiments, the cleavable linker comprises the amino acid sequence of Linker 2. In some embodiments, the cleavable linker consists of the amino acid sequence of Linker 2. In some embodiments, the cleavable linker has 1 amino acid substitution, addition, or deletion relative to the amino acid sequence of Linker 2. In some embodiments, the cleavable linker has 2 amino acid substitutions, additions, or deletions relative to the amino acid sequence of Linker 2. In some embodiments, the cleavable linker has 3 amino acid substitutions, additions, or deletions relative to the amino acid sequence of Linker 2.
In some embodiments, the cleavable linker comprises the amino acid sequence of Linker 3. In some embodiments, the cleavable linker consists of the amino acid sequence of Linker 3. In some embodiments, the cleavable linker has 1 amino acid substitution, addition, or deletion relative to the amino acid sequence of Linker 3. In some embodiments, the cleavable linker has 2 amino acid substitutions, additions, or deletions relative to the amino acid sequence of Linker 3. In some embodiments, the cleavable linker has 3 amino acid substitutions, additions, or deletions relative to the amino acid sequence of Linker 3.
In some embodiments, the cleavable linker comprises the amino acid sequence of Linker 4. In some embodiments, the cleavable linker consists of the amino acid sequence of Linker 4. In some embodiments, the cleavable linker has 1 amino acid substitution, addition, or deletion relative to the amino acid sequence of Linker 4. In some embodiments, the cleavable linker has 2 amino acid substitutions, additions, or deletions relative to the amino acid sequence of Linker 4. In some embodiments, the cleavable linker has 3 amino acid substitutions, additions, or deletions relative to the amino acid sequence of Linker 4.
In some embodiments, the amino acid substitution, addition, or deletion results in an amino acid sequence that is at least 75% identical, e.g., 77%, 80%, 82%, 85%, 88%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of any protein described herein. In some embodiments, the amino acid substitution is a conservative amino acid substitution. Among the common amino acids, for example, a “conservative amino acid substitution” is illustrated by a substitution among amino acids within each of the following groups: (1) glycine, alanine, valine, leucine, and isoleucine, (2) phenylalanine, tyrosine, and tryptophan, (3) serine and threonine, (4) aspartate and glutamate, (5) glutamine and asparagine, and (6) lysine, arginine and histidine.
In some embodiments, the cleavable linker comprises a modified amino acid or non-natural amino acid, or a modified non-natural amino acid, or a combination thereof. In some embodiments, the modified amino acid or a modified non-natural amino acid comprises a post-translational modification. In some embodiments, the cleavable linker comprises a modification including, but not limited, to acetylation, acylation, ADP-ribosylation, amidation, covalent attachment of flavin, covalent attachment of a heme moiety, covalent attachment of a nucleotide or nucleotide derivative, covalent attachment of a lipid or lipid derivative, covalent attachment of phosphatidylinositol, cross-linking, cyclization, disulfide bond formation, demethylation, formation of covalent crosslinks, formation of cystine, formation of pyroglutamate, formylation, gamma carboxylation, glycosylation, GPI anchor formation, hydroxylation, iodination, methylation, myristoylation, oxidation, proteolytic processing, phosphorylation, prenylation, racemization, selenoylation, sulfation, transfer-RNA mediated addition of amino acids to proteins such as arginylation, and ubiquitination. Modifications are made anywhere to the cleavable linker including the peptide backbone, or the amino acid side chains.
In some embodiments, the cleavable linker is cleavable by a protease. In some embodiments, the protease is present in higher levels in a disease-state microenvironment relative to levels in healthy tissue or a microenvironment that is not the disease-state microenvironment. In some embodiments, the protease comprises a tumor specific protease. In some embodiments, the protease comprises a matrix metalloprotease (MMP) or a serine protease. In some embodiments, the matrix metalloprotease comprises MMP2, MMP7, MMP9, MMP13, or MMP14. In some embodiments, the matrix metalloprotease is selected from the group consisting of MMP2, MMP7, MMP9, MMP13, and MMP14. In some embodiments, the matrix metalloprotease comprises MMP2. In some embodiments, the matrix metalloprotease comprises MMP7. In some embodiments, the matrix metalloprotease comprises MMP9. In some embodiments, the matrix metalloprotease comprises MMP13. In some embodiments, the matrix metalloprotease comprises MMP14. In some embodiments, the serine protease comprises matriptase, urokinase, or hepsin. In some embodiments, the serine protease is selected from the group consisting of matriptase, urokinase, and hepsin. In some embodiments, the serine protease comprises matriptase. In some embodiments, the serine protease comprises urokinase. In some embodiments, the serine protease comprises hepsin. In some embodiments, the cleavable linker is cleaved by a variety of proteases. In some embodiments, the cleavable linker is cleaved by at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, or more than 20 different proteases.
In some embodiments, the cleavable linker has increased rates of proteolysis as compared to the rates of proteolysis for linkers without the cleavable linker sequences. In some embodiments, the cleavable linker has increased rates of proteolysis that is at least 5× higher than the rates of proteolysis for linkers without the cleavable linker sequences. In some embodiments, the cleavable linker has increased rates of proteolysis that is at least 8× higher than the rates of proteolysis for linkers without the cleavable linker sequences. In some embodiments, the cleavable linker has increased rates of proteolysis that is at least 10× higher than the rates of proteolysis for linkers without the cleavable linker sequences. In some embodiments, the cleavable linker has increased rates of proteolysis that is at least 15× higher than the rates of proteolysis for linkers without the cleavable linker sequences. In some embodiments, the cleavable linker has increased rates of proteolysis that is at least 20× higher than the rates of proteolysis for linkers without the cleavable linker sequences. In some embodiments, the cleavable linker has increased rates of proteolysis that is at least 25× higher than the rates of proteolysis for linkers without the cleavable linker sequences. In some embodiments, the cleavable linker has increased rates of proteolysis that is at least 30× higher than the rates of proteolysis for linkers without the cleavable linker sequences. In some embodiments, the cleavable linker has increased rates of proteolysis that is at least 40× higher than the rates of proteolysis for linkers without the cleavable linker sequences. In some embodiments, the cleavable linker has increased rates of proteolysis that is at least 50× higher than the rates of proteolysis for linkers without the cleavable linker sequences. In some embodiments, the cleavable linker has increased rates of proteolysis that is at least 60× higher than the rates of proteolysis for linkers without the cleavable linker sequences. In some embodiments, the cleavable linker has increased rates of proteolysis that is at least 70× higher than the rates of proteolysis for linkers without the cleavable linker sequences. In some embodiments, the cleavable linker has increased rates of proteolysis that is at least 75× higher than the rates of proteolysis for linkers without the cleavable linker sequences. In some embodiments, the cleavable linker has increased rates of proteolysis that is at least 80× higher than the rates of proteolysis for linkers without the cleavable linker sequences. In some embodiments, the cleavable linker has increased rates of proteolysis that is at least 90× higher than the rates of proteolysis for linkers without the cleavable linker sequences. In some embodiments, the cleavable linker has increased rates of proteolysis that is at least 100× higher than the rates of proteolysis for linkers without the cleavable linker sequences. In some embodiments, the cleavable linker has increased rates of proteolysis that is at least 120× higher than the rates of proteolysis for linkers without the cleavable linker sequences. In some embodiments, the cleavable linker is cleaved by a protease. In some embodiments, the protease comprises a tumor specific protease. In some embodiments, the protease comprises a matrix metalloprotease (MMP) or a serine protease. In some embodiments, the matrix metalloprotease comprises MMP2, MMP7, MMP9, MMP13, or MMP14. In some embodiments, the serine protease comprises matriptase, urokinase, or hepsin.
In some embodiments, the cleavable linker has improved stability in human serum as compared to the stability in human serum without the cleavable linker sequences. In some embodiments, the cleavable linker has improved stability in human serum that is at least 5× higher than the stability in human serum for linkers without the cleavable linker sequences. In some embodiments, the cleavable linker has improved stability in human serum that is at least 8× higher than the stability in human serum for linkers without the cleavable linker sequences. In some embodiments, the cleavable linker has improved stability in human serum that is at least 10× higher than the stability in human serum for linkers without the cleavable linker sequences. In some embodiments, the cleavable linker has improved stability in human serum that is at least 15× higher than the stability in human serum for linkers without the cleavable linker sequences. In some embodiments, the cleavable linker has improved stability in human serum that is at least 20× higher than the stability in human serum for linkers without the cleavable linker sequences. In some embodiments, the cleavable linker has improved stability in human serum that is at least 25× higher than the stability in human serum for linkers without the cleavable linker sequences. In some embodiments, the cleavable linker has improved stability in human serum that is at least 30× higher than the stability in human serum for linkers without the cleavable linker sequences. In some embodiments, the cleavable linker has improved stability in human serum that is at least 40× higher than the stability in human serum for linkers without the cleavable linker sequences. In some embodiments, the cleavable linker has improved stability in human serum that is at least 50× higher than the stability in human serum for linkers without the cleavable linker sequences. In some embodiments, the cleavable linker has improved stability in human serum that is at least 60× higher than the stability in human serum for linkers without the cleavable linker sequences. In some embodiments, the cleavable linker has improved stability in human serum that is at least 70× higher than the stability in human serum for linkers without the cleavable linker sequences. In some embodiments, the cleavable linker has improved stability in human serum that is at least 75× higher than the stability in human serum for linkers without the cleavable linker sequences. In some embodiments, the cleavable linker has improved stability in human serum that is at least 80× higher than the stability in human serum for linkers without the cleavable linker sequences. In some embodiments, the cleavable linker has improved stability in human serum that is at least 90× higher than the stability in human serum for linkers without the cleavable linker sequences. In some embodiments, the cleavable linker has improved stability in human serum that is at least 100× higher than the stability in human serum for linkers without the cleavable linker sequences. In some embodiments, the cleavable linker has improved stability in human serum that is at least 120× higher than the stability in human serum for linkers without the cleavable linker sequences.
In some embodiments, the isolated polypeptide comprising the cleavable linker has increased rates of proteolysis as compared to an isolated polypeptide of the same amino acid sequence but comprising a cleavable linker according to the amino acid sequence of SEQ ID NO: 2.
In some embodiments, the isolated polypeptide comprising the cleavable linker has improved or equivalent serum stability as compared to an isolated polypeptide of the same amino acid sequence but comprising a cleavable linker according to the amino acid sequence of SEQ ID NO: 2.
In some embodiments, the isolated polypeptide comprising the cleavable linker has improved or equivalent in vitro tumor cell killing as compared to an isolated polypeptide of the same amino acid sequence but comprising a cleavable linker according to the amino acid sequence of SEQ ID NO: 2.
In some embodiments, the isolated polypeptide comprising the cleavable linker has improved or equivalent pharmacokinetic parameters in cynomolgus monkeys as compared to an isolated polypeptide of the same amino acid sequence but comprising a cleavable linker according to the amino acid sequence of SEQ ID NO: 2.
In some embodiments, the isolated polypeptide comprising the cleavable linker has improved or equivalent liver toxicity levels in cynomolgus monkeys as compared to an isolated polypeptide of the same amino acid sequence but comprising a cleavable linker according to the amino acid sequence of SEQ ID NO: 2.
In some embodiments, the isolated polypeptide further comprises an antigen binding domain that binds to a target antigen. In some embodiments, the antigen binding domain is C-terminal to the cleavable linker. In some embodiments, the isolated polypeptide further comprises a cytokine or cytokine fragment that binds to a cytokine receptor. In some embodiments, the cytokine or cytokine fragment is C-terminal to the cleavable linker.
In some embodiments, the cleavable linker connects a peptide to an antigen binding domain that binds to a target antigen or to a cytokine that binds to a cytokine receptor in a configuration according to Formula I:
A₁-L₁-P₁ (Formula I)
wherein A₁comprises the antigen binding domain that binds to the target antigen or the cytokine that binds to the cytokine receptor; L₁comprises the cleavable linker; P₁comprises a peptide that impairs binding of the antigen binding domain to the target antigen or impairs binding of the cytokine to the cytokine receptor. In some embodiments, P₁is connected N-terminal to the cleavable linker and A₁is connected C-terminal to the cleavable linker. In some embodiments, P₁is connected C-terminal to the cleavable linker and A₁is connected N-terminal to the cleavable linker.
In some embodiments, the isolated polypeptide is complexed with a second isolated polypeptide comprising a second antigen binding domain or a second cytokine. In some embodiments, the second isolated polypeptide is in a configuration according to Formula II:
A₂-L₂-P₂ (Formula II)
wherein A₂comprises the second antigen binding domain or the second cytokine; L₂comprises a second cleavable linker; and P₂comprises a second peptide that impairs binding of the second antigen binding domain to a second target antigen or impairs binding of the second cytokine to a second cytokine receptor.
In some embodiments, P₂is connected N-terminal to the second cleavable linker and A₂is connected C-terminal to the second cleavable linker. In some embodiments, P₂is connected C-terminal to the second cleavable linker and A₂is connected N-terminal to the second cleavable linker.
In some embodiments, the second cleavable linker comprises the amino acid sequence of SEQ ID NO: 1 (LSGRSDAG). In some embodiments, the second cleavable linker comprises the amino acid sequence of SEQ ID NO: 3 (ISSGLLSGRSDAG). In some embodiments, the second cleavable linker comprises the amino acid sequence of SEQ ID NO: 26 (AGLLAPPGGLSGRSDAG). In some embodiments, the second cleavable linker comprises the amino acid sequence of SEQ ID NO: 4 (AAGLLAPPGGLSGRSDAG). In some embodiments, the second cleavable linker comprises the amino acid sequence of SEQ ID NO: 5 (SPLGLSGRSDAG). In some embodiments, the second cleavable linker comprises the amino acid sequence of SEQ ID NO: 6 (LSGRSDAGSPLGLAG).
In some embodiments, L₁or L₂is at least 8 amino acids in length. In some embodiments, L₁or L₂is at least 10 amino acids in length but no more than 50 amino acids in length. In some embodiments, L₁or L₂is at least 10 amino acids in length but no more than 30 amino acids in length. In some embodiments, L₁or L₂is at least 18 amino acids in length. In some embodiments, L₁or L₂is at least 26 amino acids in length. In some embodiments, L₁or L₂is at least 30 amino acids in length. In some embodiments, L₁or L₂is at least 40 amino acids in length. In some embodiments, L₁or L₂is at least 50 amino acids in length.
Peptide (P₁or P₂)
In some embodiments, P₁comprises a peptide that impairs binding of the antigen binding domain to the target antigen. In some embodiments, P₁comprises a peptide that impairs binding of the cytokine to the cytokine receptor. In some embodiments, P₁is bound to A₁through ionic interactions, electrostatic interactions, hydrophobic interactions, Pi-stacking interactions, and H-bonding interactions, or a combination thereof. In some embodiments, P₁is bound to A₁at or near a cytokine receptor binding site. In some embodiments, P₁is bound to A₁at or near an antigen binding site. In some embodiments, P₁becomes unbound from A₁when L₁is cleaved by the protease thereby exposing P₁to the target antigen or cytokine receptor. In some embodiments, the protease comprises a tumor specific protease. In some embodiments, the protease comprises a matrix metalloprotease (MMP) or a serine protease. In some embodiments, the matrix metalloprotease comprises MMP2, MMP7, MMP9, MMP13, or MMP14. In some embodiments, the serine protease comprises matriptase, urokinase, or hepsin. In some embodiments, P₁impairs binding of A₁to the target antigen or cytokine receptor by non-steric blocking. In some embodiments, P₁impairs binding of A₁to the target antigen or cytokine receptor through covalent interactions. In some embodiments, P₁is not a cytokine, cytokine binding fragment, cytokine mutein, or combinations thereof of the cognate receptor of the cytokine. In some embodiments, A₁is not an antibody or fragment thereof that binds to the cytokine receptor.
In some embodiments, P₂comprises a peptide that impairs binding of the second antigen binding domain to the second target antigen. In some embodiments, P₂comprises a peptide that impairs binding of the second cytokine to the second cytokine receptor. In some embodiments, P₂is bound to A₂through ionic interactions, electrostatic interactions, hydrophobic interactions, Pi-stacking interactions, and H-bonding interactions, or a combination thereof. In some embodiments, P₂is bound to A₂at or near a cytokine receptor binding site. In some embodiments, P₂is bound to A₂at or near an antigen binding site. In some embodiments, P₂becomes unbound from A₂when L₂is cleaved by the protease thereby exposing P₂to the second target antigen or second cytokine receptor. In some embodiments, the protease comprises a tumor specific protease.
In some embodiments, the protease comprises a matrix metalloprotease (MMP) or a serine protease. In some embodiments, the matrix metalloprotease comprises MMP2, MMP7, MMP9, MMP13, or MMP14. In some embodiments, the serine protease comprises matriptase, urokinase, or hepsin. In some embodiments, P₂impairs binding of A₂to the second target antigen or second cytokine receptor by non-steric blocking. In some embodiments, P₂impairs binding of A₂to the second target antigen or second cytokine receptor through covalent interactions. In some embodiments, P₂is not a cytokine, cytokine binding fragment, cytokine mutein, or combinations thereof of the cognate receptor of the cytokine. In some embodiments, A₂is not an antibody or fragment thereof that binds to the cytokine receptor.
In some embodiments, P₁has less than 70% sequence homology to the target antigen. In some embodiments, P₁has less than 75% sequence homology to the target antigen. In some embodiments, P₁has less than 80% sequence homology to the target antigen. In some embodiments, P₁has less than 85% sequence homology to the target antigen. In some embodiments, P₁has less than 90% sequence homology to the target antigen. In some embodiments, P₁has less than 95% sequence homology to the target antigen. In some embodiments, P₁has less than 98% sequence homology to the target antigen. In some embodiments, P₁has less than 99% sequence homology to the target antigen.
In some embodiments, P₁has less than 70% sequence homology to the cytokine receptor. In some embodiments, P₁has less than 75% sequence homology to the cytokine receptor. In some embodiments, P₁has less than 80% sequence homology to the cytokine receptor. In some embodiments, P₁has less than 85% sequence homology to the cytokine receptor. In some embodiments, P₁has less than 90% sequence homology to the cytokine receptor. In some embodiments, P₁has less than 95% sequence homology to the cytokine receptor. In some embodiments, P₁has less than 98% sequence homology to the cytokine receptor. In some embodiments, P₁has less than 99% sequence homology to the cytokine receptor.
In some embodiments, P₂has less than 70% sequence homology to the second target antigen. In some embodiments, P₂has less than 75% sequence homology to the second target antigen. In some embodiments, P₂has less than 80% sequence homology to the second target antigen. In some embodiments, P₂has less than 85% sequence homology to the second target antigen. In some embodiments, P₂has less than 90% sequence homology to the second target antigen. In some embodiments, P₂has less than 95% sequence homology to the second target antigen. In some embodiments, P₂has less than 98% sequence homology to the second target antigen. In some embodiments, P₂has less than 99% sequence homology to the second target antigen.
In some embodiments, P₂has less than 70% sequence homology to the second cytokine receptor. In some embodiments, P₂has less than 75% sequence homology to the second cytokine receptor. In some embodiments, P₂has less than 80% sequence homology to the second cytokine receptor. In some embodiments, P₂has less than 85% sequence homology to the second cytokine receptor. In some embodiments, P₂has less than 90% sequence homology to the second cytokine receptor. In some embodiments, P₂has less than 95% sequence homology to the second cytokine receptor. In some embodiments, P₂has less than 98% sequence homology to the second cytokine receptor. In some embodiments, P₂has less than 99% sequence homology to the second cytokine receptor.
In some embodiments, P₁or P₂comprises a de novo amino acid sequence that shares less than 50% sequence homology to a cytokine, cytokine receptor, or antibody or fragments thereof that bind to the cytokine or cytokine receptor. In some embodiments, P₁or P₂comprises a de novo amino acid sequence that shares less than 40% sequence homology to a cytokine, cytokine receptor, or antibody or fragments thereof that bind to the cytokine or cytokine receptor. In some embodiments, P₁or P₂comprises a de novo amino acid sequence that shares less than 30% sequence homology to a cytokine, cytokine receptor, or antibody or fragments thereof that bind to the cytokine or cytokine receptor. In some embodiments, P₁or P₂comprises a de novo amino acid sequence that shares less than 20% sequence homology to a cytokine, cytokine receptor, or antibody or fragments thereof that bind to the cytokine or cytokine receptor. In some embodiments, P₁or P₂comprises a de novo amino acid sequence that shares less than 10% sequence homology to a cytokine, cytokine receptor, or antibody or fragments thereof that bind to the cytokine or cytokine receptor. In some embodiments, P₁or P₂is identified from a peptide library that contains random amino acid sequences.
In some embodiments, P₁or P₂comprises a de novo amino acid sequence that shares less than 50% sequence homology to the target antigen. In some embodiments, P₁or P₂comprises a de novo amino acid sequence that shares less than 40% sequence homology to the target antigen. In some embodiments, P₁or P₂comprises a de novo amino acid sequence that shares less than 30% sequence homology to the target antigen. In some embodiments, P₁or P₂comprises a de novo amino acid sequence that shares less than 20% sequence homology to the target antigen. In some embodiments, P₁or P₂comprises a de novo amino acid sequence that shares less than 10% sequence homology to the target antigen. In some embodiments, P₁or P₂is identified from a peptide library that contains random amino acid sequences.
In some embodiments, P₁or P₂comprises a peptide sequence of at least 5 amino acids in length. In some embodiments, P₁or P₂comprises a peptide sequence of at least 6 amino acids in length. In some embodiments, P₁or P₂comprises a peptide sequence of at least 10 amino acids in length. In some embodiments, P₁or P₂comprises a peptide sequence of at least 10 amino acids in length and no more than 20 amino acids in length. In some embodiments, P₁or P₂comprises a peptide sequence of at least 16 amino acids in length. In some embodiments, P₁or P₂comprises a peptide sequence of no more than 40 amino acids in length. In some embodiments, P₁or P₂comprises at least two cysteine amino acid residues. In some embodiments, P₁or P₂comprises a cyclic peptide or a linear peptide. In some embodiments, P₁or P₂comprises a cyclic peptide. In some embodiments, P₁or P₂comprises a linear peptide.
In some embodiments, P₁or P₂comprise a modified amino acid or non-natural amino acid, or a modified non-natural amino acid, or a combination thereof. In some embodiments, the modified amino acid or a modified non-natural amino acid comprises a post-translational modification. In some embodiments P₁or P₂comprise a modification including, but not limited to acetylation, acylation, ADP-ribosylation, amidation, covalent attachment of flavin, covalent attachment of a heme moiety, covalent attachment of a nucleotide or nucleotide derivative, covalent attachment of a lipid or lipid derivative, covalent attachment of phosphatidylinositol, cross-linking, cyclization, disulfide bond formation, demethylation, formation of covalent crosslinks, formation of cystine, formation of pyroglutamate, formylation, gamma carboxylation, glycosylation, GPI anchor formation, hydroxylation, iodination, methylation, myristoylation, oxidation, proteolytic processing, phosphorylation, prenylation, racemization, selenoylation, sulfation, transfer-RNA mediated addition of amino acids to proteins such as arginylation, and ubiquitination. Modifications are made anywhere to P₁or P₂including the peptide backbone, the amino acid side chains, and the terminus.
In some embodiments, P₁or P₂does not comprise albumin or an albumin fragment. In some embodiments, P₁or P₂does not comprise an albumin binding domain.
A₁and A₂
In some embodiments, A₁or A₂is an antigen recognizing molecule. In some embodiments, the antigen recognizing molecule is an antibody or an antibody fragment. In some embodiments, the antibody or the antibody fragment thereof comprises a single chain variable fragment, a single domain antibody, Fab, Fab′. In some embodiments, the antibody or antibody fragment thereof comprises a single chain variable fragment (scFv), a heavy chain variable domain (VH domain), a light chain variable domain (VL domain), or a variable domain (VHH) of a camelid derived single domain antibody. In some embodiments, the antibody or antibody fragment thereof comprises a single-chain variable fragment. In some embodiments, the antibody or antibody fragment thereof is humanized or human.
In some embodiments, A₁or A₂is a Fab. In some embodiments, the Fab comprises (a) a Fab light chain polypeptide; and (b) a Fab heavy chain polypeptide. In some embodiments, L₁or L₂is bound to N-terminus of the Fab light chain polypeptide. In some embodiments L₁or L₂is bound to N-terminus of the Fab heavy chain polypeptide. In some embodiments, L₁or L₂is bound to C-terminus of the Fab light chain polypeptide. In some embodiments, L₁or L₂is bound to C-terminus of the Fab heavy chain polypeptide.
In some embodiments, A₁or A₂is a single chain variable fragment (scFv). In some embodiments, L₁or L₂is bound to N-terminus of the scFv. In some embodiments, L₁or L₂is bound to C-terminus of the scFv. In some embodiments, the scFv comprises a light chain variable domain and a heavy chain variable domain. In some embodiments, L₁or L₂is bound to a N-terminus of the light chain variable domain of the single chain variable fragment (scFv). In some embodiments, L₁or L₂is bound to a N-terminus of the heavy chain variable domain of the single chain variable fragment (scFv).
In some embodiments, the antibody or antibody fragment thereof comprises an epidermal growth factor receptor (EGFR) binding domain. In some embodiments, the antibody or antibody fragment thereof comprises a cluster of differentiation 3 (CD3) binding domain. In some embodiments, the antibody or antibody fragment thereof comprises a cluster of differentiation 3 epsilon (CD3e) binding domain. In some embodiments, the target antigen comprises EGFR. In some embodiments, the target antigen comprises CD3. In some embodiments, the target antigen comprises CD3ε.
