# Patent

## Title
Single-chain antibodies and other heteromultimers

## Abstract

The invention provides engineered heteromultimeric protein complexes constructed using one, two, or three tethers and methods for making, using, and purifying such complexes, such as antibodies with different binding properties.

## Background
This application is a continuation of International Application No. PCT/US2013/025365 having an international filing date of Feb. 8, 2013, the entire contents of which are incorporated herein by reference, and which claims the benefit of priority under 35 U.S.C. §119 to U.S. Provisional Application Ser. No. 61/597,486, filed Feb. 10, 2012, the disclosure of which is incorporated herein by reference in its entirety.


SEQUENCE LISTING
The instant application contains a Sequence Listing which has been submitted in ASCII format via EFS-Web and is hereby incorporated by reference in its entirety. Said ASCII copy, created on Jul. 31, 2014, is named P4733C1_SequenceListing.txt and is 7,543 bytes in size.
FIELD OF THE INVENTION
This invention relates to novel engineered proteins and protein complexes, including heteromultimers (e.g., single-chain antibodies, multi-chain antibodies, and immunoadhesin-antibody complexes) with mono- or multi-specificity, methods of constructing them and producing them. This invention also relates to the new application of technologies useful in obtaining the mono- or multi-specific heteromultimers. The heteromultimers generated by the methods provided herein are useful as a therapeutic for any disease or pathological condition as well as any other use in which use of an antibody is advantageous.
BACKGROUND OF THE INVENTION
Developing technologies for producing antibodies or other heteromultimers with different binding characteristics (e.g., monospecific or multispecific) that are useful and scalable for commercial and therapeutic purposes has been elusive. Many methods have been tried, but nearly all suffer significant drawbacks such as being poorly soluble or inexpressible in mammalian cells, demonstrating low yield of heterodimer formation, being technically challenging to manufacture or immunogenic, exhibiting short half-life in vivo, or being unstable, among other problems (e.g., Hollinger et al., (1993) PNAS 90:6444-6448; U.S. Pat. No. 5,932,448; U.S. Pat. No. 6,833,441; U.S. Pat. No. 5,591,828; U.S. Pat. No. 7,129,330; U.S. Pat. No. 7,507,796; Fischer et al., (2007) Pathobiology 74:3-14; Booy (2006) Arch. Immunol. Ther. Exp. 54:85-101; Cao et al., (2003) 55: 171-197; and Marvin et al., (2006) Current Opinion in Drug Discovery & Development 9(2): 184-193). Thus, there is a need for improved technologies and processes to make antibodies or other heteromultimers with different binding characteristics.
SUMMARY OF THE INVENTION
The present invention provides heteromultimers (e.g., novel single-chain antibodies (scAbs), multi-chain antibodies (mcAbs), and immunoadhesin-antibody complexes) and methods of creating, manufacturing, and using the heteromultimers. In one aspect, the invention features a heteromultimeric single-chain antibody including a HeteroDimerization (HD) tether, which links a first heavy chain variable (VH) domain to a second VH domain, wherein the heteromultimer includes one or more heavy chain constant (CH) domains selected from a first CH2 domain, a first CH3 domain, a second CH2 domain, and a second CH3 domain. In one embodiment, the heteromultimer includes at least one pair of heavy chain constant domains. In another embodiment, the heteromultimer may include a hinge domain positioned between a VH and CH2 domain on one or both heavy chains. In another embodiment, the heteromultimer includes a first and/or second CH1 domain. The one or two CH1 domains are positioned C-terminal to one or both VH domains and N-terminal to one or both hinge domains, or one or both CH2 domains in the absence of the hinge domains. In particular embodiments, the heteromultimer may also include one or two light chain variable (VL) domains, which are linked N-terminal to the first and/or second VH domains by one or two CLH tethers (Cognate LC-HC tether). In some embodiments, the heteromultimer further includes one or two light chain constant (CL) domains, which are each positioned C-terminal to one or both VL domains and immediately N-terminal to one or both CLH tethers.
In another aspect, the invention features a heteromultimeric single-chain antibody including a single polypeptide with the following domains positioned relative to each other in an N-terminal to C-terminal direction as follows: VL1-CL1-CLH tether1-VH1-CH11-hinge1-CH21-CH31-HD tether-VL2-CL2-CLH tether2-VH2-CH12-hinge2-CH22-CH32.