In some embodiments, A₁or A₂binds to a polypeptide that is part of a TCR-CD3 complex on the effector cell. In some embodiments, the target antigen is an anti-CD3 effector cell antigen. In some embodiments, the polypeptide that is part of the TCR-CD3 complex is human CD3ε. In some embodiments, A₁or A₂comprises an anti-CD3e single-chain variable fragment. In some embodiments, A₁or A₂comprises an anti-CD3e single-chain variable fragment that has a K_Dbinding of 1 μM or less to CD3 on CD3 expressing cells. In some embodiments, A_tor A₂comprises a variable light chain and variable heavy chain each of which is capable of specifically binding to human CD3. In some embodiments, A₁or A₂comprises complementary determining regions (CDRs) selected from the group consisting of muromonab-CD3 (OKT3), otelixizumab (TRX4), teplizumab (MGA031), visilizumab (Nuvion), SP34, X35, VIT3, BMA030 (BW264/56), CLB-T3/3, CRIS7, YTH12.5, F111-409, CLB-T3.4.2, TR-66, WT32, SPv-T3b, 11D8, XIII-141, XIII-46, XIII-87, 12F6, T3/RW2-8C8, T3/RW2-4B6, OKT3D, M-T301, SMC2, F101.01, UCHT-1, WT-31, 15865, 15865v12, 15865v16, and 15865v19.
In some embodiments, A₁or A₂is a soluble T cell receptor (TCR). Native TCRs are transmembrane receptors expressed on the surface of T cells that recognize antigens bound to major histocompatibility complex molecules (MHC). Native TCRs are heterodimeric and comprise an alpha polypeptide chain and a beta polypeptide chain linked through a disulfide bond. The alpha polypeptide chain and the beta polypeptide chain are expressed as part of a complex with accessory proteins which include, for example, two CD3 epsilon polypeptides, one CD3 gamma polypeptide, one CD3 delta polypeptide, and two CD3 zeta polypeptides. When a TCR engages with a target antigen and MHC, the T cell is activated resulting in a series of signaling events mediated by associated enzymes, co-receptors, adapter molecules, and activated or released transcription factors.
In native TCRs, the alpha polypeptide chain and the beta polypeptide chain comprise an extracellular domain, a transmembrane domain, and a cytoplasmic domain. Each extracellular domain comprises a variable region (V), a joining region (J), and a constant region (C). The constant region is N-terminal to the transmembrane domain, and the transmembrane domain is N-terminal to the cytoplasmic domain. The variable regions of both the alpha polypeptide chain and the beta polypeptide chain comprise three hypervariable or complementarity determining regions (CDRs). The beta polypeptide chain usually contains a short diversity region between the variable and joining regions. The three CDRs are embedded into a framework sequence, with one CDR being the hypervariable region named CDR3. The alpha chain variable region (Vα) and the beta chain variable region (Vβ) are of several types that are distinguished by their framework sequences, CDR1 and CDR2 sequences, and a partly defined CDR3 sequence.
TCRs are described using the International Immunogenetics (IMGT) TCR nomenclature. The Vα in IMGT nomenclature is referred to by a unique “TRAV” number. In the same way, Vβ is referred to by a unique “TRBV” number. The corresponding joining and constant regions are referred to as TRAJ and TRAC, respectively for the α joining and constant regions, and TRBJ and TRBC, respectively for the β joining and constant regions. The sequences defined by the IMGT nomenclature are known in the art and are contained within the online IMGT public database.
In some embodiments, the soluble TCR is a single chain TCR comprising a variable region of a TCR alpha extracellular domain, or fragment thereof, and a variable region of a TCR beta extracellular domain, or fragment thereof. In some embodiments, the soluble TCR comprises an alpha TCR polypeptide comprising a TCR alpha extracellular domain and a beta TCR polypeptide comprising a TCR beta extracellular domain.
In some embodiments, the soluble TCR is a single chain TCR comprising a variable region of a TCR alpha extracellular domain, or fragment thereof, and a variable region of a TCR beta extracellular domain, or fragment thereof. In some embodiments, the soluble TCR comprises an alpha TCR polypeptide comprising a TCR alpha extracellular domain and a beta TCR polypeptide comprising a TCR beta extracellular domain. In some embodiments, L₁is bound to N-terminus of the alpha TCR polypeptide. In some embodiments, L₁is bound to N-terminus of the beta TCR polypeptide. In some embodiments, A₂is bound to C-terminus of the alpha TCR polypeptide. In some embodiments, A₂is bound to N-terminus of the alpha TCR polypeptide. In some embodiments, A₂is bound to C-terminus of the beta TCR polypeptide. In some embodiments, A₂is bound to N-terminus of the beta TCR polypeptide. In some embodiments, L₁is bound to N-terminus of the alpha TCR polypeptide and A₂is bound to N-terminus of the beta TCR polypeptide. In some embodiments, L₁is bound to N-terminus of the alpha TCR polypeptide and A₂is bound to C-terminus of the beta TCR polypeptide. In some embodiments, L₁is bound to N-terminus of the alpha TCR polypeptide and A₂is bound to C-terminus of the alpha TCR polypeptide. In some embodiments, L₁is bound to N-terminus of the beta TCR polypeptide and A₂is bound to N-terminus of the alpha TCR polypeptide. In some embodiments, L₁is bound to N-terminus of the beta TCR polypeptide and A₂is bound to C-terminus of the beta TCR polypeptide. In some embodiments, L₁is bound to N-terminus of the beta TCR polypeptide and A₂is bound to C-terminus of the alpha TCR polypeptide.
In some embodiments, the polypeptide or polypeptide complex has weaker binding affinity for the target antigen or second target antigen as compared to the binding affinity for the target antigen or second target antigen of a polypeptide or polypeptide complex that does not have P₁or P₂or L₁or L₂. In some embodiments, the polypeptide or polypeptide complex has weaker binding affinity for the target antigen or second target antigen that is at least 5× higher than the binding affinity for the target antigen of a form of the polypeptide or polypeptide complex that does not have P₁or P₂or L₁or L₂. In some embodiments, the polypeptide or polypeptide complex has weaker binding affinity for the target antigen or second target antigen that is at least 8× higher than the binding affinity for the target antigen or second target antigen of a form of the polypeptide or polypeptide complex that does not have P₁or P₂or L₁or L₂. In some embodiments, the polypeptide or polypeptide complex has weaker binding affinity for the target antigen or second target antigen that is at least 10× higher than the binding affinity for the target antigen or second target antigen of a form of the polypeptide or polypeptide complex that does not have P₁or P₂or L₁or L₂. In some embodiments, the polypeptide or polypeptide complex has weaker binding affinity for the target antigen or second target antigen that is at least 20× higher than the binding affinity for the target antigen or second target antigen of a form of the polypeptide or polypeptide complex that does not have P₁or P₂or L₁or L₂. In some embodiments, the polypeptide or polypeptide complex has weaker binding affinity for the target antigen or second target antigen that is at least 25× higher than the binding affinity for the target antigen or second target antigen of a form of the polypeptide or polypeptide complex that does not have P₁or P₂or L₁or L₂. In some embodiments, the polypeptide or polypeptide complex has weaker binding affinity for the target antigen or second target antigen that is at least 30× higher than the binding affinity for the target antigen or second target antigen of a form of the polypeptide or polypeptide complex that does not have P₁or P₂or L₁or L₂. In some embodiments, the polypeptide or polypeptide complex has weaker binding affinity for the target antigen or second target antigen that is at least 40× higher than the binding affinity for the target antigen or second target antigen of a form of the polypeptide or polypeptide complex that does not have P₁or P₂or L₁or L₂. In some embodiments, the polypeptide or polypeptide complex has weaker binding affinity for the target antigen or second target antigen that is at least 50× higher than the binding affinity for the target antigen or second target antigen of a form of the polypeptide or polypeptide complex that does not have P₁or P₂or L₁or L₂. In some embodiments, the polypeptide or polypeptide complex has weaker binding affinity for the target antigen or second target antigen that is at least 60× higher than the binding affinity for the target antigen or second target antigen of a form of the polypeptide or polypeptide complex that does not have P₁or P₂or L₁or L₂. In some embodiments, the polypeptide or polypeptide complex has weaker binding affinity for the target antigen or second target antigen that is at least 70× higher than the binding affinity for the target antigen or second target antigen of a form of the polypeptide or polypeptide complex that does not have P₁or P₂or L₁or L₂. In some embodiments, the polypeptide or polypeptide complex has weaker binding affinity for the target antigen or second target antigen that is at least 75× higher than the binding affinity for the target antigen or second target antigen of a form of the polypeptide or polypeptide complex that does not have P₁or P₂or L₁or L₂. In some embodiments, the polypeptide or polypeptide complex has weaker binding affinity for the target antigen or second target antigen that is at least 80× higher than the binding affinity for the target antigen or second target antigen of a form of the polypeptide or polypeptide complex that does not have P₁or P₂or L₁or L₂. In some embodiments, the polypeptide or polypeptide complex has weaker binding affinity for the target antigen or second target antigen that is at least 90× higher than the binding affinity for the target antigen or second target antigen of a form of the polypeptide or polypeptide complex that does not have P₁or P₂or L₁or L₂. In some embodiments, the polypeptide or polypeptide complex has weaker binding affinity for the target antigen or second target antigen that is at least 100× higher than the binding affinity for the target antigen or second target antigen of a form of the polypeptide or polypeptide complex that does not have P₁or P₂or L₁or L₂. In some embodiments, the polypeptide or polypeptide complex has weaker binding affinity for the target antigen or second target antigen that is at least 120× higher than the binding affinity for the target antigen or second target antigen of a form of the polypeptide or polypeptide complex that does not have P₁or P₂or L₁or L₂.
In some embodiments, the polypeptide or polypeptide complex has weaker binding affinity for the target antigen or second target antigen as compared to the binding affinity for the target antigen or second target antigen of the polypeptide or polypeptide complex in which L₁or L₂has been cleaved. In some embodiments, the polypeptide or polypeptide complex has weaker binding affinity for the target antigen or second target antigen that is at least 5× higher than the binding affinity for the target antigen or second target antigen of the polypeptide or polypeptide complex in which L₁or L₂has been cleaved. In some embodiments, the polypeptide or polypeptide complex has weaker binding affinity for the target antigen or second target antigen that is at least 8× higher than the binding affinity for the target antigen or second target antigen of the polypeptide or polypeptide complex in which L₁or L₂has been cleaved. In some embodiments, the polypeptide or polypeptide complex has weaker binding affinity for the target antigen or second target antigen that is at least 10× higher than the binding affinity for the target antigen or second target antigen of the polypeptide or polypeptide complex in which L₁or L₂has been cleaved. In some embodiments, the polypeptide or polypeptide complex has weaker binding affinity for the target antigen or second target antigen that is at least 20× higher than the binding affinity for the target antigen or second target antigen of the polypeptide or polypeptide complex in which L₁or L₂has been cleaved. In some embodiments, the polypeptide or polypeptide complex has weaker binding affinity for the target antigen or second target antigen that is at least 25× higher than the binding affinity for the target antigen or second target antigen of the polypeptide or polypeptide complex in which L₁or L₂has been cleaved. In some embodiments, the polypeptide or polypeptide complex has weaker binding affinity for the target antigen or second target antigen that is at least 30× higher than the binding affinity for the target antigen or second target antigen of the polypeptide or polypeptide complex in which L₁or L₂has been cleaved. In some embodiments, the polypeptide or polypeptide complex has weaker binding affinity for the target antigen or second target antigen that is at least 40× higher than the binding affinity for the target antigen or second target antigen of the polypeptide or polypeptide complex in which L₁or L₂has been cleaved. In some embodiments, the polypeptide or polypeptide complex has weaker binding affinity for the target antigen or second target antigen that is at least 50× higher than the binding affinity for the target antigen or second target antigen of the polypeptide or polypeptide complex in which L₁or L₂has been cleaved. In some embodiments, the polypeptide or polypeptide complex has weaker binding affinity for the target antigen or second target antigen that is at least 60× higher than the binding affinity for the target antigen or second target antigen of the polypeptide or polypeptide complex in which L₁or L₂has been cleaved. In some embodiments, the polypeptide or polypeptide complex has weaker binding affinity for the target antigen or second target antigen that is at least 70× higher than the binding affinity for the target antigen or second target antigen of the polypeptide or polypeptide complex in which L₁or L₂has been cleaved. In some embodiments, the polypeptide or polypeptide complex has weaker binding affinity for the target antigen or second target antigen that is at least 75× higher than the binding affinity for the target antigen or second target antigen of the polypeptide or polypeptide complex in which L₁or L₂has been cleaved. In some embodiments, the polypeptide or polypeptide complex has weaker binding affinity for the target antigen or second target antigen that is at least 80× higher than the binding affinity for the target antigen or second target antigen of the polypeptide or polypeptide complex in which L₁or L₂has been cleaved. In some embodiments, the polypeptide or polypeptide complex has weaker binding affinity for the target antigen or second target antigen that is at least 90× higher than the binding affinity for the target antigen or second target antigen of the polypeptide or polypeptide complex in which L₁or L₂has been cleaved. In some embodiments, the polypeptide or polypeptide complex has weaker binding affinity for the target antigen or second target antigen that is at least 100× higher than the binding affinity for the target antigen or second target antigen of the polypeptide or polypeptide complex in which L₁or L₂has been cleaved. In some embodiments, the polypeptide or polypeptide complex has weaker binding affinity for the target antigen or second target antigen that is at least 120× higher than the binding affinity for the target antigen or second target antigen of the polypeptide or polypeptide complex in which L₁or L₂has been cleaved. In some embodiments, L₁or L₂is cleaved by a protease. In some embodiments, the protease comprises a tumor specific protease. In some embodiments, the protease comprises a matrix metalloprotease (MMP) or a serine protease. In some embodiments, the matrix metalloprotease comprises MMP2, MMP7, MMP9, MMP13, or MMP14. In some embodiments, the serine protease comprises matriptase, urokinase, or hepsin.
In some embodiments, A₁or A₂is a cytokine or cytokine fragment. In some embodiments, A₁or A₂is a mutein of the cytokine or the cytokine fragment. In some embodiments, the cytokine or the cytokine fragment is a mutein of the cytokine or the cytokine fragment.
Cytokines are a diverse group of small peptides, including chemokines, interferons, interleukins, lymphokines, adipokines, mesenchymal growth factors, and tumor necrosis factors, which are involved in intercellular signaling in a variety of biological pathways. They are particularly important in immune and inflammatory responses. Signaling occurs following recognition of the cytokine by a corresponding cytokine receptor, which are transmembrane receptors comprising an extracellular domain for ligand binding and an intracellular domain that allows signal transduction.
The diversity of cytokines comes with a corresponding diversity in cytokine receptors, which can comprise a single chain or subunit or dimeric/multimeric domains. Cytokine receptors include Type I cytokine receptors, exemplified by interleukin receptors, and Type II cytokine receptors, exemplified by interferon receptors, both of which comprise a cytokine receptor homology domain (CHD). The CHD of Type I cytokine receptors share a common amino acid motif (WSXWS (SEQ ID NO: 27)), while Type II cytokine receptors lack this motif. Cytokine receptors can include an alpha subunit, beta subunit, gamma subunit, or dimeric, or trimeric combinations thereof. In one example, a high affinity receptor for IL-2 comprises an IL-2Rα subunit, IL-2Rβ subunit, and IL-2Rγ subunit, an intermediate affinity receptor for IL-2 comprises only the IL-2Rβ subunit and IL-2Rγ subunit, and low affinity receptor for IL-2 comprises only the IL-2Rα subunit.
In some embodiments, the cytokine is a chemokine, an interferon, an interleukin, a lymphokine, an adipokine, a growth factor, or a tumor necrosis factor. In some embodiments, the interferon (IFN) is IFNα, IFNβ, IFNγ, or a fragment thereof. In some embodiments, the interleukin (IL) is IL-2, IL-4, IL-6, IL-7, IL-10, IL-12, IL-15, IL-21, or a fragment thereof. In some embodiments, the growth factor is granulocyte-macrophage colony-stimulating factor (GM-CSF) or a fragment thereof. In some embodiments the cytokine is TGF-γ.
In some embodiments, a cytokine mutein is a variant of a wild-type cytokine. In some embodiments, a cytokine mutein is a mutant of a wild-type cytokine. In some embodiments, the cytokine mutein comprises at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, or more than 50 amino acid substitutions relative to a wild-type cytokine. In some embodiments, the cytokine mutein comprises no more than 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, or more than 50 amino acid substitutions relative to a wild-type cytokine. In some embodiments, the cytokine mutein is a non-naturally occurring cytokine. In some embodiments, the cytokine mutein comprises at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, or more than 50 amino acid substitutions relative to a naturally occurring cytokine. In some embodiments, the cytokine mutein comprises no more than 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, or more than 50 amino acid substitutions relative to a naturally occurring cytokine.
In some embodiments, the cytokine or cytokine fragment binds to a cytokine receptor. In some embodiments, the cytokine receptor is a receptor for a chemokine, an interferon, an interleukin, a lymphokine, an adipokine, a growth factor, or a tumor necrosis factor. In some embodiments, the cytokine receptor is a type I cytokine receptor or a type II cytokine receptor. In some embodiments, the cytokine receptor is a dimer or a trimer. In some embodiments, the cytokine receptor comprises an alpha subunit, a beta subunit, a gamma subunit, or any combination thereof. For example, in some embodiments, the cytokine receptor comprises an alpha subunit, a beta subunit, and a gamma subunit. In another example, in some embodiments, the cytokine receptor comprises a beta subunit and a gamma subunit. In some embodiments, the cytokine receptor comprises an alpha subunit and a beta subunit.
In some embodiments, the polypeptide or polypeptide complex has a weaker binding affinity for its cytokine receptor as compared to the binding affinity for the cytokine receptor of a polypeptide or polypeptide complex that does not have P₁or P₂or L₁or L₂. In some embodiments, the polypeptide or polypeptide complex has weaker binding affinity for its cytokine receptor that is at least 5× weaker than the binding affinity for the cytokine receptor of a form of the polypeptide or polypeptide complex that does not have P₁or P₂or L₁or L₂. In some embodiments, the polypeptide or polypeptide complex has weaker binding affinity for its cytokine receptor that is at least 8× weaker than the binding affinity for the cytokine receptor of a form of the polypeptide or polypeptide complex that does not have P₁or P₂or L₁or L₂. In some embodiments, the polypeptide or polypeptide complex has weaker binding affinity for its cytokine receptor that is at least 10× weaker than the binding affinity for the cytokine receptor of a form of the polypeptide or polypeptide complex that does not have P₁or P₂or L₁or L₂. In some embodiments, the polypeptide or polypeptide complex has weaker binding affinity for its cytokine receptor that is at least 20× weaker than the binding affinity for the cytokine receptor of a form of the polypeptide or polypeptide complex that does not have P₁or P₂or L₁or L₂. In some embodiments, the polypeptide or polypeptide complex has weaker binding affinity for its cytokine receptor that is at least 25× weaker than the binding affinity for the cytokine receptor of a form of the polypeptide or polypeptide complex that does not have P₁or P₂or L₁or L₂. In some embodiments, the polypeptide or polypeptide complex has weaker binding affinity for its cytokine receptor that is at least 30× weaker than the binding affinity for the cytokine receptor of a form of the polypeptide or polypeptide complex that does not have P₁or P₂or L₁or L₂. In some embodiments, the polypeptide or polypeptide complex has weaker binding affinity for its cytokine receptor that is at least 40× weaker than the binding affinity for the cytokine receptor of a form of the polypeptide or polypeptide complex that does not have P₁or P₂or L₁or L₂. In some embodiments, the polypeptide or polypeptide complex has weaker binding affinity for its cytokine receptor that is at least 50× weaker than the binding affinity for the cytokine receptor of a form of the polypeptide or polypeptide complex that does not have P₁or P₂or L₁or L₂In some embodiments, the polypeptide or polypeptide complex has weaker binding affinity for its cytokine receptor that is at least 60× weaker than the binding affinity for the cytokine receptor of a form of the polypeptide or polypeptide complex that does not have P₁or P₂or L₁or L₂In some embodiments, the polypeptide or polypeptide complex has weaker binding affinity for its cytokine receptor that is at least 70× weaker than the binding affinity for the cytokine receptor of a form of the polypeptide or polypeptide complex that does not have P₁or P₂or L₁or L₂. In some embodiments, the polypeptide or polypeptide complex has weaker binding affinity for its cytokine receptor that is at least 75× weaker than the binding affinity for the cytokine receptor of a form of the polypeptide or polypeptide complex that does not have P₁or P₂or L₁or L₂. In some embodiments, the polypeptide or polypeptide complex has weaker binding affinity for its cytokine receptor that is at least 80× weaker than the binding affinity for the cytokine receptor of a form of the polypeptide or polypeptide complex that does not have P₁or P₂or L₁or L₂. In some embodiments, the polypeptide or polypeptide complex has weaker binding affinity for its cytokine receptor that is at least 90× weaker than the binding affinity for the cytokine receptor of a form of the polypeptide or polypeptide complex that does not have P₁or P₂or L₁or L₂. In some embodiments, the polypeptide or polypeptide complex has weaker binding affinity for its cytokine receptor that is at least 100× weaker than the binding affinity for the cytokine receptor of a form of the polypeptide or polypeptide complex that does not have P₁or P₂or L₁or L₂. In some embodiments, the polypeptide or polypeptide complex has weaker binding affinity for its cytokine receptor that is at least 120× weaker than the binding affinity for the cytokine receptor of a form of the polypeptide or polypeptide complex that does not have P₁or P₂or L₁or L₂. In some embodiments, the polypeptide or polypeptide complex has weaker binding affinity for its cytokine receptor that is at least 150× weaker than the binding affinity for the cytokine receptor of a form of the polypeptide or polypeptide complex that does not have P₁or P₂or L₁or L₂. In some embodiments, the cytokine or cytokine fragment comprises an interferon, GM-CSF, IL-2, IL-7, IL-12, IL-15, or IL-21. In some embodiments, the cytokine or cytokine fragment comprises IL-2, IL-12, IL-6, IL-4, IL-10, or TGF-3. In some embodiments, the cytokine receptor comprises an interferon receptor, GM-CSF receptor, IL-2 receptor, IL-7 receptor, IL-12 receptor, IL-15 receptor, or IL-21 receptor. In some embodiments, the cytokine receptor comprises IL-2 receptor, IL-12 receptor, IL-6 receptor, IL-4 receptor, IL-10 receptor, or TGF-β receptor.
In some embodiments, the polypeptide or polypeptide complex has weaker binding affinity for its cytokine receptor as compared to the binding affinity for the cytokine receptor of the polypeptide or polypeptide complex in which L₁or L₂has been cleaved. In some embodiments, the polypeptide or polypeptide complex has weaker binding affinity for its cytokine receptor that is at least 5× weaker than the binding affinity for the cytokine receptor of the polypeptide or polypeptide complex in which L₁or L₂has been cleaved. In some embodiments, the polypeptide or polypeptide complex has weaker binding affinity for its cytokine receptor that is at least 8× weaker than the binding affinity for the cytokine receptor of the polypeptide or polypeptide complex in which L₁or L₂has been cleaved. In some embodiments, the polypeptide or polypeptide complex has weaker binding affinity for its cytokine receptor that is at least 10× weaker than the binding affinity for the cytokine receptor of the polypeptide or polypeptide complex in which L₁or L₂has been cleaved. In some embodiments, the polypeptide or polypeptide complex has weaker binding affinity for its cytokine receptor that is at least 15× weaker than the binding affinity for the cytokine receptor of the polypeptide or polypeptide complex in which L₁or L₂has been cleaved. In some embodiments, the polypeptide or polypeptide complex has weaker binding affinity for its cytokine receptor that is at least 20× weaker than the binding affinity for the cytokine receptor of the polypeptide or polypeptide complex in which L₁or L₂has been cleaved. In some embodiments, the polypeptide or polypeptide complex has weaker binding affinity for its cytokine receptor that is at least 25× weaker than the binding affinity for the cytokine receptor of the polypeptide or polypeptide complex in which L₁or L₂has been cleaved. In some embodiments, the polypeptide or polypeptide complex has weaker binding affinity for its cytokine receptor that is at least 30× weaker than the binding affinity for the cytokine receptor of the polypeptide or polypeptide complex in which L₁or L₂has been cleaved. In some embodiments, the polypeptide or polypeptide complex has weaker binding affinity for its cytokine receptor that is at least 40× weaker than the binding affinity for the cytokine receptor of the polypeptide or polypeptide complex in which L₁or L₂has been cleaved. In some embodiments, the polypeptide or polypeptide complex has weaker binding affinity for its cytokine receptor that is at least 50× weaker than the binding affinity for the cytokine receptor of the polypeptide or polypeptide complex in which L₁or L₂has been cleaved. In some embodiments, the polypeptide or polypeptide complex has weaker binding affinity for its cytokine receptor that is at least 60× weaker than the binding affinity for the cytokine receptor of the polypeptide or polypeptide complex in which L₁or L₂has been cleaved. In some embodiments, the polypeptide or polypeptide complex has weaker binding affinity for its cytokine receptor that is at least 70× weaker than the binding affinity for the cytokine receptor of the polypeptide or polypeptide complex in which L₁or L₂has been cleaved. In some embodiments, the polypeptide or polypeptide complex has weaker binding affinity for its cytokine receptor that is at least 75× weaker than the binding affinity for the cytokine receptor of the polypeptide or polypeptide complex in which L₁or L₂has been cleaved. In some embodiments, the polypeptide or polypeptide complex has weaker binding affinity for its cytokine receptor that is at least 80× weaker than the binding affinity for the cytokine receptor of the polypeptide or polypeptide complex in which L₁or L₂has been cleaved. In some embodiments, the polypeptide or polypeptide complex has weaker binding affinity for its cytokine receptor that is at least 90× weaker than the binding affinity for the cytokine receptor of the polypeptide or polypeptide complex in which L₁or L₂has been cleaved. In some embodiments, the polypeptide or polypeptide complex has weaker binding affinity for its cytokine receptor that is at least 100× weaker than the binding affinity for the cytokine receptor of the polypeptide or polypeptide complex in which L₁or L₂has been cleaved. In some embodiments, the cytokine or cytokine fragment comprises an interferon, GM-CSF, IL-2, IL-7, IL-12, IL-15, or IL-21. In some embodiments, the cytokine receptor comprises an interferon receptor, GM-CSF receptor, IL-2 receptor, IL-7 receptor, IL-12 receptor, IL-15 receptor, or IL-21 receptor. In some embodiments, L₁or L₂is cleaved by a protease. In some embodiments, the protease comprises a tumor specific protease. In some embodiments, the protease comprises a matrix metalloprotease (MMP) or a serine protease. In some embodiments, the matrix metalloprotease comprises MMP2, MMP7, MMP9, MMP13, or MMP14. In some embodiments, the serine protease comprises matriptase, urokinase, or hepsin.

Half-Life Extending Moiety

In some embodiments, P₁is further linked to a half-life extending moiety. In some embodiments, P₁is further linked to a half-life extending moiety in a configuration according to Formula Ia
A₁-L₁-P₁-L₃-H₁ (Formula Ia)
wherein H₁is the half-life extending moiety and L₃is a linker that connects H₁to P₁. In some embodiments, L₃is a non-cleavable linker. In some embodiments, the half-life extending moiety (H₁) does not block A₁binding to the target antigen. In some embodiments, the half-life extending moiety (H₁) does not have binding affinity to A₁. In some embodiments, the half-life extending moiety (H₁) does not have binding affinity to the target antigen. In some embodiments, the half-life extending moiety (H₁) does not shield A₁from the target antigen. In some embodiments, the half-life extending moiety (H₁) is not directly linked to A₁.
In some embodiments, the half-life extending moiety (H₁) does not block A₁binding to the cytokine receptor. In some embodiments, the half-life extending moiety (H₁) does not have binding affinity to the cytokine or cytokine receptor. In some embodiments, the half-life extending moiety (H₁) does not shield the cytokine or cytokine fragment from the cytokine receptor. In some embodiments, the half-life extending moiety (H₁) is not directly linked to the cytokine or cytokine fragment.
In some embodiments, H₁comprises an amino acid sequence that has repetitive sequence motifs. In some embodiments, H₁comprises an amino acid sequence that has highly ordered secondary structure. “Highly ordered secondary structure,” as used in this context, means that at least about 50%, or about 70%, or about 80%, or about 90%, of amino acid residues of H₁contribute to secondary structure, as measured or determined by means, including, but not limited to, spectrophotometry (e.g. by circular dichroism spectroscopy in the “far-UV” spectral region (190-250 nm), and computer programs or algorithms, such as the Chou-Fasman algorithm and the Gamier-Osguthorpe-Robson (“GOR”) algorithm.
In some embodiments, H₁comprises a polymer. In some embodiments, the polymer is polyethylene glycol (PEG). In some embodiments, H₁comprises albumin. In some embodiments, H₁comprises a Fc domain. In some embodiments, the albumin is serum albumin. In some embodiments, the albumin is human serum albumin. In some embodiments, H₁comprises a polypeptide, a ligand, or a small molecule. In some embodiments, the polypeptide, the ligand or the small molecule binds serum protein or a fragment thereof, a circulating immunoglobulin or a fragment thereof, or CD35/CR1. In some embodiments, the serum protein comprises a thyroxine-binding protein, a transthyretin, a 1-acid glycoprotein, a transferrin, transferrin receptor or a transferrin-binding portion thereof, a fibrinogen, or an albumin. In some embodiments, the circulating immunoglobulin molecule comprises IgG1, IgG2, IgG3, IgG4, s1gA, IgM or IgD. In some embodiments, the serum protein is albumin. In some embodiments, the polypeptide is an antibody. In some embodiments, the antibody comprises a single domain antibody, a single chain variable fragment or a Fab. In some embodiments, the antibody comprises a single domain antibody. In some embodiments, the antibody comprises a single domain antibody that binds to albumin. In some embodiments, the antibody comprises a single domain antibody that binds to human serum albumin. In some embodiments, the antibody is a human or humanized antibody. In some embodiments, the single domain antibody is selected from the group consisting of 645gH1gL1, 645dsgH5gL4, 23-13-A01-sc02, A10m3 or a fragment thereof, DOM7r-31, DOM7h-11-15, Alb-1, Alb-8, Alb-23, 10G, 10GE, and SA21.
In some embodiments, H₁comprises a single domain antibody. In some embodiments, H₁comprises a single domain antibody that binds to albumin. In some embodiments, H₁comprises a single domain antibody that binds to human serum albumin.
In some embodiments, H₁comprise a modified amino acid or non-natural amino acid, or a modified non-natural amino acid, or a combination thereof. In some embodiments, the modified amino acid or a modified non-natural amino acid comprises a post-translational modification. In some embodiments, H₁comprise a modification including, but not limited to acetylation, acylation, ADP-ribosylation, amidation, covalent attachment of flavin, covalent attachment of a heme moiety, covalent attachment of a nucleotide or nucleotide derivative, covalent attachment of a lipid or lipid derivative, covalent attachment of phosphatidylinositol, cross-linking, cyclization, disulfide bond formation, demethylation, formation of covalent crosslinks, formation of cystine, formation of pyroglutamate, formylation, gamma carboxylation, glycosylation, GPI anchor formation, hydroxylation, iodination, methylation, myristoylation, oxidation, proteolytic processing, phosphorylation, prenylation, racemization, selenoylation, sulfation, transfer-RNA mediated addition of amino acids to proteins such as arginylation, and ubiquitination. Modifications are made anywhere to H₁including the peptide backbone, the amino acid side chains, and the terminus.