In another aspect, the invention features a multi-chain antibody heteromultimer including three polypeptide chains, where the first and second polypeptide chains are identical and each forms a light chain (LC) and the third polypeptide chain forms a first heavy chain (HC) and second HC. The first and second polypeptide chains each include a VL and CL domain. The third polypeptide chain includes two VH domains, an HD tether, one or two hinge domains, and one or more heavy chain constant domains selected from a first CH1 domain, a first CH2 domain, a first CH3 domain, a second CH1 domain, a second CH2 domain, and a second CH3 domain, wherein the components of the second polypeptide chain are positioned relative to each other in an N-terminal to C-terminal direction as follows: VH1-optional CH11-optional hinge1-optional CH21-optional CH31-HD tether-VH2-optional CH12-optional hinge2-optional CH22-optional CH32.
In another aspect, the invention features a multi-chain antibody heteromultimer including two polypeptide chains, where the first polypeptide chain forms a first light chain (LC) and the second polypeptide chain forms a first heavy chain (HC), second LC, and second HC. The first polypeptide chain includes a first VL and CL domain. The second polypeptide chain includes two VH domains, an HD tether, a second VL domain, a second CL domain, a CLH tether, one or two hinge domains, and one or more heavy chain constant domains selected from a first CH1 domain, a first CH2 domain, a first CH3 domain, a second CH1 domain, a second CH2 domain, and a second CH3 domain, wherein the components of the second polypeptide chain are positioned relative to each other in an N-terminal to C-terminal direction as follows: VH1-optional CH11-optional hinge1-optional CH21-optional CH31-HD tether-VL2-CL2-CLH tether-VH2-optional CH12-optional hinge2-optional CH22-optional CH32.
In another aspect, the invention features a multi-chain antibody heteromultimer including two polypeptide chains, where the first polypeptide chain forms a first LC, first HC, and second HC, and the second polypeptide chain forms a second LC. The first polypeptide chain includes two VH domains, an HD tether, a first VL domain, a first CL domain, a CLH tether, one or two hinge domains, and one or more heavy chain constant domains selected from a first CH1 domain, a first CH2 domain, a first CH3 domain, a second CH1 domain, a second CH2 domain, and a second CH3 domain, wherein the components of the second polypeptide chain are positioned relative to each other in an N-terminal to C-terminal direction as follows: VL1-CL1-CLH tether-VH1-optional CH11-optional hinge1-optional CH21-optional CH31-HD tether-VH2-optional CH12-optional hinge2-optional CH22-optional CH32. The second polypeptide chain includes a second VL and CL domain.
In another aspect, the invention features a heteromultimer including two polypeptide chains, where the first polypeptide includes an immunoadhesin that includes an adhesin and one or more heavy chain constant domains (e.g., CH21 and/or CH31), the second polypeptide forms a half-antibody that includes a VH domain and one or more heavy chain constant domains (e.g., CH1, CH22, and/or CH32), and the first and second polypeptide chains are linked to one another by an HD tether to form a single polypeptide chain. The components of the heteromultimer are positioned relative to each other in an N-terminal to C-terminal direction as follows: adhesin-optional CH21-optional CH31-HD tether-VH-optional CH1-optional CH22-optional CH32. The HD tether facilitates interaction between the one or more constant domains of the immunoadhesin and the half-antibody. In one embodiment, a CLH tether facilitates the interaction between light chain and heavy chain components of the half-antibody to yield a heteromultimer with components positioned relative to each other in an N-terminal to C-terminal direction as follows: adhesin-optional CH21-optional CH31-HD tether-VL-CL-CLH tether-VH-optional CH1-optional CH22-optional CH32. In another embodiment, the VL and CL domains of the light chain of the half-antibody are provided by a second polypeptide, which associates with the heavy chain of the half-antibody of the first polypeptide chain to form a light chain-heavy chain cognate pair. In another embodiment, the immunoadhesin portion of the heteromultimer may include an amino acid spacer between its adhesin and heavy chain constant domain components. The spacer, in one embodiment, includes glycine (G) and serine (S) residues, for example, as GGS repeats. In another embodiment, the spacer is between 10-80 amino acids in length, for example, between 20-40 residues in length.
The heteromultimer of the invention may include an HD tether of between 15-100 amino acids in length. In a particular embodiment, the HD tether is between 30-39 amino acids in length, for example, 30, 31, 32, 33, 34, 35, 36, 37, 38, or 39 amino acids in length. The tether, in one embodiment, includes glycine (G) and serine (S) residues. In another embodiment, the tether includes GGS repeats. In a preferred embodiment, the tether includes 8 to 9 GGS repeats (SEQ ID NO: 19).