Polynucleotides Encoding Polypeptides or Polypeptide Complexes

Disclosed herein, in some embodiments, are isolated recombinant nucleic acid molecules encoding polypeptides or polypeptide complexes as disclosed herein. Described herein, in some embodiments, are isolated recombinant nucleic acid molecules encoding polypeptides comprising a cleavable linker.
As disclosed herein, in some embodiments, are isolated recombinant nucleic acid molecules encoding polypeptides comprising a cleavable linker according to the amino acid sequence of SEQ ID NO: 1 (LSGRSDAG).
In some embodiments, the cleavable linker comprises the amino acid sequence of SEQ ID NO: 3 (ISSGLLSGRSDAG). In some embodiments, the cleavable linker comprises the amino acid sequence of SEQ ID NO: 26 (AGLLAPPGGLSGRSDAG). In some embodiments, the cleavable linker comprises the amino acid sequence of SEQ ID NO: 4 (AAGLLAPPGGLSGRSDAG). In some embodiments, the cleavable linker comprises the amino acid sequence of SEQ ID NO: 5 (SPLGLSGRSDAG). In some embodiments, the cleavable linker comprises the amino acid sequence of SEQ ID NO: 6 (LSGRSDAGSPLGLAG).
Disclosed herein, in some embodiments, are isolated recombinant nucleic acid molecules encoding an isolated polypeptide comprising a cleavable linker according to the amino acid sequence of Linker 1 (ISSGLLSGRSDAG) (SEQ ID NO: 3), Linker 2 (AAGLLAPPGGLSGRSDAG) (SEQ ID NO: 4), Linker 3 (SPLGLSGRSDAG) (SEQ ID NO: 5), or Linker 4 (LSGRSDAGSPLGLAG) (SEQ ID NO: 6), or an isolated polypeptide comprising a cleavable linker that has 1, 2, or 3 amino acid substitutions, additions, or deletions relative to the amino acid sequence of Linker 1, Linker 2, Linker 3, or Linker 4. Disclosed herein, in some embodiments, are isolated recombinant nucleic acid molecules encoding an isolated polypeptide comprising a cleavable linker according to the amino acid sequence of Linker 1 (ISSGLLSGRSDAG) (SEQ ID NO: 3). Disclosed herein, in some embodiments, are isolated recombinant nucleic acid molecules encoding an isolated polypeptide comprising a cleavable linker according to the amino acid sequence of Linker 2 (AAGLLAPPGGLSGRSDAG) (SEQ ID NO: 4). Disclosed herein, in some embodiments, are isolated recombinant nucleic acid molecules encoding an isolated polypeptide comprising a cleavable linker according to the amino acid sequence of Linker 3 (SPLGLSGRSDAG) (SEQ ID NO: 5). Disclosed herein, in some embodiments, are isolated recombinant nucleic acid molecules encoding an isolated polypeptide comprising a cleavable linker according to the amino acid sequence of Linker 4 (LSGRSDAGSPLGLAG) (SEQ ID NO: 6).
Disclosed herein, in some embodiments, are isolated recombinant nucleic acid molecules encoding an isolated polypeptide comprising a cleavable linker according to the amino acid sequence LSGRSDAG (SEQ ID NO: 1).
Disclosed herein, in some embodiments, are isolated recombinant nucleic acid molecules encoding polypeptides or polypeptide complexes according to Formula I:
A₁-L₁-P₁ (Formula I)
wherein A₁comprises the antigen binding domain that binds to the target antigen or the cytokine that binds to the cytokine receptor; L₁comprises the cleavable linker; and P₁comprises a peptide that impairs binding of the antigen binding domain to the target antigen or impairs binding of the cytokine to the cytokine receptor.
Disclosed herein, in some embodiments, are isolated recombinant nucleic acid molecules encoding polypeptides or polypeptide complexes comprising Formula I:
A₁-L₁-P₁ (Formula I)
wherein A₁comprises the antigen binding domain that binds to the target antigen or the cytokine that binds to the cytokine receptor; L₁comprises the cleavable linker; and P₁comprises a peptide that impairs binding of the antigen binding domain to the target antigen or impairs binding of the cytokine to the cytokine receptor. Disclosed herein, in some embodiments, are isolated recombinant nucleic acid molecules encoding polypeptides or polypeptide complexes according to Formula I:
A₁-L₁-P₁ (Formula I)
wherein A₁is the antigen binding domain that binds to the target antigen or the cytokine that binds to the cytokine receptor; L₁is the cleavable linker; and P₁is a peptide that impairs binding of the antigen binding domain to the target antigen or impairs binding of the cytokine to the cytokine receptor. Disclosed herein, in some embodiments, are isolated recombinant nucleic acid molecules encoding polypeptides or polypeptide complexes comprising Formula I:
A₁-L₁-P₁ (Formula I)
wherein A₁is the antigen binding domain that binds to the target antigen or the cytokine that binds to the cytokine receptor; L₁is the cleavable linker; and P₁is a peptide that impairs binding of the antigen binding domain to the target antigen or impairs binding of the cytokine to the cytokine receptor.
Disclosed herein, in some embodiments, are polypeptides or polypeptide complexes, wherein the isolated polypeptide is complexed with a second isolated polypeptide comprising a second antigen binding domain or a second cytokine. Disclosed herein, in some embodiments, are isolated recombinant nucleic acid molecules encoding polypeptides or polypeptide complexes according to Formula II:
A₂-L₂-P₂ (Formula II)
wherein A₂comprises the second antigen binding domain or the second cytokine; L₂comprises a second cleavable linker; and P₂comprises a second peptide that impairs binding of the second antigen binding domain to a second target antigen or impairs binding of the second cytokine to a second cytokine receptor. Disclosed herein, in some embodiments, are isolated recombinant nucleic acid molecules encoding polypeptides or polypeptide complexes comprising Formula II:
A₂-L₂-P₂ (Formula II)
wherein A₂comprises the second antigen binding domain or the second cytokine; L₂comprises a second cleavable linker; and P₂comprises a second peptide that impairs binding of the second antigen binding domain to a second target antigen or impairs binding of the second cytokine to a second cytokine receptor. Disclosed herein, in some embodiments, are isolated recombinant nucleic acid molecules encoding polypeptides or polypeptide complexes according to Formula II:
A₂-L₂-P₂ (Formula II)
wherein A₂is the second antigen binding domain or the second cytokine; L₂is a second cleavable linker; and P₂is a second peptide that impairs binding of the second antigen binding domain to a second target antigen or impairs binding of the second cytokine to a second cytokine receptor. Disclosed herein, in some embodiments, are isolated recombinant nucleic acid molecules encoding polypeptides or polypeptide complexes comprising Formula II:
A₂-L₂-P₂ (Formula II)
wherein A₂is the second antigen binding domain or the second cytokine; L₂is a second cleavable linker; and P₂is a second peptide that impairs binding of the second antigen binding domain to a second target antigen or impairs binding of the second cytokine to a second cytokine receptor.

Pharmaceutical Compositions

Disclosed herein, in some embodiments, are pharmaceutical compositions comprising: (a) the polypeptides or polypeptide complexes as disclosed herein; and (b) a pharmaceutically acceptable excipient.
In some embodiments, the pharmaceutical composition comprises (a) the polypeptides or polypeptide complexes comprising a cleavable linker according to the amino acid sequence of SEQ ID NO: 1 (LSGRSDAG) and (b) a pharmacetically acceptable excipient.
In some embodiments, the pharmaceutical composition comprises (a) the polypeptides or polypeptide complexes comprising a cleavable linker according to the amino acid sequence of SEQ ID NO: 3 (ISSGLLSGRSDAG) and (b) a pharmacetically acceptable excipient.
In some embodiments, the pharmaceutical composition comprises (a) the polypeptides or polypeptide complexes comprising a cleavable linker according to the amino acid sequence of SEQ ID NO: 26 (AGLLAPPGGLSGRSDAG) and (b) a pharmacetically acceptable excipient.
In some embodiments, the pharmaceutical composition comprises (a) the polypeptides or polypeptide complexes comprising a cleavable linker according to the amino acid sequence of SEQ ID NO: 4 (AAGLLAPPGGLSGRSDAG) and (b) a pharmacetically acceptable excipient.
In some embodiments, the pharmaceutical composition comprises (a) the polypeptides or polypeptide complexes comprising a cleavable linker according to the amino acid sequence of SEQ ID NO: 5 (SPLGLSGRSDAG) and (b) a pharmacetically acceptable excipient.
In some embodiments, the pharmaceutical composition comprises (a) the polypeptides or polypeptide complexes comprising a cleavable linker according to the amino acid sequence of SEQ ID NO: 6 (LSGRSDAGSPLGLAG) and (b) a pharmacetically acceptable excipient.
In some embodiments, the pharmaceutical composition comprises (a) the polypeptides or polypeptide complexes comprising a cleavable linker according to the amino acid sequence of Linker 1 (ISSGLLSGRSDAG) (SEQ ID NO: 3), Linker 2 (AAGLLAPPGGLSGRSDAG) (SEQ ID NO: 4), Linker 3 (SPLGLSGRSDAG) (SEQ ID NO: 5), or Linker 4 (LSGRSDAGSPLGLAG) (SEQ ID NO: 6), or the polypeptides or polypeptide complexes comprising a cleavable linker that has 1, 2, or 3 amino acid substitutions, additions, or deletions relative to the amino acid sequence of Linker 1, Linker 2, Linker 3, or Linker 4 and (b) a pharmacetically acceptable excipient. In some embodiments, the pharmaceutical composition comprises (a) the polypeptides or polypeptide complexes comprising a cleavable linker according to the amino acid sequence of Linker 1 (ISSGLLSGRSDAG) (SEQ ID NO: 3) and (b) a pharmacetically acceptable excipient. In some embodiments, the pharmaceutical composition comprises (a) the polypeptides or polypeptide complexes comprising a cleavable linker according to the amino acid sequence of Linker 2 (AAGLLAPPGGLSGRSDAG) (SEQ ID NO: 4) and (b) a pharmacetically acceptable excipient. In some embodiments, the pharmaceutical composition comprises (a the polypeptides or polypeptide complexes comprising a cleavable linker according to the amino acid sequence of Linker 3 (SPLGLSGRSDAG) (SEQ ID NO: 5) and (b) a pharmacetically acceptable excipient. In some embodiments, the pharmaceutical composition comprises (a) the polypeptides or polypeptide complexes comprising a cleavable linker according to the amino acid sequence of Linker 4 (LSGRSDAGSPLGLAG) (SEQ ID NO: 6) and (b) a pharmacetically acceptable excipient. In some embodiments, the pharmaceutical composition comprises (a) the polypeptides or polypeptide complexes comprising a cleavable linker according to the the amino acid sequence LSGRSDAG (SEQ ID NO: 1) and (b) a pharmacetically acceptable excipient.
In some embodiments, the pharmaceutical composition comprises (a) isolated polypeptide polypeptides or polypeptide complexes according to Formula I:
A₁-L₁-P₁ (Formula I)
wherein A₁comprises the antigen binding domain that binds to the target antigen or the cytokine that binds to the cytokine receptor; L₁comprises the cleavable linker; and P₁comprises a peptide that impairs binding of the antigen binding domain to the target antigen or impairs binding of the cytokine to the cytokine receptor; and (b) a pharmacetically acceptable excipient. In some embodiments, the pharmaceutical composition comprises (a) isolated polypeptide polypeptides or polypeptide complexes comprising Formula I:
A₁-L₁-P₁ (Formula I)
wherein A₁comprises the antigen binding domain that binds to the target antigen or the cytokine that binds to the cytokine receptor; L₁comprises the cleavable linker; and P₁comprises a peptide that impairs binding of the antigen binding domain to the target antigen or impairs binding of the cytokine to the cytokine receptor; and (b) a pharmacetically acceptable excipient. In some embodiments, the pharmaceutical composition comprises (a) isolated polypeptide polypeptides or polypeptide complexes according to Formula I:
A₁-L₁-P₁ (Formula I)
wherein A₁is the antigen binding domain that binds to the target antigen or the cytokine that binds to the cytokine receptor; L₁is the cleavable linker; and P₁is a peptide that impairs binding of the antigen binding domain to the target antigen or impairs binding of the cytokine to the cytokine receptor; and (b) a pharmacetically acceptable excipient. In some embodiments, the pharmaceutical composition comprises (a) isolated polypeptide polypeptides or polypeptide complexes comprising Formula I:
A₁-L₁-P₁ (Formula I)
wherein A₁is the antigen binding domain that binds to the target antigen or the cytokine that binds to the cytokine receptor; L₁is the cleavable linker; and P₁is a peptide that impairs binding of the antigen binding domain to the target antigen or impairs binding of the cytokine to the cytokine receptor; and (b) a pharmacetically acceptable excipient.
Disclosed herein, in some embodiments, are polypeptides or polypeptide complexes, wherein the isolated polypeptide is complexed with a second isolated polypeptide comprising a second antigen binding domain or a second cytokine. In some embodiments, the pharmaceutical composition comprises (a) isolated polypeptide polypeptides or polypeptide complexes according to Formula II:
A₂-L₂-P₂ (Formula II)
wherein A₂comprises the second antigen binding domain or the second cytokine; L₂comprises a second cleavable linker; and P₂comprises a second peptide that impairs binding of the second antigen binding domain to a second target antigen or impairs binding of the second cytokine to a second cytokine receptor; and (b) a pharmacetically acceptable excipient. In some embodiments, the pharmaceutical composition comprises (a) isolated polypeptide polypeptides or polypeptide complexes comprising Formula II:
A₂-L₂-P₂ (Formula II)
wherein A₂comprises the second antigen binding domain or the second cytokine; L₂comprises a second cleavable linker; and P₂comprises a second peptide that impairs binding of the second antigen binding domain to a second target antigen or impairs binding of the second cytokine to a second cytokine receptor; and (b) a pharmacetically acceptable excipient. In some embodiments, the pharmaceutical composition comprises (a) isolated polypeptide polypeptides or polypeptide complexes according to Formula II:
A₂-L₂-P₂ (Formula II)
wherein A₂is the second antigen binding domain or the second cytokine; L₂is a second cleavable linker; and P₂is a second peptide that impairs binding of the second antigen binding domain to a second target antigen or impairs binding of the second cytokine to a second cytokine receptor; and (b) a pharmacetically acceptable excipient. In some embodiments, the pharmaceutical composition comprises (a) isolated polypeptide polypeptides or polypeptide complexes comprising Formula II:
A₂-L₂-P₂ (Formula II)
wherein A₂is the second antigen binding domain or the second cytokine; L₂is a second cleavable linker; and P₂is a second peptide that impairs binding of the second antigen binding domain to a second target antigen or impairs binding of the second cytokine to a second cytokine receptor; and (b) a pharmacetically acceptable excipient.
In some embodiments, the polypeptide or polypeptide complex further comprises a detectable label, a therapeutic agent, or a pharmacokinetic modifying moiety. In some embodiments, the detectable label comprises a fluorescent label, a radiolabel, an enzyme, a nucleic acid probe, or a contrast agent.
For administration to a subject, the polypeptide or polypeptide complex as disclosed herein, may be provided in a pharmaceutical composition together with one or more pharmaceutically acceptable carriers or excipients. The term “pharmaceutically acceptable carrier” includes, but is not limited to, any carrier that does not interfere with the effectiveness of the biological activity of the ingredients and that is not toxic to the patient to whom it is administered. Examples of suitable pharmaceutical carriers are well known in the art and include phosphate buffered saline solutions, water, emulsions, such as oil/water emulsions, various types of wetting agents, sterile solutions etc. Such carriers can be formulated by conventional methods and can be administered to the subject at a suitable dose. Preferably, the compositions are sterile. These compositions may also contain adjuvants such as preservative, emulsifying agents and dispersing agents. Prevention of the action of microorganisms may be ensured by the inclusion of various antibacterial and antifungal agents.
The pharmaceutical composition may be in any suitable form, (depending upon the desired method of administration). It may be provided in unit dosage form, may be provided in a sealed container and may be provided as part of a kit. Such a kit may include instructions for use. It may include a plurality of said unit dosage forms.
The pharmaceutical composition may be adapted for administration by any appropriate route, including a parenteral (e.g., subcutaneous, intramuscular, or intravenous) route. Such compositions may be prepared by any method known in the art of pharmacy, for example by mixing the active ingredient with the carrier(s) or excipient(s) under sterile conditions.
Dosages of the substances of the present disclosure can vary between wide limits, depending upon the disease or disorder to be treated, the age and condition of the individual to be treated, etc. and a physician will ultimately determine appropriate dosages to be used.
Table 1 provides the amino acid sequences of constructs described herein.

TABLE 1

Summary of Amino Acid Sequences

Construct	Construct	Amino Acid Sequence	SEQ ID
ID	Description	(N to C)	NO:

LINKER SEQUENCES

Linker-0	Cleavable linker	ISSGLLSGRSDNH	2
	(control)

Linker-1	Cleavable linker	ISSGLLSGRSDAG	3

Linker-2	Cleavable linker	AAGLLAPPGGLSGRSDAG	4

Linker-3	Cleavable linker	SPLGLSGRSDAG	5

Linker-4	Cleavable linker	LSGRSDAGSPLGLAG	6

Linker-5	Cleavable linker	LSGRSDAG	1

Linker-6	Cleavable linker	AGLLAPPGGLSGRSDAG	26

PEPTIDE MASK SEQUENCES

Peptide-1	anti-EGFR peptide	QGQSGQLSCEGWAMNREQCRA	7
	mask

Peptide-2	anti-EGFR peptide	GGPCRSHIDVAKPICV	8
	mask

Peptide-3	anti-CD3 peptide	QGQSGQGYLWGCEWNCGGITT	9
	mask

Peptide-4	anti-CD3 peptide	QGQSGSGYLWGCEWNCAGITT	10
	mask

HALF-LIFE EXTENDING MOIETIES

HE-1	10G single domain	EVQLVESGGGLVQPGNSLRLSCAASGFTFSKFGMSWVR	11
	antibody	QAPGKGLEWVSSISGSGRDTLYADSVKGRFTISRDNAKT
		TLYLQMNSLRPEDTAVYYCTIGGSLSVSSQGTLVTVSS

FULL LENGTH CONSTRUCTS

PC-1	Light Chain	QGQSGQLSCEGWAMNREQCRAGSSGGSGGSGGSGISSG	12
	Sequence: N-	LLSGRSDNHGSSGTDILLTQSPVILSVSPGERVSFSCRASQ
	[Peptide-1]-[Linker-	SIGTNIHWYQQRTNGSPRLLIKYASESISGIPSRFSGSGSGT
	0]-[anti-EGFR Fab	DFTLSINSVESEDIADYYCQQNNNWPTTFGAGTKLELKR
	light chain]-C	TVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQ
	(control)	WKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADY
		EKHKVYACEVTHQGLSSPVTKSFNRGEC

PC-1	Heavy Chain	EVQLVESGGGLVQPGNSLRLSCAASGFTFSKFGMSWVR	13
	Sequence: N-[10G	QAPGKGLEWVSSISGSGRDTLYADSVKGRFTISRDNAKT
	SDA]-[Peptide-3]-	TLYLQMNSLRPEDTAVYYCTIGGSLSVSSQGTLVTVSSG
	[Linker-0]-[anti-CD3	GGGSGGGSQGQSGQGYLWGCEW
	scFv (light chain-	NCGGITTGSSGGSGGSGGISSGLLSGRSDNHGGGSQTVVT
	heavy chain)]-[anti-	QEPSLTVSPGGTVTLTCRSSTGAVTTSNYANWVQQKPGQ
	EGFR Fab heavy	APRGLIGGTNKRAPGTPARFSGSLLGGKAALTLSGVQPE
	chain]-C	DEAEYYCALWYSNLWVFGGGTKLTVLGGGGSGGGGSG
	(control)	GGGSEVQLVESGGGLVQPGGSLKLSCAASGFTFNTYAM
		NWVRQAPGKGLEWVARIRSKYNNYATYYADSVKDRFTI
		SRDDSKNTAYLQMNNLKTEDTAVYYCVRHGNFGNSYV
		SWFAYWGQGTLVTVSSGGGGSQVQLKQSGPGLVQPSQS
		LSITCTVSGFSLTNYGVHWVRQSPGKGLEWLGVIWSGGN
		TDYNTPFTSRLSINKDNSKSQVFFKMNSLQSNDTAIYYCA
		RALTYYDYEFAYWGQGTLVTVSAASTKGPSVFPLAPSSK
		STSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPA
		VLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVD
		KKVEPKSCGGHHHHHHHHGGGLNDIFEAQKIEWHE

PC-2	Light Chain	GGPCRSHIDVAKPICVGGGGSGGSISSGLLSGRSDAGGGG	14
	Sequence: N-	SDILLTQSPVILSVSPGERVSFSCRASQSIGTNIHWYQQRT
	[Peptide-2]-[Linker-	NGSPRLLIKYASESISGIPSRFSGSGSGTDFTLSINSVESEDI
	1]-[anti-EGFR Fab	ADYYCQQNNNWPTTFGAGTKLELKRTVAAPSVFIFPPSD
	light chain]-C	EQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQ
		ESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQ
		GLSSPVTKSFNRGEC

PC-2	Heavy Chain	EVQLVESGGGLVQPGNSLRLSCAASGFTFSKFGMSWVR	15
	Sequence: N-[10G	QAPGKGLEWVSSISGSGRDTLYADSVKGRFTISRDNAKT
	SDA]-[Peptide-4]-	TLYLQMNSLRPEDTAVYYCTIGGSLSVSSQGTLVTVSSG
	[Linker-1]-[anti-CD3	GGGSGGGSQGQSGQGYLWGCEWNCAGITTGSSGGSGGS
	scFv (light chain-	GGISSGLLSGRSDAGGGGSQTVVTQEPSLTVSPGGTVTLT
	heavy chain)]-[anti-	CRSSTGAVTTSNYANWVQQKPGQAPRGLIGGTNKRAPG
	EGFR Fab heavy	TPARFSGSLLGGKAALTLSGVQPEDEAEYYCALWYSNL
	chain]-C	WVFGGGTKLTVLGGGGSGGGGSGGGGSEVQLVESGGG
		LVQPGGSLKLSCAASGFTFNTYAMNWVRQAPGKGLEW
		VARIRSKYNNYATYYADSVKDRFTISRDDSKNTAYLQM
		NNLKTEDTAVYYCVRHGNFGNSYVSWFAYWGQGTLVT
		VSSGGGGSQVQLKQSGPGLVQPSQSLSITCTVSGFSLTNY
		GVHWVRQSPGKGLEWLGVIWSGGNTDYNTPFTSRLSIN
		KDNSKSQVFFKMNSLQSNDTAIYYCARALTYYDYEFAY
		WGQGTLVTVSAASTKGPSVFPLAPSSKSTSGGTAALGCL
		VKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSS
		VVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCAAA
		HHHHHHHH

PC-3	Light Chain	GGPCRSHIDVAKPICVGGGGSSGGSAAGLLAPPGGLSGRS	16
	Sequence: N-	DAGGGGSDILLTQSPVILSVSPGERVSFSCRASQSIGTNIH
	[Peptide-2]-[Linker-	WYQQRTNGSPRLLIKYASESISGIPSRFSGSGSGTDFTLSIN
	2]-[anti-EGFR Fab	SVESEDIADYYCQQNNNWPTTFGAGTKLELKRTVAAPSV
	light chain]-C	FIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNAL
		QSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYA
		CEVTHQGLSSPVTKSFNRGEC

PC-3	Heavy Chain	EVQLVESGGGLVQPGNSLRLSCAASGFTFSKFGMSWVR	17
	Sequence: N-[10G	QAPGKGLEWVSSISGSGRDTLYADSVKGRFTISRDNAKT
	SDA]-[Peptide-4]-	TLYLQMNSLRPEDTAVYYCTIGGSLSVSSQGTLVTVSSG
	[linker Linker-2]-	GGGSGGGSQGQSGQGYLWGCEWNCAGITTGSSGGSAA
	[anti-CD3 scFv (light	GLLAPPGGLSGRSDAGGGGSQTVVTQEPSLTVSPGGTVT
	chain-heavy chain)]-	LTCRSSTGAVTTSNYANWVQQKPGQAPRGLIGGTNKRA
	[anti-EGFR Fab	PGTPARFSGSLLGGKAALTLSGVQPEDEAEYYCALWYSN
	heavy chain]-C	LWVFGGGTKLTVLGGGGSGGGGSGGGGSEVQLVESGG
		GLVQPGGSLKLSCAASGFTFNTYAMNWVRQAPGKGLE
		WVARIRSKYNNYATYYADSVKDRFTISRDDSKNTAYLQ
		MNNLKTEDTAVYYCVRHGNFGNSYVSWFAYWGQGTLV
		TVSSGGGGSQVQLKQSGPGLVQPSQSLSITCTVSGFSLTN
		YGVHWVRQSPGKGLEWLGVIWSGGNTDYNTPFTSRLSI
		NKDNSKSQVFFKMNSLQSNDTAIYYCARALTYYDYEFA
		YWGQGTLVTVSAASTKGPSVFPLAPSSKSTSGGTAALGC
		LVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLS
		SVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCAA
		AHHHHHHHH

PC-4	Light Chain	GGPCRSHIDVAKPICVGGGGSGGGGSPLGLSGRSDAGGG	18
	Sequence: N-	GSDILLTQSPVILSVSPGERVSFSCRASQSIGTNIHWYQQR
	[Peptide-2]-[Linker-	TNGSPRLLIKYASESISGIPSRFSGSGSGTDFTLSINSVESED
	3]-[anti-EGFR Fab	IADYYCQQNNNWPTTFGAGTKLELKRTVAAPSVFIFPPS
	light chain]-C	DEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNS
		QESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTH
		QGLSSPVTKSFNRGEC

PC-4	Heavy Chain	EVQLVESGGGLVQPGNSLRLSCAASGFTFSKFGMSWVR	19
	Sequence: N-[10G	QAPGKGLEWVSSISGSGRDTLYADSVKGRFTISRDNAKT
	SDA]-[Peptide-4]-	TLYLQMNSLRPEDTAVYYCTIGGSLSVSSQGTLVTVSSG
	[Linker-3]-[anti-CD3	GGGSGGGSQGQSGQGYLWGCEWNCAGITTGSSGGSGG
	scFv (light chain-	GSGGSPLGLSGRSDAGGGGSQTVVTQEPSLTVSPGGTVT
	heavy chain)]-[anti-	LTCRSSTGAVTTSNYANWVQQKPGQAPRGLIGGTNKRA
	EGFR Fab heavy	PGTPARFSGSLLGGKAALTLSGVQPEDEAEYYCALWYSN
	chain]-C	LWVFGGGTKLTVLGGGGSGGGGSGGGGSEVQLVESGG
		GLVQPGGSLKLSCAASGFTFNTYAMNWVRQAPGKGLE
		WVARIRSKYNNYATYYADSVKDRFTISRDDSKNTAYLQ
		MNNLKTEDTAVYYCVRHGNFGNSYVSWFAYWGQGTLV
		TVSSGGGGSQVQLKQSGPGLVQPSQSLSITCTVSGFSLTN
		YGVHWVRQSPGKGLEWLGVIWSGGNTDYNTPFTSRLSI
		NKDNSKSQVFFKMNSLQSNDTAIYYCARALTYYDYEFA
		YWGQGTLVTVSAASTKGPSVFPLAPSSKSTSGGTAALGC
		LVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLS
		SVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCAA
		AHHHHHHHH

PC-5	Light Chain	GGPCRSHIDVAKPICVGGGGSGGLSGRSDAGSPLGLAGS	20
	Sequence: N-	GGSDILLTQSPVILSVSPGERVSFSCRASQSIGTNIHWYQQ
	[Peptide-2]-[Linker-	RTNGSPRLLIKYASESISGIPSRFSGSGSGTDFTLSINSVESE
	4]-[anti-EGFR Fab	DIADYYCQQNNNWPTTFGAGTKLELKRTVAAPSVFIFPP
	light chain]-C	SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGN
		SQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVT
		HQGLSSPVTKSFNRGEC

PC-5	Heavy Chain	EVQLVESGGGLVQPGNSLRLSCAASGFTFSKFGMSWVR	21
	Sequence: N-[10G	QAPGKGLEWVSSISGSGRDTLYADSVKGRFTISRDNAKT
	SDA]-[Peptide-4]-	TLYLQMNSLRPEDTAVYYCTIGGSLSVSSQGTLVTVSSG
	[Linker-4]-[anti-CD3	GGGSGGGSQGQSGQGYLWGCEWNCAGITTGSSGGSGGL
	scFv (light chain-	SGRSDAGSPLGLAGSGGGSQTVVTQEPSLTVSPGGTVTL
	heavy chain)]-[anti-	TCRSSTGAVTTSNYANWVQQKPGQAPRGLIGGTNKRAP
	EGFR Fab heavy	GTPARFSGSLLGGKAALTLSGVQPEDEAEYYCALWYSNL
	chain]-C	WVFGGGTKLTVLGGGGSGGGGSGGGGSEVQLVESGGG
		LVQPGGSLKLSCAASGFTFNTYAMNWVRQAPGKGLEW
		VARIRSKYNNYATYYADSVKDRFTISRDDSKNTAYLQM
		NNLKTEDTAVYYCVRHGNFGNSYVSWFAYWGQGTLVT
		VSSGGGGSQVQLKQSGPGLVQPSQSLSITCTVSGFSLTNY
		GVHWVRQSPGKGLEWLGVIWSGGNTDYNTPFTSRLSIN
		KDNSKSQVFFKMNSLQSNDTAIYYCARALTYYDYEFAY
		WGQGTLVTVSAASTKGPSVFPLAPSSKSTSGGTAALGCL
		VKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSS
		VVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCAAA
		HHHHHHHH

PC-6	N-[anti-EGFR Fab	QILLTQSPVILSVSPGERVSFSCRASQSIGTNIHWYQQRTN	22
	heavy chain]-C	GSPRLLIKYASESISGIPSRFSGSGSGTDFTLSINSVESEDIA
		DYYCQQNNNWPTTFGAGTKLELKRTVAAPSVFIFPPSDE
		QLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQE
		SVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQG
		LSSPVTKSFNRGEC

PC-6	N-[anti-CD3 scFv	QTVVTQEPSLTVSPGGTVTLTCRSSTGAVTTSNYANWVQ	23
	(light chain-heavy	QKPGQAPRGLIGGTNKRAPGTPARFSGSLLGGKAALTLS
	chain)]-[anti-EGFR	GVQPEDEAEYYCALWYSNLWVFGGGTKLTVLGGGGSG
	Fab heavy chain]-C	GGGSGGGGSEVQLVESGGGLVQPGGSLKLSCAASGFTFN
		TYAMNWVRQAPGKGLEWVARIRSKYNNYATYYADSVK
		DRFTISRDDSKNTAYLQMNNLKTEDTAVYYCVRHGNFG
		NSYVSWFAYWGQGTLVTVSSGGGGSQVQLKQSGPGLV
		QPSQSLSITCTVSGFSLTNYGVHWVRQSPGKGLEWLGVI
		WSGGNTDYNTPFTSRLSINKDNSKSQVFFKMNSLQSQDT
		AIYYCARALTYYDYEFAYWGQGTLVTVSAASTKGPSVF
		PLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTS
		GVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHK
		PSNTKVDKKVEPKSCGGHHHHHHHHGGGLNDIFEAQKI
		EWHE

PC-7	N-[anti-EGFR Fab	DILLTQSPVILSVSPGERVSFSCRASQSIGTNIHWYQQRTN	24
	heavy chain]-C	GSPRLLIKYASESISGIPSRFSGSGSGTDFTLSINSVESEDIA
		DYYCQQNNNWPTTFGAGTKLELKRTVAAPSVFIFPPSDE
		QLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQE
		SVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQG
		LSSPVTKSFNRGEC

PC-7	N-[anti-CD3 scFv	QTVVTQEPSLTVSPGGTVTLTCRSSTGAVTTSNYANWVQ	25
	(light chain-heavy	QKPGQAPRGLIGGTNKRAPGTPARFSGSLLGGKAALTLS
	chain)]-[anti-EGFR	GVQPEDEAEYYCALWYSNLWVFGGGTKLTVLGGGGSG
	Fab heavy chain]-C	GGGSGGGGSEVQLVESGGGLVQPGGSLKLSCAASGFTFN
		TYAMNWVRQAPGKGLEWVARIRSKYNNYATYYADSVK
		DRFTISRDDSKNTAYLQMNNLKTEDTAVYYCVRHGNFG
		NSYVSWFAYWGQGTLVTVSSGGGGSQVQLKQSGPGLV
		QPSQSLSITCTVSGFSLTNYGVHWVRQSPGKGLEWLGVI
		WSGGNTDYNTPFTSRLSINKDNSKSQVFFKMNSLQSNDT
		AIYYCARALTYYDYEFAYWGQGTLVTVSAASTKGPSVF
		PLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTS
		GVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHK
		PSNTKVDKKVEPKSCGGHHHHHHHHGGGLNDIFEAQKI
		EWHE

Polypeptides or polypeptide complexes, in some embodiments, comprise a sequence set forth in Table 1. In some embodiments, the sequence comprises at least or about 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NOs: 1, 2, 4, 5, 7, 8, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25. In some instances, the sequence comprises at least or about 95% homology to SEQ ID NOs: 1, 2, 4, 5, 7, 8, 9, 12, 13, 14, 15, 16, 17, 18, 1⁹, 20, 21, 22, 23, 24, or 25. In some instances, the sequence comprises at least or about 97% homology to SEQ ID NOs: 1, 2, 4, 5, 7, 8, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25. In some instances, the sequence comprises at least or about 99% homology to SEQ ID NOs: 1, 2, 4, 5, 7, 8, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25. In some instances, the sequence comprises at least or about 100% homology to SEQ ID NOs: 1, 2, 4, 5, 7, 8, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25. In some instances, the sequence comprises at least a portion having at least or about 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 220, 230, 240, 250, 260, 270, 280, 290, 300, 310, 320, 330, 340, 350, 360, 370, 380, 390, 400, or more than 400 amino acids of SEQ ID NOs: 1, 2, 4, 5, 7, 8, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25.
Percent (%) sequence identity with respect to a reference polypeptide sequence is the percentage of amino acid residues in a candidate sequence that are identical with the amino acid residues in the reference 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 known for instance, using publicly available computer software such as BLAST, BLAST-2, ALIGN or Megalign (DNASTAR) software. Appropriate parameters for aligning sequences are able to be determined, including algorithms needed to achieve maximal alignment over the full length of the sequences being compared. For purposes herein, however, % amino acid sequence identity values are generated using the sequence comparison computer program ALIGN-2. The ALIGN-2 sequence comparison computer program was authored by Genentech, Inc., and the source code has been filed with user documentation in the U.S. Copyright Office, Washington D.C., 20559, where it is registered under U.S. Copyright Registration No. TXU510087. The ALIGN-2 program is publicly available from Genentech, Inc., South San Francisco, Calif., or may be compiled from the source code. The ALIGN-2 program should be compiled for use on a UNIX operating system, including digital UNIX V4.0D. All sequence comparison parameters are set by the ALIGN-2 program and do not vary.
In situations where ALIGN-2 is employed for amino acid sequence comparisons, the % amino acid sequence identity of a given amino acid sequence A to, with, or against a given amino acid sequence B (which can alternatively be phrased as a given amino acid sequence A that has or comprises a certain % amino acid sequence identity to, with, or against a given amino acid sequence B) is calculated as follows: 100 times the fraction X/Y, where X is the number of amino acid residues scored as identical matches by the sequence alignment program ALIGN-2 in that program's alignment of A and B, and where Y is the total number of amino acid residues in B. It will be appreciated that where the length of amino acid sequence A is not equal to the length of amino acid sequence B, the % amino acid sequence identity of A to B will not equal the % amino acid sequence identity of B to A. Unless specifically stated otherwise, all % amino acid sequence identity values used herein are obtained as described in the immediately preceding paragraph using the ALIGN-2 computer program.