The heteromultimer of the invention may also include one or more CLH tethers. In one embodiment, the one or more CLH tethers are each between 10-80 amino acids in length. In a particular embodiment, the one or more CLH tethers are each between 20-40 amino acids in length. The tether, in one embodiment, includes glycine (G) and serine (S) residues. In another embodiment, the tether includes GGS repeats.
In another embodiment, one or more of the HD and CLH tethers of the invention are cleavable by one or more of the following endopeptidases: furin, urokinase, thrombin, tissue plasminogen activator (tPa), genenase, Lys-C, Arg-C, Asp-N, Glu-C, Factor Xa, tobacco etch virus protease (TEV), enterokinase, human rhinovirus C3 protease (HRV C3), or kininogenase. In a preferred embodiment, at least one of the tethers is cleavable by furin. In another embodiment, at least one of the one or more of the tethers of the invention is cleavable in two sites at or near the N- and C-terminus of the tether. Preferably for the HD tether, one of the two cleavage sites is a furin cleavage site and the other cleavage site is a Lys-C cleavage site. Preferably for CLH tethers, both N- and C-terminal cleavage sites of the one or more CLH tethers are cleavable by furin. In certain embodiments, the furin cleavage site comprises the amino acid sequence RKRKRR (SEQ ID NO:9). In certain other embodiments, the furin cleavage site comprises the amino acid sequence RHRQPR (SEQ ID NO:10). In one embodiment, endopeptidase cleavage occurs in situ. In certain embodiment, the endopeptidase is recombinantly expressed in a host cell. In another embodiment, endopeptidase cleavage occurs upon addition of the endopeptidase following purification.
The heteromultimer of the invention may have one or more (e.g., two) CLH tethers which each include one or more cleavage sites for one or more of the following specific exopeptidases: Carboxypeptidase A, Carboxypeptidase B, plasma Carboxypeptidase B (also known as Carboxypeptidase U or thrombin-activatable fibrinolysis inhibitor (TAFI)), Carboxypeptidase D, Carboxypeptidase E (also known as enkephalin convertase or Carboxypeptidase H), Carboxypeptidase M, Carboxypeptidase N, or Carboxypeptidase Z. In a preferred embodiment, the heteromultimer of the invention is cleavable by a Carboxypeptidase B exopeptidase. In one embodiment, exopeptidase cleavage occurs in situ. In certain embodiment, the exopeptidase is recombinantly expressed in a host cell. In another embodiment, exopeptidase cleavage occurs upon addition of the exopeptidase following purification. As used herein, Carboxypeptidase B may refer to the class of carboxypeptidases or the specific carboxypeptidase. As a class, Carboxypeptidase B includes all specific carboxypeptidases except Carboxypeptidase A. As a specific carboxypeptidase, Carboxypeptidase B is also known as Carboxypeptidase U or TAFI. One of skill in the art can readily discern the distinction between Carboxypeptidase B as a class and Carboxypeptidase B as a specific exopeptidase, depending on the context in which the term is used.
In yet another embodiment, the heteromultimer of the invention may include one or more hinge domains, including but not limited to hinge domains that include Glu216 to Pro230 of human IgG1. In some embodiments, one or both hinge domains include a mutation that removes a Lys-C endopeptidase cleavage site. In one example, the mutation that removes a Lys-C endopeptidase cleavage site is a K222A substitution (EU numbering system).
The heteromultimer of the invention may be monospecific. In one embodiment, the monospecific heteromultimer of the invention comprises two half-antibodies that bind the same epitope target but may bind with different affinities. In another embodiment, the monospecific heteromultimer of the invention includes a half-antibody associated with an immunoadhesin that each are specific for the same binding partner or eptiope.
The heteromultimer of the invention may be bispecific or multispecific. In one embodiment, the heteromultimer is capable of binding at least two antigens. In another embodiment, the heteromultimer is capable of binding at least two epitopes on the same antigen. In yet another embodiment, the bispecific or multispecific heteromultimer of the invention includes a half-antibody associated with an immunoadhesin, each of which is specific for a different binding partner or epitope.
In another embodiment, the heteromultimer of the invention includes a constant region conjugated to a cytotoxic agent.