Production of Polypeptides Comprising Cleavable Linkers

In some embodiments, polypeptides described herein (e.g., antibodies and its binding fragments) are produced using any method known in the art to be useful for the synthesis of polypeptides (e.g., antibodies), in particular, by chemical synthesis or by recombinant expression, and are preferably produced by recombinant expression techniques.
In some instances, an antibody or its binding fragment thereof is expressed recombinantly, and the nucleic acid encoding the antibody or its binding fragment is assembled from chemically synthesized oligonucleotides (e.g., as described in Kutmeier et al., 1994, BioTechniques 17:242), which involves the synthesis of overlapping oligonucleotides containing portions of the sequence encoding the antibody, annealing and ligation of those oligonucleotides, and then amplification of the ligated oligonucleotides by PCR.
Alternatively, a nucleic acid molecule encoding an antibody is optionally generated from a suitable source (e.g., an antibody cDNA library, or cDNA library generated from any tissue or cells expressing the immunoglobulin) by PCR amplification using synthetic primers hybridizable to the 3′ and 5′ ends of the sequence or by cloning using an oligonucleotide probe specific for the particular gene sequence.
In some instances, an antibody or its binding is optionally generated by immunizing an animal, such as a mouse, to generate polyclonal antibodies or, more preferably, by generating monoclonal antibodies, e.g., as described by Kohler and Milstein (1975, Nature 256:495-497) or, as described by Kozbor et al. (1983, Immunology Today 4:72) or Cole et al. (1985 in Monoclonal Antibodies and Cancer Therapy, Alan R. Liss, Inc., pp. 77-96). Alternatively, a clone encoding at least the Fab portion of the antibody is optionally obtained by screening Fab expression libraries (e.g., as described in Huse et al., 1989, Science 246:1275-1281) for clones of Fab fragments that bind the specific antigen or by screening antibody libraries (See, e.g., Clackson et al., 1991, Nature 352:624; Hane et al., 1997 Proc. Natl. Acad. Sci. USA 94:4937).
In some embodiments, techniques developed for the production of “chimeric antibodies” (Morrison et al., 1984, Proc. Natl. Acad. Sci. 81:851-855; Neuberger et al., 1984, Nature 312:604-608; Takeda et al., 1985, Nature 314:452-454) by splicing genes from a mouse antibody molecule of appropriate antigen specificity together with genes from a human antibody molecule of appropriate biological activity are used. A chimeric antibody is a molecule in which different portions are derived from different animal species, such as those having a variable region derived from a murine monoclonal antibody and a human immunoglobulin constant region.
In some embodiments, techniques described for the production of single chain antibodies (U.S. Pat. No. 4,694,778; Bird, 1988, Science 242:423-42; Huston et al., 1988, Proc. Natl. Acad. Sci. USA 85:5879-5883; and Ward et al., 1989, Nature 334:544-54) are adapted to produce single chain antibodies. Single chain antibodies are formed by linking the heavy and light chain fragments of the Fv region via an amino acid bridge, resulting in a single chain polypeptide. Techniques for the assembly of functional Fv fragments in E. coli are also optionally used (Skerra et al., 1988, Science 242:1038-1041).
In some embodiments, an expression vector comprising the nucleotide sequence of an antibody or the nucleotide sequence of an antibody is transferred to a host cell by conventional techniques (e.g., electroporation, liposomal transfection, and calcium phosphate precipitation), and the transfected cells are then cultured by conventional techniques to produce the antibody. In specific embodiments, the expression of the antibody is regulated by a constitutive, an inducible or a tissue, specific promoter.
In some embodiments, a variety of host-expression vector systems is utilized to express an antibody, or its binding fragment described herein. Such host-expression systems represent vehicles by which the coding sequences of the antibody is produced and subsequently purified, but also represent cells that are, when transformed or transfected with the appropriate nucleotide coding sequences, express an antibody or its binding fragment in situ. These include, but are not limited to, microorganisms such as bacteria (e.g., E. coli and B. subtilis) transformed with recombinant bacteriophage DNA, plasmid DNA or cosmid DNA expression vectors containing an antibody or its binding fragment coding sequences; yeast (e.g., Saccharomyces Pichia) transformed with recombinant yeast expression vectors containing an antibody or its binding fragment coding sequences; insect cell systems infected with recombinant virus expression vectors (e.g., baculovirus) containing an antibody or its binding fragment coding sequences; plant cell systems infected with recombinant virus expression vectors (e.g., cauliflower mosaic virus (CaMV) and tobacco mosaic virus (TMV)) or transformed with recombinant plasmid expression vectors (e.g., Ti plasmid) containing an antibody or its binding fragment coding sequences; or mammalian cell systems (e.g., COS, CHO, BH, 293, 293T, 3T3 cells) harboring recombinant expression constructs containing promoters derived from the genome of mammalian cells (e.g., metallothionein promoter) or from mammalian viruses (e.g. the adenovirus late promoter; the vaccinia virus 7.5K promoter).
For long-term, high-yield production of recombinant proteins, stable expression is preferred. In some instances, cell lines that stably express an antibody are optionally engineered. Rather than using expression vectors that contain viral origins of replication, host cells are transformed with DNA controlled by appropriate expression control elements (e.g., promoter, enhancer, sequences, transcription terminators, polyadenylation sites, etc.), and a selectable marker. Following the introduction of the foreign DNA, engineered cells are then allowed to grow for 1-2 days in an enriched media, and then are switched to a selective media. The selectable marker in the recombinant plasmid confers resistance to the selection and allows cells to stably integrate the plasmid into their chromosomes and grow to form foci that in turn are cloned and expanded into cell lines. This method can advantageously be used to engineer cell lines which express the antibody or its binding fragments.
In some instances, a number of selection systems are used, including but not limited to the herpes simplex virus thymidine kinase (Wigler et al., 1977, Cell 11:223), hypoxanthine-guanine phosphoribosyltransferase (Szybalska & Szybalski, 192, Proc. Natl. Acad. Sci. USA 48:202), and adenine phosphoribosyltransferase (Lowy et al., 1980, Cell 22:817) genes are employed in tk-, hgprt- or aprt- cells, respectively. Also, antimetabolite resistance are used as the basis of selection for the following genes: dhfr, which confers resistance to methotrexate (Wigler et al., 1980, Proc. Natl. Acad. Sci. USA 77:357; O'Hare et al., 1981, Proc. Natl. Acad. Sci. USA 78:1527); gpt, which confers resistance to mycophenolic acid (Mulligan & Berg, 1981, Proc. Natl. Acad. Sci. USA 78:2072); neo, which confers resistance to the aminoglycoside G-418 (Clinical Pharmacy 12:488-505; Wu and Wu, 1991, Biotherapy 3:87-95; Tolstoshev, 1993, Ann. Rev. Pharmacol. Toxicol. 32:573-596; Mulligan, 1993, Science 260:926-932; and Morgan and Anderson, 1993, Ann. Rev. Biochem. 62:191-217; May 1993, TIB TECH 11(5):155-215) and hygro, which confers resistance to hygromycin (Santerre et al., 1984, Gene 30:147). Methods commonly known in the art of recombinant DNA technology which can be used are described in Ausubel et al. (eds., 1993, Current Protocols in Molecular Biology, John Wiley & Sons, NY; Kriegler, 1990, Gene Transfer and Expression, A Laboratory Manual, Stockton Press, NY; and in Chapters 12 and 13, Dracopoli et al. (eds), 1994, Current Protocols in Human Genetics, John Wiley & Sons, NY.; Colberre-Garapin et al., 1981, J. Mol. Biol. 150:1).
In some instances, the expression levels of an antibody are increased by vector amplification (for a review, see Bebbington and Hentschel, the use of vectors based on gene amplification for the expression of cloned genes in mammalian cells in DNA cloning, Vol. 3. (Academic Press, New York, 1987)). When a marker in the vector system expressing an antibody is amplifiable, an increase in the level of inhibitor present in culture of host cell will increase the number of copies of the marker gene. Since the amplified region is associated with the nucleotide sequence of the antibody, production of the antibody will also increase (Crouse et al., 1983, Mol. Cell Biol. 3:257).
In some instances, any method known in the art for purification of an antibody is used, for example, by chromatography (e.g., ion exchange, affinity, particularly by affinity for the specific antigen after Protein A, and sizing column chromatography), centrifugation, differential solubility, or by any other standard technique for the purification of proteins.

Expression Vectors

In some embodiments, vectors include any suitable vectors derived from either a eukaryotic or prokaryotic sources. In some cases, vectors are obtained from bacteria (e.g. E. coli), insects, yeast (e.g. Pichia pastoris), algae, or mammalian sources. Exemplary bacterial vectors include pACYC177, pASK75, pBAD vector series, pBADM vector series, pET vector series, pETM vector series, pGEX vector series, pHAT, pHAT2, pMal-c2, pMal-p2, pQE vector series, pRSET A, pRSET B, pRSET C, pTrcHis2 series, pZA31-Luc, pZE21-MCS-1, pFLAG ATS, pFLAG CTS, pFLAG MAC, pFLAG Shift-12c, pTAC-MAT-1, pFLAG CTC, or pTAC-MAT-2.
Exemplary insect vectors include pFastBac1, pFastBac DUAL, pFastBac ET, pFastBac HTa, pFastBac HTb, pFastBac HTc, pFastBac M30a, pFastBact M30b, pFastBac, M30c, pVL1392, pVL1393, pVL1393 M10, pVL1393 M11, pVL1393 M12, FLAG vectors such as pPolh-FLAG1 or pPolh-MAT 2, or MAT vectors such as pPolh-MAT1, or pPolh-MAT2.
In some cases, yeast vectors include Gateway® pDEST™ 14 vector, Gateway® pDEST™ 15 vector, Gateway® pDEST™ 17 vector, Gateway® pDEST™ 24 vector, Gateway® pYES-DEST52 vector, pBAD-DEST49 Gateway® destination vector, pAO815 Pichia vector, pFLD1 Pichi pastoris vector, pGAPZA,B, & C Pichia pastoris vector, pPIC3.5K Pichia vector, pPIC6 A, B, & C Pichia vector, pPIC9K Pichia vector, pTEF1/Zeo, pYES2 yeast vector, pYES2/CT yeast vector, pYES2/NT A, B, & C yeast vector, or pYES3/CT yeast vector.
Exemplary algae vectors include pChlamy-4 vector or MCS vector.
Examples of mammalian vectors include transient expression vectors or stable expression vectors. Mammalian transient expression vectors may include pRK5, p3xFLAG-CMV 8, pFLAG-Myc-CMV 19, pFLAG-Myc-CMV 23, pFLAG-CMV 2, pFLAG-CMV 6a, b, c, pFLAG-CMV 5.1, pFLAG-CMV 5a, b, c, p3xFLAG-CMV 7.1, pFLAG-CMV 20, p3xFLAG-Myc-CMV 24, pCMV-FLAG-MAT1, pCMV-FLAG-MAT2, pBICEP-CMV 3, or pBICEP-CMV 4. Mammalian stable expression vector may include pFLAG-CMV 3, p3xFLAG-CMV 9, p3xFLAG-CMV 13, pFLAG-Myc-CMV 21, p3xFLAG-Myc-CMV 25, pFLAG-CMV 4, p3xFLAG-CMV 10, p3xFLAG-CMV 14, pFLAG-Myc-CMV 22, p3xFLAG-Myc-CMV 26, pBICEP-CMV 1, or pBICEP-CMV 2.
In some instances, a cell-free system is a mixture of cytoplasmic and/or nuclear components from a cell and is used for in vitro nucleic acid synthesis. In some cases, a cell-free system utilizes either prokaryotic cell components or eukaryotic cell components. Sometimes, a nucleic acid synthesis is obtained in a cell-free system based on for example Drosophila cell, Xenopus egg, or HeLa cells. Exemplary cell-free systems include, but are not limited to, E. coli S30 Extract system, E. coli T7 S30 system, or PURExpress®.

Host Cells

In some embodiments, a host cell includes any suitable cell such as a naturally derived cell or a genetically modified cell. In some instances, a host cell is a production host cell. In some instances, a host cell is a eukaryotic cell. In other instances, a host cell is a prokaryotic cell. In some cases, a eukaryotic cell includes fungi (e.g., yeast cells), animal cell or plant cell. In some cases, a prokaryotic cell is a bacterial cell. Examples of bacterial cell include gram-positive bacteria or gram-negative bacteria. Sometimes the gram-negative bacteria is anaerobic, rod-shaped, or both.
In some instances, gram-positive bacteria include Actinobacteria, Firmicutes or Tenericutes. In some cases, gram-negative bacteria include Aquificae, Deinococcus-Thermus, Fibrobacteres-Chlorobi/Bacteroidetes (FCB group), Fusobacteria, Gemmatimonadetes, Nitrospirae, Planctomycetes-Verrucomicrobia/Chlamydiae (PVC group), Proteobacteria, Spirochaetes or Synergistetes. Other bacteria can be Acidobacteria, Chloroflexi, Chrysiogenetes, Cyanobacteria, Deferribacteres, Dictyoglomi, Thermodesulfobacteria or Thermotogae. A bacterial cell can be Escherichia coli, Clostridium botulinum, or Coli bacilli.
Exemplary prokaryotic host cells include, but are not limited to, BL21, Machl™, DH10B™, TOP10, DH5α, DH10Bac™, OmniMax™, MegaX™, DH12S™, INV110, TOP10F′, INVαF, TOP10/P3, ccdB Survival, PIR1, PIR2, Stbl2™, Stbl3™, or Stbl4™.
In some instances, animal cells include a cell from a vertebrate or from an invertebrate. In some cases, an animal cell includes a cell from a marine invertebrate, fish, insects, amphibian, reptile, or mammal. In some cases, a fungus cell includes a yeast cell, such as brewer's yeast, baker's yeast, or wine yeast.
Fungi include ascomycetes such as yeast, mold, filamentous fungi, basidiomycetes, or zygomycetes. In some instances, yeast includes Ascomycota or Basidiomycota. In some cases, Ascomycota includes Saccharomycotina (true yeasts, e.g. Saccharomyces cerevisiae (baker's yeast)) or Taphrinomycotina (e.g. Schizosaccharomycetes (fission yeasts)). In some cases, Basidiomycota includes Agaricomycotina (e.g. Tremellomycetes) or Pucciniomycotina (e.g. Microbotryomycetes).
Exemplary yeast or filamentous fungi include, for example, the genus: Saccharomyces, Schizosaccharomyces, Candida, Pichia, Hansenula, Kluyveromyces, Zygosaccharomyces, Yarrowia, Trichosporon, Rhodosporidi, Aspergillus, Fusarium, or Trichoderma. Exemplary yeast or filamentous fungi include, for example, the species: Saccharomyces cerevisiae, Schizosaccharomyces pombe, Candida utilis, Candida boidini, Candida albicans, Candida tropicalis, Candida stellatoidea, Candida glabrata, Candida krusei, Candida parapsilosis, Candida guilliermondii, Candida viswanathii, Candida lusitaniae, Rhodotorula mucilaginosa, Pichia metanolica, Pichia angusta, Pichia pastoris, Pichia anomala, Hansenula polymorpha, Kluyveromyces lactis, Zygosaccharomyces rouxii, Yarrowia lipolytica, Trichosporon pullulans, Rhodosporidium toru-Aspergillus niger, Aspergillus nidulans, Aspergillus awamori, Aspergillus oryzae, Trichoderma reesei, Yarrowia lipolytica, Brettanomyces bruxellensis, Candida stellata, Schizosaccharomyces pombe, Torulaspora delbrueckii, Zygosaccharomyces bailii, Cryptococcus neoformans, Cryptococcus gattii, or Saccharomyces boulardii.
Exemplary yeast host cells include, but are not limited to, Pichia pastoris yeast strains such as GS115, KM71H₁, SMD1168, SMD1 168H, and X-33; and Saccharomyces cerevisiae yeast strain such as INVSc1.
In some instances, additional animal cells include cells obtained from a mollusk, arthropod, annelid or sponge. In some cases, an additional animal cell is a mammalian cell, e.g., from a primate, ape, equine, bovine, porcine, canine, feline or rodent. In some cases, a rodent includes mouse, rat, hamster, gerbil, hamster, chinchilla, fancy rat, or guinea pig.
Exemplary mammalian host cells include, but are not limited to, 293A cell line, 293FT cell line, 293F cells, 293 H cells, CHO DG44 cells, CHO-S cells, CHO-K1 cells, FUT8 KO CHOK1, Expi293F™ cells, F1p-In™ T-REx™ 293 cell line, F1p-In™-293 cell line, F1p-In™-3T3 cell line, F1p-In™-BHK cell line, F1p-In™-CHO cell line, F1p-In™-CV-1 cell line, F1p-In™-Jurkat cell line, FreeStyle™ 293-F cells, FreeStyle™ CHO-S cells, GripTite™ 293 MSR cell line, GS-CHO cell line, HepaRG™ cells, T-REx™ Jurkat cell line, Per.C6 cells, T-REx™-293 cell line, T-REx™-CHO cell line, and T-REx™-HeLa cell line.
In some instances, a mammalian host cell is a stable cell line, or a cell line that has incorporated a genetic material of interest into its own genome and has the capability to express the product of the genetic material after many generations of cell division. In some cases, a mammalian host cell is a transient cell line, or a cell line that has not incorporated a genetic material of interest into its own genome and does not have the capability to express the product of the genetic material after many generations of cell division.
Exemplary insect host cells include, but are not limited to, Drosophila S2 cells, Sf9 cells, Sf21 cells, High Five™ cells, and expresSF+® cells.
In some instances, plant cells include a cell from algae. Exemplary insect cell lines include, but are not limited to, strains from Chlamydomonas reinhardtii 137c, or Synechococcus elongatus PPC 7942.

Articles of Manufacture

In another aspect of the invention, an article of manufacture containing materials useful for the treatment, prevention and/or diagnosis of the disorders described above is provided. The article of manufacture comprises a container and a label or package insert on or associated with the container. Suitable containers include, for example, bottles, vials, syringes, IV solution bags, etc. The containers may be formed from a variety of materials such as glass or plastic. The container holds a composition which is by itself or combined with another composition effective for treating, preventing and/or diagnosing the condition and may have a sterile access port (for example the container may be an intravenous solution bag or a vial having a stopper that is pierceable by a hypodermic injection needle). At least one active agent in the composition is a bispecific antibody comprising a first antigen-binding site that specifically binds to CD3 and a second antigen-binding site that specifically binds to a tumor antigen.
The label or package insert indicates that the composition is used for treating the condition of choice. Moreover, the article of manufacture may comprise (a) a first container with a composition contained therein, wherein the composition comprises the bispecific antibody of the invention; and (b) a second container with a composition contained therein, wherein the composition comprises a further cytotoxic or otherwise therapeutic agent. The article of manufacture in this embodiment of the invention may further comprise a package insert indicating that the 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.

Methods of Treatment

In some embodiments, the isolated polypeptide comprising the cleavable linkers described herein are used in a method of treating cancer. In some embodiments, the cancer has cells that express EGFR. In some embodiments, the polypeptides or polypeptide complexes described herein are used in a method of treating colorectal cancer (CRC), squamous cell carcinoma of the head and Neck (SCCHN), non-small cell lung cancer (NSCLC), prostate cancer, breast cancer, colon/rectum cancer, head and neck cancer, esophagogastric cancer, liver cancer, glioblastoma, cervical cancer, ovarian cancer, bladder cancer, kidney cancer, or pancreatic cancer. In some embodiments, the polypeptides or polypeptide complexes described herein are used in a method of treating subjects who are resistant to EGFR inhibitor treatment. In some embodiments, the polypeptides or polypeptide complexes described herein are used in a method of treating subjects who harbor KRAS mutations. In some embodiments, the polypeptides or polypeptide complexes described herein are used in a method of treating subjects who are resistant to EGFR inhibitor treatment and harbor KRAS mutations.
While preferred embodiments of the present invention have been shown and described herein, it will be obvious to those skilled in the art that such embodiments are provided by way of example only. Numerous variations, changes, and substitutions will now occur to those skilled in the art without departing from the invention. It should be understood that various alternatives to the embodiments of the invention described herein may be employed in practicing the invention. It is intended that the following claims define the scope of the invention and that methods and structures within the scope of these claims and their equivalents be covered thereby.

EMBODIMENTS

Embodiment 1 comprises an isolated polypeptide comprising a cleavable linker according to the amino acid sequence of SEQ ID NO: 1 (LSGRSDAG).
Embodiment 2 comprises an isolated polypeptide of embodiment 1, wherein the cleavable linker comprises the amino acid sequence of SEQ ID NO: 3 (ISSGLLSGRSDAG).
Embodiment 3 comprises an isolated polypeptide of any one of embodiments 1-2, wherein the cleavable linker comprises the amino acid sequence of SEQ ID NO: 26 (AGLLAPPGGLSGRSDAG).
Embodiment 4 comprises an isolated polypeptide of any one of embodiments 1-3, wherein the cleavable linker comprises the amino acid sequence of SEQ ID NO: 4 (AAGLLAPPGGLSGRSDAG).
Embodiment 5 comprises an isolated polypeptide of any one of embodiments 1-4, wherein the cleavable linker comprises the amino acid sequence of SEQ ID NO: 5 (SPLGLSGRSDAG).
Embodiment 6 comprises an isolated polypeptide of any one of embodiments 1-5, wherein the cleavable linker comprises the amino acid sequence of SEQ ID NO: 6 (LSGRSDAGSPLGLAG).
Embodiment 7 comprises an isolated polypeptide of any one of embodiments 1-6, wherein the cleavable linker is cleavable by a protease.
Embodiment 8 comprises an isolated polypeptide of embodiment 7, wherein the protease comprises a tumor specific protease.
Embodiment 9 comprises an isolated polypeptide of any one of embodiments 7-8, wherein the protease comprises a matrix metalloprotease (MMP) or a serine protease.
Embodiment 10 comprises an isolated polypeptide of embodiment 9, wherein the matrix metalloprotease comprises MMP2, MMP7, MMP9, MMP13, or MMP14.
Embodiment 11 comprises an isolated polypeptide of embodiment 9, wherein the serine protease comprises matriptase, urokinase, or hepsin.
Embodiment 12 comprises an isolated polypeptide of any one of embodiments 1-11, wherein the isolated polypeptide further comprises an antigen binding domain that binds to a target antigen.
Embodiment 13 comprises an isolated polypeptide of embodiment 12, wherein the antigen binding domain is C-terminal to the cleavable linker.
Embodiment 14 comprises an isolated polypeptide of any one of embodiments 1-11, wherein the isolated polypeptide further comprises a cytokine or cytokine fragment that binds to a cytokine receptor.
Embodiment 15 comprises an isolated polypeptide of embodiment 14, wherein the cytokine or cytokine fragment is C-terminal to the cleavable linker.
Embodiment 16 comprises an isolated polypeptide of any one of embodiments 1-15, wherein the cleavable linker connects a peptide to an antigen binding domain that binds to a target antigen or to a cytokine or cytokine fragment that binds to a cytokine receptor in a configuration according to Formula I: A₁-L₁-P₁wherein A₁comprises the antigen binding domain that binds to the target antigen or the cytokine or cytokine fragment that binds to the cytokine receptor; L₁comprises the cleavable linker; P₁comprises a peptide that impairs binding of the antigen binding domain to the target antigen or impairs binding of the cytokine to the cytokine receptor.
Embodiment 17 comprises an isolated polypeptide of embodiment 16, wherein P₁is connected N-terminal to the cleavable linker and A₁is connected C-terminal to the cleavable linker.
Embodiment 18 comprises an isolated polypeptide of embodiment 16, wherein P₁is connected C-terminal to the cleavable linker and A₁is connected N-terminal to the cleavable linker.
Embodiment 19 comprises an isolated polypeptide of any one of embodiments 16-18, wherein P₁is bound to A₁through ionic interactions, electrostatic interactions, hydrophobic interactions, Pi-stacking interactions, and H-bonding interactions, or a combination thereof.
Embodiment 20 comprises an isolated polypeptide of any one of embodiments 16-19, wherein P₁has less than 70% sequence homology to the target antigen or the cytokine receptor.
Embodiment 21 comprises an isolated polypeptide of any one of embodiments 16-20, wherein P₁comprises a peptide sequence of at least 10 amino acids in length.
Embodiment 22 comprises an isolated polypeptide of any one of embodiments 16-21, wherein P₁comprises a peptide sequence of at least 10 amino acids in length and no more than 20 amino acids in length.
Embodiment 23 comprises an isolated polypeptide of any one of embodiments 16-22, wherein P₁comprises a peptide sequence of at least 16 amino acids in length.
Embodiment 24 comprises an isolated polypeptide of any one of embodiments 16-23, wherein P₁comprises a peptide sequence of no more than 40 amino acids in length.
Embodiment 25 comprises an isolated polypeptide of any one of embodiments 16-24, wherein P₁comprises a cyclic peptide or a linear peptide.
Embodiment 26 comprises an isolated polypeptide of any one of embodiments 16-25, wherein P₁comprises a cyclic peptide.
Embodiment 27 comprises an isolated polypeptide of any one of embodiments 16-26, wherein P₁is further linked to a half-life extending moiety.
Embodiment 28 comprises an isolated polypeptide of embodiment 27, wherein the half-life extending moiety is a single-domain antibody.
Embodiment 29 comprises an isolated polypeptide of embodiment 28, wherein the single domain antibody comprises 10G.
Embodiment 30 comprises an isolated polypeptide of any one of embodiments 16-29, wherein A₁comprises an antibody, a single chain variable fragment (scFv), a heavy chain variable domain (VH domain), a light chain variable domain (VL domain), a variable domain (VHH) of a camelid derived single domain antibody, a Fab, a Fab′, a Fab light chain polypeptide, or a Fab heavy chain polypeptide.
Embodiment 31 comprises an isolated polypeptide of any one of embodiments 16-30, wherein the target antigen comprises a tumor antigen.
Embodiment 32 comprises an isolated polypeptide of any one of embodiments 30-31, wherein A₁comprises the Fab light chain polypeptide or the Fab heavy chain polypeptide.
Embodiment 33 comprises an isolated polypeptide of any one of embodiments 16-32, wherein A₁comprises an epidermal growth factor receptor (EGFR) binding domain.
Embodiment 34 comprises an isolated polypeptide of any one of embodiments 16-30, wherein the target antigen comprises an effector cell antigen.
Embodiment 35 comprises an isolated polypeptide of embodiment 34, wherein A₁comprises the scFv.
Embodiment 36 comprises an isolated polypeptide of embodiment 35, wherein the scFv comprises an anti-CD3e single chain variable fragment.
Embodiment 37 comprises an isolated polypeptide of any one of embodiments 16-29, wherein A₁comprises the cytokine.
Embodiment 38 comprises an isolated polypeptide of embodiment 37, wherein the cytokine or cytokine fragment is a wild-type cytokine.
Embodiment 39 comprises an isolated polypeptide of embodiment 37, wherein the cytokine or cytokine fragment is a mutein of the cytokine.
Embodiment 40 comprises an isolated polypeptide of any one of embodiments 37-39, wherein the cytokine receptor is an interferon receptor or an interleukin receptor.
Embodiment 41 comprises an isolated polypeptide of any one of embodiments 37-40, wherein the cytokine receptor comprises an interferon receptor, GM-CSF receptor, IL-2 receptor, IL-4 receptor, IL-6 receptor, IL-7 receptor, IL-10 receptor, IL-12 receptor, IL-15 receptor, IL-21 receptor, or TGF-β receptor.
Embodiment 42 comprises an isolated polypeptide of any one of embodiments 37-41, wherein the cytokine or cytokine fragment comprises an interferon, GM-CSF, IL-2, IL-7, IL-12, IL-15, or IL-21.
Embodiment 43 comprises an isolated polypeptide of any one of embodiments 37-42, wherein the cytokine or cytokine fragment comprises an IL-2, IL-12, IL-6, IL-4, IL-10, or TGFβ.
Embodiment 44 comprises an isolated polypeptide of any one of embodiments 1-43, wherein the isolated polypeptide is complexed with a second isolated polypeptide comprising a second antigen binding domain or a second cytokine or second cytokine fragment.
Embodiment 45 comprises an isolated polypeptide of embodiment 44, wherein the second isolated polypeptide is in a configuration according to Formula II: A₂-L₂-P₂wherein A₂comprises the second antigen binding domain or the second cytokine; L₂comprises a second cleavable linker; P₂comprises a second peptide that impairs binding of the second antigen binding domain to a second target antigen or impairs binding of the second cytokine or second cytokine fragment to a second cytokine receptor.
Embodiment 46 comprises an isolated polypeptide of embodiment 45, wherein the second cleavable linker comprises the amino acid sequence of SEQ ID NO: 1 (LSGRSDAG).
Embodiment 47 comprises an isolated polypeptide of any one of embodiments 45-46, wherein the second cleavable linker comprises the amino acid sequence of SEQ ID NO: 3 (ISSGLLSGRSDAG).
Embodiment 48 comprises an isolated polypeptide of any one of embodiments 45-47, wherein the second cleavable linker comprises the amino acid sequence of SEQ ID NO: 26 (AGLLAPPGGLSGRSDAG).
Embodiment 49 comprises an isolated polypeptide of any one of embodiments 45-48, wherein the second cleavable linker comprises the amino acid sequence of SEQ ID NO: 4 (AAGLLAPPGGLSGRSDAG).
Embodiment 50 comprises an isolated polypeptide of any one of embodiments 45-49, wherein the second cleavable linker comprises the amino acid sequence of SEQ ID NO: 5 (SPLGLSGRSDAG).
Embodiment 51 comprises an isolated polypeptide of any one of embodiments 45-50, wherein the second cleavable linker comprises the amino acid sequence of SEQ ID NO: 6 (LSGRSDAGSPLGLAG).
Embodiment 52 comprises an isolated polypeptide of any one of embodiments 45-51, wherein P₂is connected N-terminal to the second cleavable linker and A₂is connected C-terminal to the second cleavable linker.
Embodiment 53 comprises an isolated polypeptide of any one of embodiments 45-51, wherein P₂is connected C-terminal to the second cleavable linker and A₂is connected N-terminal to the second cleavable linker.
Embodiment 54 comprises an isolated polypeptide of any one of embodiments 45-53, wherein P₂is bound to A₂through ionic interactions, electrostatic interactions, hydrophobic interactions, P₁-stacking interactions, and H-bonding interactions, or a combination thereof.
Embodiment 55 comprises an isolated polypeptide of any one of embodiments 45-54, wherein P₂has less than 70% sequence homology to the second target antigen or the second cytokine receptor.
Embodiment 56 comprises an isolated polypeptide of any one of embodiments 45-55, wherein P₂comprises a peptide sequence of at least 10 amino acids in length.
Embodiment 57 comprises an isolated polypeptide of any one of embodiments 45-56, wherein P₂comprises a peptide sequence of at least 10 amino acids in length and no more than 20 amino acids in length.
Embodiment 58 comprises an isolated polypeptide of any one of embodiments 45-57, wherein P₂comprises a peptide sequence of at least 16 amino acids in length.
Embodiment 59 comprises an isolated polypeptide of any one of embodiments 45-56, wherein P₂comprises a peptide sequence of no more than 40 amino acids in length.
Embodiment 60 comprises an isolated polypeptide of any one of embodiments 45-59, wherein P₂comprises a cyclic peptide or a linear peptide.
Embodiment 61 comprises an isolated polypeptide of any one of embodiments 45-60, wherein P₂comprises a cyclic peptide.
Embodiment 62 comprises an isolated polypeptide of any one of embodiments 45-61, wherein A₂comprises an antibody, a single chain variable fragment (scFv), a heavy chain variable domain (VH domain), a light chain variable domain (VL domain), a variable domain (VHH) of a camelid derived single domain antibody, a Fab, a Fab′, a Fab light chain polypeptide, or a Fab heavy chain polypeptide.
Embodiment 63 comprises an isolated polypeptide of any one of embodiments 45-62, wherein the second target antigen comprises a tumor antigen.
Embodiment 64 comprises an isolated polypeptide of embodiment 62, wherein A₂comprises the Fab light chain polypeptide or the Fab heavy chain polypeptide.
Embodiment 65 comprises an isolated polypeptide of any one of embodiments 45-64, wherein A₂comprises an epidermal growth factor receptor (EGFR) binding domain.
Embodiment 66 comprises an isolated polypeptide of any one of embodiments 45-62, wherein the second target antigen comprises an effector cell antigen.
Embodiment 67 comprises an isolated polypeptide of embodiment 62, wherein A₂comprises the scFv.
Embodiment 68 comprises an isolated polypeptide of any one of embodiments 66-67, wherein the scFv comprises an anti-CD3e single chain variable fragment.
Embodiment 69 comprises an isolated polypeptide of any one of embodiments 45-61, wherein A₂comprises the second cytokine.
Embodiment 70 comprises an isolated polypeptide of embodiment 69, wherein the second cytokine or second cytokine fragment is a wild-type cytokine.
Embodiment 71 comprises an isolated polypeptide of embodiment 69, wherein the second cytokine or second cytokine fragment is a mutein of the cytokine.
Embodiment 72 comprises an isolated polypeptide of any one of embodiments 69-71, wherein the second cytokine receptor is an interferon receptor or an interleukin receptor.
Embodiment 73 comprises an isolated polypeptide of any one of embodiments 69-72, wherein the second cytokine receptor comprises an interferon receptor, GM-CSF receptor, IL-2 receptor, IL-4 receptor, IL-6 receptor, IL-7 receptor, IL-10 receptor, IL-12 receptor, IL-15 receptor, IL-21 receptor, or TGF-β receptor.
Embodiment 74 comprises an isolated polypeptide of any one of embodiments 69-73, wherein the second cytokine or second cytokine fragment comprises an interferon, GM-CSF, IL-2, IL-7, IL-12, IL-15, or IL-21.
Embodiment 75 comprises an isolated polypeptide of any one of embodiments 69-74, wherein the second cytokine or second cytokine fragment comprises an IL-2, IL-12, IL-6, IL-4, IL-10, or TGFβ.
Embodiment 76 comprises a pharmaceutical composition comprising: the isolated polypeptide comprising a cleavable linker of any one of the above embodiments; and a pharmaceutically acceptable excipient.
Embodiment 77 comprises an isolated recombinant nucleic acid molecule encoding the isolated polypeptide comprising a cleavable linker of any one of the above embodiments.
Embodiment 78 comprises a vector comprising the isolated recombinant nucleic acid molecule according to Embodiment 77.
Embodiment 79 comprises a method of producing an isolated polypeptide comprising a cleavable linker according to any of the above embodiments comprising culturing a cell under conditions that lead to expression of the polypeptide, wherein the cell comprises the vector of embodiment 78.
Embodiment 80 comprises a method of manufacturing an isolated polypeptide comprising a cleavable linker, the method comprising: (a) culturing a cell comprising the recombinant nucleic acid molecule of embodiment 77 under conditions that lead to expression of the polypeptide, and (b) isolating the polypeptide.

Examples

Example 1. Proteolysis Rates and Serum Stability

The polypeptide complexes were evaluated for tumor and serum protease activity.
Briefly, polypeptide complexes PC-1, PC-2, PC-3, PC-4, and PC-5 were generated comprising peptide masks genetically fused to the polypeptide complexes using cleavable linkers recognized by various tumor proteases. The polypeptide complexes were exposed to various tumor proteases. Cleavage rate was determined when the polypeptide complexes were exposed to MMP2, MMP7, MMP9, MMP13, MMP14, uPa, MTSP1, and Hepsin. The data for apparent cleavage rate and relative serum stability are seen in Tables 2-4.

TABLE 2

Apparent Cleavage Rate Comparisons

Tumor
Proteases	PC-1	PC-2	PC-3	PC-4	PC-5

MMP2	45	45	5	5	5
	10 < r < 10	10 < r < 10	>10	>10	>10
MMP7	<2.5 × 10	<2.5 × 10³	45	5	5
			10 < r < 10	>10	>10
MMP9	<2.5 ×10	<2.5 × 10³	45	5	5
			10 <r<10	>10	>10
MMP13	45	45	5	5	5
	10 < r < 10	10 < r < 10	>10	>10	>10
MMP14	45	45	45	45	45
	10 < r < 10	10 < r < 10	10 < r < 10	10 < r < 10	10 < r < 10
uPa	2.5 × 10³< r < 10⁴	2.5 × 10³< r < 10	2.5 × 10³< r < 10⁴	2.5 × 10³< r < 10⁴	2.5 × 10³< r < 10⁴
MTSP1	2.5 × 10³< r < 10⁴	2.5 × 10³< r < 10⁴	45	45	45
			10 < r < 10	10 < r < 10	10 < r < 10
Hepsin	5	5	45	45	45
	>10	>10	10 < r < 10	10 < r <10	10 < r < 10

TABLE 3

Apparent Cleavage Rate Constants
Apparent Cleavage Rate Constants (M⁻¹ s⁻¹) (EGFR side)

Tumor
Protease	PC-1	PC-2	PC-3	PC-4	PC-5

MMP2	1.99E+04	2.47E+04	3.63E+05	3.29E+05	3.48E+05
MMP7	1.50E+02	1.57E+02	1.34E+04	1.76E+05	9.15E+04
MMP9	2.35E+03	5.00E+01	4.10E+04	2.36E+05	2.82E+05
MMP13	1.89E+04	1.20E+04	1.56E+05	2.75E+05	3.80E+05
MMP14	1.01E+04	1.07E+04	2.78E+04	1.42E+04	1.95E+04
uPa	8.39E+03	4.32E+03	3.41E+03	4.03E+03	5.88E+03
MTSP1	9.96E+03	8.63E+03	3.83E+04	3.92E+04	5.65E+04
Hepsin	2.53E+05	2.53E+05	7.00E+04	4.26E+04	8.28E+04

TABLE 4

Relative Serum Stability
Relative serum stability (% cleavage per day)
(EGFR side/CD3e side)

Serum	PC-1	PC-2	PC-3	PC-4	PC-5

Human	0.51%/	0.52%/	0.44%/	0.44%/	0.72%/
	0.56%	0.65%	0.63%	0.82%	0.71%

The data shows that serum proteolytic activity is greater than blood. The data also shows the cleavable linker sequences have increased rates of proteolysis while retaining stability in human serum.

Example 2. Confirmation of Comparable Masking with Cleavable Linkers

The polypeptide complexes were evaluated for EGFR and CD36 binding.
Briefly, the binding of polypeptide complexes PC-1, PC-2, PC-3, PC-4, and PC-5 comprising EGFR masking was determined. As seen in FIG. 1A, EGFR masking blocks binding for the various polypeptide complexes. Following cleavage by the tumor protease MTSP1, the polypeptide complexes are able to bind (FIG. 1B).
Details of the EGFR binding shifts are seen in Tables 5-8.