In another embodiment, the heteromultimer may include two heavy chain constant domains (e.g., two CH3 domains) having a protuberance or cavity, wherein the protuberance or cavity of one heavy chain constant domain (e.g., CH31 domain) is positionable into the cavity or protuberance, respectively, of the second heavy chain constant domain (e.g., CH32 domain). Preferably, the two constant domains meet at an interface comprising the protuberance and cavity. In yet another embodiment, the heteromultimer may include at least one light chain constant domain and one heavy chain constant domain interface (e.g., a CL/CH1 interface), wherein the light chain constant domain (e.g., CL domain) and heavy chain constant domain (e.g., CH1 domain) interact, at least in part, by a protuberance-cavity interaction.
In another embodiment, the heteromultimer of the invention includes a CH2 domain mutation in either its CH21 or CH22 that results in an antibody with altered effector functions. In a preferred embodiment, the CH2 domain mutation is a N297 mutation. In certain embodiments, the N297 mutation is an N297A mutation. In certain other embodiments, the CH2 domain further comprises a D256A mutation.
In a further aspect, the invention features methods for producing a heteromultimer. In another aspect, the invention features polynucleotides encoding heteromultimers of the invention. In additional aspects, the invention features vectors including the polynucleotides of the invention and a host cell including the vectors. In one embodiment, the host cell is a mammalian cell. In a preferred embodiment, the mammalian cell is a CHO cell. In another embodiment, the host cell is a prokaryotic cell. In a further embodiment, the prokaryotic cell is an E. coli cell. In an additional aspect, the invention features a method of producing a heteromultimer that includes culturing the host cell that comprises the vector with heteromultimer-encoding polynucleotides in a culture medium. Preferably, the heteromultimer is recovered from the host cell or the host cell's culture medium.
In a further aspect, the invention provides single-chain antibodies comprising a single polypeptide comprising the following domains positioned relative to each other in an N-terminal to C-terminal direction: VL1-CL1-CLH tether1-VH1-CH11-hinge1-CH21-CH31-HD tether-VL2-CL2-CLH tether2-VH2-CH12-hinge2-CH22-CH32, wherein the CLH tether1, CLH tether2 and HD tether each comprises an amino acid sequence cleavable by furin endopeptidase. In certain embodiments of the aspect, the furin cleavable sequence comprises the amino acid sequence RKRKRR (SEQ ID NO: 9), while in other embodiments, the furin cleavable sequence comprises the amino acid sequence RHRQPR (SEQ ID NO: 10). In related aspects, the invention provides polynucleotide molecules encoding the single-chain antibody of the invention, vectors comprising the polynucleotides, and host cells comprising the vectors. In certain embodiments, the host cell is a mammalian cell, including without limitation, a CHO cell. In certain other embodiments, the host cell is a prokaryotic cell, including without limitation, an E. coli cell. In a further related aspect, the invention provides methods of producing the single-chain antibody comprising culturing the host cell that comprises the vector in a culture medium. In certain embodiments, the method further comprises the step of recovering said single-chain antibody from said host cell or said culture medium.
Other features and advantages of the invention will be apparent from the following Detailed Description, the Drawings, and the Claims.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 is a schematic diagram showing the structure of an exemplary heteromultimeric single-chain antibody comprising three cleavable tethers. Endopeptidase cleavage sites are indicated by the triangles. Also depicted is an optional K222A mutation.
FIG. 2 is a schematic diagram showing the arrangement of an exemplary heteromultimeric single-chain antibody's LCs, HCs, tethers, and cleavage sites. The cleavage sites are exemplified by RKRKRRG(GGS)6GRSRKRR (SEQ ID NO:14) and (GGS)(8-10) RSRKRR (SEQ ID NOs:15-17). The furin recognition site is illustrated as RXRXRR (SEQ ID NO:8).
FIG. 3A is an example of a heteromultimeric single-chain antibody after furin cleavage. The residues in parentheses (RKRKRR (SEQ ID NO:9), and RKRKR (SEQ ID NO:18)) indicate residues that may be removed by endogenous exopeptidases prior to purification over the Protein A column resulting in ragged C-termini. Also depicted is an optional K222A mutation.
FIG. 3B is an example of a heteromultimeric single-chain antibody after furin, Lys-C, and exopeptidase (e.g., Carboxypeptidase B) treatment. Also depicted is an optional K222A mutation.