TABLE 5

Step	Time	pH

Baseline: Octet buffer	60 sec	pH 7.4
Load: 30 nM EGFR-biotin	300 sec	pH 7.4
(2.169 ug/mL)
Biocytin quench (100 uM)	300 sec	pH 7.4
Baseline: Octet buffer	90 sec	pH 7.4
Association:	300 sec	pH 7.4
25 nM PC-2
25 nM PC-3
25 nM PC-4
25 nM PC-5
25 nM PC-2 + MTSP1
25 nMPC-3 + MTSP1
25 nM PC-4 + MTSP1
25 nM PC-5 + MTSP1
Dissociation: Octet buffer	600 sec	pH 7.4

TABLE 6

	Loading	Conc.		KD
Sample ID	Sample ID	(nM)	KD (M)	Error	kon(1/Ms)	kdis(1/s)	Full R{circumflex over ( )}2	Full X{circumflex over ( )}2	Response

PC-2	EGFR	25	No significant binding
PC-3	EGFR	25	No significant binding
PC-4	EGFR	25	No significant binding
PC-5	EGFR	25	No significant binding

PC-2 + MTSP1	EGFR	25	1.34E−09	2.87E−11	3.48E+05	4.66E−04	0.9735	2.3843	1.5573
PC-3 + MTSP1	EGFR	25	9.46E−10	1.99E−11	4.72E+05	4.46E−04	0.9684	2.3105	1.5016
PC-4 + MTSP1	EGFR	25	1.19E−09	2.56E−11	3.82E+05	4.54E−04	0.9715	2.45	1.553
PC-5 + MTSP1	EGFR	25	1.45E−09	2.98E−11	3.50E+05	5.07E−04	0.9728	1.9973	1.4156

TABLE 7

Step	Time	pH

Baseline: Octet buffer	60 sec	pH 7.4
Load: 30 nM EGFR-biotin	300 sec	pH 7.4
(2.169 ug/mL)
Biocytin quench (100 uM)	300 sec	pH 7.4
Baseline: 5% human serum	300 sec	pH 7.4
Association:	300 sec	pH 7.4
30 nM PC-1,
30 nM PC-1 + MTSP1
30 nM PC-6,
buffer
Dissociation: 5% human	600 sec	pH 7.4
serum

TABLE 8

	Loading	Conc.		KD
Sample ID	Sample ID	(nM)	KD (M)	Error	kon(1/Ms)	kdis(1/s)	Full R{circumflex over ( )}2	Full X{circumflex over ( )}2	Response

PC-1	EGFR-	50	No significant binding
	biotin

PC-1 + MTSP1	EGFR-	50	1.91E−09	3.85E−11	2.60E+05	4.98E−04	0.965	1.7318	1.2733
	biotin
PC-6	EGFR-	50	1.77E−09	3.19E−11	4.93E+05	8.72E−04	0.9535	1.4956	1.0938
	biotin
buffer	EGFR-	50	<1.0E−12	6.00E−09	1.29E+04	<1.0E−07	0.5559	0.1511	0.0151
	biotin

The polypeptide complexes were also evaluated for CD3E binding. Briefly, the binding of the polypeptide complexes PC-1, PC-2, PC-3, PC-4, and PC-5 comprising CD3ε masking was determined. As seen in FIG. 2A, the masks block binding for the various polypeptide complexes. Following cleavage by the tumor protease MTSP1, the polypeptide complexes are able to bind (FIG. 2B).
Details of the CD3ε binding shifts are seen in Tables 9-12.

TABLE 9

Step	Time	pH

Baseline: Octet buffer	60 sec	pH 7.4
Load: 30 nM CD3e-biotin	300 sec	pH 7.4
(0.465 ug/mL)
Biocytin quench (100 uM)	300 sec	pH 7.4
Baseline: Octet buffer	90 sec	pH 7.4
Association:	300 sec	pH 7.4
25 nM PC-2
25 nM PC-3
25 nM PC-4
25 nM PC-5
25 nM PC-2 + MTSP1
25 nM PC-3 + MTSP1
25 nM PC-4 + MTSP1
25 nM PC-5 + MTSP1
Dissociation: Octet buffer	600 sec	pH 7.4

TABLE 10

	Loading	Conc.
Sample ID	Sample ID	(nM)	KD (M)	KD Error	kon(1/Ms)	kdis(1/s)	Full R{circumflex over ( )}2	Full X{circumflex over ( )}2	Response

PC-2	CD3e	25	No significant binding
PC-3	CD3e	25	No significant binding
PC-4	CD3e	25	No significant binding
PC-5	CD3e	25	No significant binding

PC-2 + MTSP1	CD3e	25	1.41E−08	3.66E−10	2.37E+05	3.33E−03	0.9829	1.2588	1.0342
PC-3 + MTSP1	CD3e	25	1.00E−08	2.60E−10	3.37E+05	3.37E−03	0.976	2.078	1.1036
PC-4 + MTSP1	CD3e	25	1.19E−08	3.14E−10	2.78E+05	3.30E−03	0.9786	1.5272	1.0227
PC-5 + MTSP1	CD3e	25	1.32E−08	3.33E−10	2.91E+05	3.84E−03	0.9832	1.452	1.0526

TABLE 11

Step	Time	pH

Baseline: Octet buffer	60 sec	pH 7.4
Load: 30nM CD3e-biotin	300 sec	pH 7.4
(0.46ug/mL)
Biocytin quench (IOOuM)	300 sec	pH 7.4
Baseline: 5% human serum	300 sec	pH 7.4
Association:	300 sec	pH 7.4
30nMPC-l,
30nM PC-1 + MTSP1
30nM PC-6,
buffer
Dissociation: 5% human serum	600 sec	pH 7.4

TABLE 12

	Loading	Conc.		KD
Sample ID	Sample ID	(nM)	KD (M)	Error	kon(1/Ms)	kdis(1/s)	Full R{circumflex over ( )}2	Full X{circumflex over ( )}2	Response

PC-1	CD3e-	50	No significant binding
	biotin

PC-1 + MTSP1	CD3e-	50	3.15E−08	1.01E−09	1.25E+05	3.95E−03	0.9774	2.6058	1.2556
	biotin
PC-6	CD3e-	50	2.26E−08	6.81E−10	1.33E+05	3.02E−03	0.9702	4.4245	1.5652
	biotin

buffer	CD3e-	50	No significant binding
	biotin

The polypeptide complexes binding was evaluated using enzyme linked immunosorbent assays (ELISAs). Biotinylated peptides were captured on neutravidin coated plates. A secondary antibody was used to detect bound polypeptide complex. Data for PC-2, PC-3, PC-4, PC-5, PC-1, and PC-6 comprising the mask and following cleavage of the mask is seen in FIGS. 3A-3B and EC50 binding data is summarized in Tables 13-14.

TABLE 13

EC50 nM	Masked	Cleaved	Shift

PC-2	21.29	0.13	169.5
PC-3	23.47	0.12	198.2
PC-4	20.59	0.15	139.3
PC-5	18.28	0.13	143.5
PC-1	44.79	—	282.8
PC-6	—	0.16	—

TABLE 14

EC50 nM	Masked	Cleaved	Shift

PC-2	2.082	0.101	20.6x
PC-3	1.792	0.1007	17.8x
PC-4	2.439	0.119	20.5x
PC-5	2.665	0.121	22.0x
PC-1	4.598	0.1383	33.2x
PC-6	—	0.069	—

Example 3. Confirmation of Comparable T-Cell Shifts with Cleavable Linkers

The polypeptide complexes were next evaluated in functional in vitro tumor cell killing and related T cell activation studies.
Briefly, HCT116 cells were seeded onto 96 well tissue culture treated flat bottom plates and allowed to adhere overnight. The following day, culture medium and nonadherent cells were removed and replaced with fresh medium containing titrated the polypeptide complexes at concentrations indicated. The data for PC-2, PC-3, PC-4, PC-5, PC-1, and PC-6 is seen in FIGS. 4A-4E and Tables 15-16.

TABLE 15

Tumor cell viability, IC50 (pM)

Cytotox							PC-2 +	PC-3 +	PC-4 +	PC-5 +
time	PC-6	PC-1	PC-2	PC-3	PC-4	PC-5	MTSP1	MTSP1	MTSP1	MTSP1

24 hr	1.13	555.6	326.6	578.3	539.9	869.4	0.2377	0.2811	0.3557	0.2294
48 hr	0.4675	460.9	301.8	389.1	419.7	499.6	0.1998	0.1843	0.1596	0.2197
72 hr	0.5507	763.5	389.3	444	522.6	588.6	0.2632	0.2402	0.218	0.3065
96 hr	0.7548	1023	475.3	511.8	659.1	712.9	0.3296	0.3099	0.2809	0.394
120 hr			577.5	589.6	773.2	824.2	0.3901	0.3679	0.3351	0.4737

TABLE 16

Tumor cell viability, Functional Shift

Cytotox							PC-2 +	PC-3 +	PC-4 +	PC-5 +
time	PC-6	PC-1	PC-2	PC-3	PC-4	PC-5	MTSP1	MTSP1	MTSP1	MTSP1

24 hr	1x	491.7x	289x	511.8x	477.8x	769.4x	0.2x	0.2x	0.3x	0.2x
48 hr	1x	985.9x	645.6x	832.3x	897.8x	1068.7x	0.4x	0.4x	0.3x	0.5x
72 hr	1x	1386.4x	706.9x	806.2x	949x	1068.8x	0.5x	0.4x	0.4x	0.6x
96 hr	1x	1355.3x	629.7x	678.1x	873.2x	944.5x	0.4x	0.4x	0.4x	0.5x
120 hr			765.1x	781.1x	1024.4x	1091.9x	0.5x	0.5x	0.4x	0.6x

Example 4. In Vivo Cynomolgus Monkey PK Comparison

The polypeptide complexes were assessed for pharmacokinetic and safety in cynomolgus monkey.
Cynomolgus Monkeys
Young naïve male cynomolgus monkeys were paired housed by group and identified by unique body tattoo. All animals were acclimated to housing conditions for 3 days prior to the start of the study. Prior to initiation all animals had undergone a physical examination by the study veterinarian. Only animals that, in the opinion of the study veterinarian, were healthy and otherwise met the criteria were admitted to the study. Food was withheld overnight prior to dosing. Purina 5049 was provided daily in amounts appropriate for the size of the animal. Tap water was provided ad libitum via automatic watering device.
Pharmacokinetics
Polypeptide complex pharmacokinetics for polypeptide complexes PC-1, PC-2, PC-3, PC-4, and PC-5 were determined in naïve male cynomolgus monkeys weighing 2-3 kg. Briefly, two group housed monkeys were used per dosing group and allowed to acclimate to their surroundings prior to dosing. Animals were sedated with Ketamine HCL 10-20 mg/kg IM prior to dosing and bleeding. Concentrated test articles were diluted in sterile phosphate buffered saline and administered to animals at a quantity relative to the animals' mass in kg. The dose for each test article was administered intravenously at 1 mL/kg dosing volume. For dosing, the left and right limbs were clipped and prepped with alcohol. The saphenous vein was identified, and a standard catheter was placed for IV bolus infusion (in either the left or right limb). The test article dosing solution was attached to the catheter via syringe and the bolus infusion occurred via manual compression of the syringe.
For blood collections, animals were sedated using ketamine, the femoral triangle was prepared, and blood was collected from the femoral vein using a 22G 1.5 inch needle, vacutainer sheath, and collection tube. Following venipuncture, manual compression of the vein was maintained until hemostasis was achieved. Blood collections were based on weight of the animals and did not exceed AGI maximum bleeds as set forth by IACUC. Blood was collected in EDTA tubes and processed to plasma. The blood samples were centrifuged cold at 3000×g for 10 min to separate cells from plasma. The plasma supernatant was harvested and stored frozen prior to analysis.
The concentration of the polypeptide complexes in cyno plasma samples was determined by ELISA. Briefly, anti-histag capture antibody was coated directly on ELISA plates. Standard dilutions of polypeptide complex in cyno serum were used to generate a calibration curve to which animal PK test samples could be compared. Standards and test samples were added to the plate and incubated cold overnight. Several different dilutions of test samples were used to make sure signals landed within appropriate dynamic range of the standard curve. Plates were washed and incubated with an anti-human HRP detection antibody for a brief time. Plates were washed, developed, and stopped using standard ELISA techniques. Standard curves plotting absorbance at 450 nm versus known polypeptide complex concentration were used to calculate the concentration of unknown test articles in each mouse PK plasma sample. Concentration of polypeptide complexes were plotted versus time and fit to a standard two stage distribution and elimination pharmacokinetic model. The calculated pharmacokinetic and parameters for polypeptide complexes PC-1, PC-7, PC-4, and PC-5 from cynomolgus monkey are shown in FIGS. 5A-5D and Tables 17-20.

TABLE 17

	Dose	C_max	T_1/2	Vd	CL	AUC_(0→d7)
Construct	(ug/kg)	(nM)	(hr)	(L)	(ml/h/kg)	(nM · min)

PC-1	100	51	100	0.06	0.14	165,895
PC-2	100
PC-3	100
PC-4	100	48	91	0.07	0.16	221,875
PC-5	100	61	97	0.05	0.12	244,051

TABLE 18

Cyno PK Parameters

					CL
	Dose	C_max	T_1/2	Vd	(ml/
Construct	(ug/kg)	(nM)	(hr)	(L)	h/kg)

PC-1	300	153	109	0.06	0.13
PC-1	100	51	100	0.06	0.14
PC-7	10	1.7	1.2	0.24	47
PC-7	3	0.17	0.3	0.68	491

TABLE 19

	Dose	C_max	T_1/2	Vd	CL
Construct	(ug/kg)	(nM)	(hr)	(L)	(ml/h/kg)

PC-1	100	51	100	0.06	0.14

TABLE 20

Parameter	PC-2 100 ug/kg	PC-3 100 ug/kg	Units

CMAX	40.37	53.78	nM
t1/2	69.44	104.57	hr
Vd	0.08	0.06	L
VSS	0.06	0.11	L
CL	0.26	0.13	mL/hr/kg
BW	3.00	3.00	kg
7 day AUC	207834	305952	nM · min

Example 5. In Vivo Cynomolgus Monkey Cytokine Release

Cytokine release was measured in cynomolgus monkeys.
Cytokines present in plasma post treatment were measured using the non-human primate Th1/Th2 cytometric bead array assay kit from BD Biosciences (Cat no. 557800) according to the manufacturer's instructions. Data is shown in FIGS. 6A-61 ) and Table 21.

TABLE 21

Property	PC-7	PC-7	PC-1	PC-2	PC-3	PC-4	PC-5

	3 ug/kg	10 ug/kg	100 ug/kg

Plasma Cytokine Levels (Cmax pg/ml)

IL-6	1,932	5,352	BQL	TBD	TBD	234	493
TNFα	1,267	2,497	BQL	TBD	TBD	BQL	BQL
IFNγ	BQL	109	BQL	TBD	TBD	BQL	BQL
IL-2	87	412	BQL	TBD	TBD	BQL	BQL

Example 6. In Vivo Cynomolgus Monkey Liver ALT/AST

ALT/AST levels were measured. As seen in FIGS. 7A and 7B and Table 22, polypeptide complexes prevented liver toxicity in cynomolgus monkeys.

TABLE 22

	PC-1	PC-2	PC-3	PC-4	PC-5

Property

100 ug/kg

Plasma Levels (U/L)

ALT	18	TBD	TBD	40	41
AST	9	TBD	TBD	40	51

While preferred embodiments of the present invention have been shown and described herein, it will be obvious to those skilled in the art that such embodiments are provided by way of example only. Numerous variations, changes, and substitutions will now occur to those skilled in the art without departing from the invention. It should be understood that various alternatives to the embodiments of the invention described herein may be employed in practicing the invention. It is intended that the following claims define the scope of the invention and that methods and structures within the scope of these claims and their equivalents be covered thereby.

Claims

1-30. (canceled)

31. An isolated polypeptide comprising a cleavable linker according to the amino acid sequence of SEQ ID NO: 4 (AAGLLAPPGGLSGRSDAG).

32. The isolated polypeptide of claim 31, wherein the cleavable linker is cleavable by a protease.

33. The isolated polypeptide of claim 32, wherein the protease comprises a tumor specific protease.

34. The isolated polypeptide of claim 32, wherein the protease comprises a matrix metalloprotease (MMP) or a serine protease.

35. The isolated polypeptide of claim 34, wherein the matrix metalloprotease comprises MMP2, MMP7, MMP9, MMP13, or MMP14.

36. The isolated polypeptide of claim 34, wherein the serine protease comprises matriptase, urokinase, or hepsin.

37. The isolated polypeptide of claim 31, wherein the isolated polypeptide further comprises an antigen binding domain that binds to a target antigen.

38. The isolated polypeptide of claim 37, wherein the cleavable linker connects a peptide to the antigen binding domain that binds to the target antigen in a configuration according to Formula I: A₁-L₁-P₁wherein A₁comprises the antigen binding domain that binds to the target antigen; L₁comprises the cleavable linker; P₁comprises a peptide that impairs binding of the antigen binding domain to the target antigen; and wherein P₁is connected C-terminal to L₁and A₁is connected N-terminal to L₁, or P₁is connected N-terminal to L₁and A₁is connected C-terminal to L₁.

39. The isolated polypeptide of claim 38, wherein P₁is further linked to a half-life extending moiety, and wherein the half-life extending moiety is a single-domain antibody.

40. The isolated polypeptide of claim 38, wherein A₁comprises an antibody, a single chain variable fragment (scFv), a heavy chain variable domain (VH domain), a light chain variable domain (VL domain), a variable domain (VHH) of a camelid derived single domain antibody, a Fab, a Fab′, a Fab light chain polypeptide, or a Fab heavy chain polypeptide.

41. The isolated polypeptide of claim 40, wherein A₁comprises the scFv.

42. The isolated polypeptide of claim 41, wherein the scFv comprises an anti-CD3e single chain variable fragment.

43. A complex comprising the isolated polypeptide of claim 37 and a second isolated polypeptide comprising a second antigen binding domain.

44. The isolated polypeptide of claim 43, wherein the second isolated polypeptide is in a configuration according to Formula II: A₂-L₂-P₂wherein A₂comprises the second antigen binding domain; L₂comprises a second cleavable linker; P₂comprises a second peptide that impairs binding of the second antigen binding domain to a second target antigen; wherein the second antigen binding domain comprises a Fab light chain polypeptide or a Fab heavy chain polypeptide and the second target antigen comprises a tumor antigen.

45. The isolated polypeptide of claim 44, wherein the second cleavable linker comprises the amino acid sequence of SEQ ID NO: 1 (LSGRSDAG).

46. The isolated polypeptide of claim 44, wherein the second cleavable linker comprises the amino acid sequence of SEQ ID NO: 3 (ISSGLLSGRSDAG).

47. The isolated polypeptide of claim 44, wherein the second cleavable linker comprises the amino acid sequence of SEQ ID NO: 26 (AGLLAPPGGLSGRSDAG).

48. The isolated polypeptide of claim 44, wherein the second cleavable linker comprises the amino acid sequence of SEQ ID NO: 4 (AAGLLAPPGGLSGRSDAG).

49. The isolated polypeptide of claim 44, wherein the second cleavable linker comprises the amino acid sequence of SEQ ID NO: 5 (SPLGLSGRSDAG).

50. The isolated polypeptide of claim 44, wherein the second cleavable linker comprises the amino acid sequence of SEQ ID NO: 6 (LSGRSDAGSPLGLAG).