FIG. 4 is an exemplary conjugated heteromultimeric single-chain antibody prior to cleavage to remove the tethers. Also depicted is an optional conjugated moiety, e.g., toxin, antibiotic, etc., and optional K222A mutation.
FIG. 5A is a schematic diagram showing the structure of an exemplary heteromultimeric multi-chain antibody containing one cleavable tether. The two untethered LCs may be expressed independently of the tether-containing polypeptide. The untethered LCs may be expressed in the same cell or in a different cell as the linked heavy chains. The untethered LC may be expressed on the same or different plasmid. Also depicted is an optional conjugated moiety, e.g., toxin, antibiotic, etc., and optional K222A mutation.
FIG. 5B is a schematic diagram showing the structure of an exemplary heteromultimeric multi-chain antibody containing two cleavable tethers. The HD tether links a first HC to a second HC indirectly by a tethered LC. The untethered LC may be expressed independently of the tether-containing polypeptide. The untethered LC may be expressed in the same cell or in a different cell as the linked heavy chains. The untethered LC may be expressed on the same or different plasmid. Also depicted is an optional K222A mutation.
FIG. 5C is a schematic diagram showing the structure of an exemplary heteromultimeric multi-chain antibody containing two cleavable tethers. The HD tether links a first HC to a second HC directly. The untethered LC may be expressed independently of the tether-containing polypeptide. The untethered LC may be expressed in the same cell or in a different cell as the linked heavy chains. The untethered LC may be expressed on the same or different plasmid. Also depicted is an optional K222A mutation.
FIGS. 6A-6D are graphs showing the results from an Octet analysis. (A) A composite of the graphs shown in B-D. (B) The exemplary heteromultimeric single-chain antibody binds both antigen 1 and antigen 2 simultaneously. (C and D) Antibody 1 and antibody 2 do not cross react with each other's antigen, but do bind their respective antigen. The x-axis is time in seconds. The y-axis is a relative absorbance. Reference is made to Example 3.



DETAILED DESCRIPTION OF THE INVENTION
Unwanted heavy-chain homodimerization typically occurs when generating monospecific or multispecific (e.g., bispecific) antibodies or other heteromultimers having different binding properties with multiple polypeptide chains. We have discovered this common problem can be circumvented by the generation of single-chain monospecific or multispecific heteromultimers, whose assembly is directed by one or more tethers. Without being bound by theory, we believe that the HD tether enables the binding of distinct Fc heavy-chain components with a high degree of accuracy and efficiency, yielding a functional heteromultimer comprising two-half molecules (e.g., two half-antibodies) which bind the same target or different targets with the same or different binding affinity. The heteromultimer with linked heavy-chain components may additionally include distinct light-chain components, yielding a functional single-chain monospecific or multispecific heteromultimer (e.g., antibody) with a complete complement of heavy and light chains. Additional tethers according to the present invention can be used to link the light and heavy chains of a heteromultimer and thereby aid in the proper association of each light chain to its cognate heavy chain.
Use of the methods for making heteromultimers described herein allows for the production of a substantially homogeneous population of monospecific or multispecific heteromultimers generated from a single or multiple polypeptide sequences. The heteromultimers generated by the methods described herein can be useful for recognition of more than one target in a pathogenic pathway or for co-localization of a specific target (e.g., a tumor cell) and an agent directed against the target (e.g., a T cell). In addition, the heteromultimers described herein are advantageous because they eliminate the need for combination therapy to target two antigens and the risk associated with providing two or more therapeutics to a subject.
I. Definitions
The term “antibody” herein is used in the broadest sense and refers to any immunoglobulin (Ig) molecule comprising two heavy chains and two light chains, and any fragment, mutant, variant or derivation thereof so long as they exhibit the desired biological activity (e.g., epitope binding activity). Examples of antibodies include monoclonal antibodies, polyclonal antibodies, bispecific antibodies, multispecific antibodies, and antibody fragments.
The Kabat numbering system is generally used when referring to a residue in the variable domain (approximately residues 1-107 of the light chain and residues 1-113 of the heavy chain) (e.g., Kabat et al., Sequences of Immunological Interest. 5th Ed. Public Health Service, National Institutes of Health, Bethesda, Md. (1991)). The “EU numbering system” or “EU index” is generally used when referring to a residue in an immunoglobulin heavy chain constant region (e.g., the EU index reported in Kabat et al., supra). The “EU index as in Kabat” refers to the residue numbering of the human IgG1 EU antibody. Unless stated otherwise herein, references to residue numbers in the variable domain of antibodies means residue numbering by the Kabat numbering system. Unless stated otherwise herein, references to residue numbers in the heavy chain constant domain of antibodies means residue numbering by the EU numbering system.
A naturally occurring basic 4-chain antibody unit is a heterotetrameric glycoprotein composed of two identical light chains (LCs) and two identical heavy chains (HCs) (an IgM antibody consists of 5 of the basic heterotetramer units along with an additional polypeptide called J chain, and therefore contains 10 antigen binding sites, while secreted IgA antibodies can polymerize to form polyvalent assemblages comprising 2-5 of the basic 4-chain units along with J chain). In the case of IgGs, the 4-chain unit is generally about 150,000 daltons. Each LC is linked to an HC by one covalent disulfide bond, while the two HCs are linked to each other by one or more disulfide bonds depending on the HC isotype. Each HC and LC also has regularly spaced intrachain disulfide bridges. Each HC has, at the N-terminus, a variable domain (VH) followed by three constant domains (CH1, CH2, CH3) for each of the α and γ chains and four Cj domains for μ and ε isotypes. Each LC has, at the N-terminus, a variable domain (VL) followed by a constant domain (CL) at its other end. The VL is aligned with the VH and the CL is aligned with the first constant domain of the heavy chain (CH1). CH1 can be connected to the second constant domain of the heavy chain (CH2) by a hinge region. Particular amino acid residues are believed to form an interface between the light chain and heavy chain variable domains. The pairing of a VH and VL together forms a single antigen-binding site. For the structure and properties of the different classes of antibodies, see, e.g., Basic and Clinical Immunology, 8th edition, Daniel P. Stites, Abba I. Ten and Tristram G. Parslow (eds.), Appleton & Lange, Norwalk, Conn., 1994, page 71 and Chapter 6.
“Hinge region” is generally defined as stretching from Glu216 to Pro230 of human IgG1 (Burton, Molec. Immunol. 22: 161-206 (1985)). Hinge regions of other IgG isotypes may be aligned with the IgG1 sequence by placing the first and last cysteine residues forming inter-heavy chain S—S bonds in the same positions.
The “lower hinge region” of an Fc region is normally defined as the stretch of residues immediately C-terminal to the hinge region, i.e., residues 233 to 239 of the Fc region. Prior to the present invention, FcgammaR binding was generally attributed to amino acid residues in the lower hinge region of an IgG Fc region.
The “CH2 domain” of a human IgG Fc region usually extends from about residues 231 to about 340 of the IgG. The CH2 domain is unique in that it is not closely paired with another domain. Rather, two N-linked branched carbohydrate chains are interposed between the two CH2 domains of an intact native IgG molecule. It has been speculated that the carbohydrate may provide a substitute for the domain-domain pairing and help stabilize the CH2 domain. Burton, Molec. Immunol. 22: 161-206 (1985).
The “CH3 domain” comprises the stretch of residues C-terminal to a CH2 domain in an Fc region (i.e., from about amino acid residue 341 to about amino acid residue 447 of an IgG).
The light chain (LC) from any vertebrate species can be assigned to one of two clearly distinct types, called kappa and lambda, based on the amino acid sequences of their constant domains. Depending on the amino acid sequence of the constant domain of their heavy chains (CH), immunoglobulins can be assigned to different classes or isotypes. There are five classes of immunoglobulins: IgA, IgD, IgE, IgG, and IgM, having heavy chains designated α, δ, γ, ε, and μ, respectively. The γ and α classes are further divided into subclasses on the basis of relatively minor differences in CH sequence and function, e.g., humans express the following subclasses: IgG1, IgG2, IgG3, IgG4, IgA1, and IgA2.
The term “variable” refers to the fact that certain segments of the variable domains differ extensively in sequence among antibodies. The V domain mediates antigen binding and defines specificity of a particular antibody for its particular antigen. However, the variability is not evenly distributed across the 110-amino acid span of the variable domains. Instead, the V regions consist of relatively invariant stretches called framework regions (FRs) of 15-30 amino acids separated by shorter regions of extreme variability called “hypervariable regions” that are each 9-12 amino acids long. The variable domains of native heavy and light chains each comprise four FRs, largely adopting a beta-sheet configuration, connected by three hypervariable regions, which form loops connecting, and in some cases forming part of, the beta-sheet structure. The hypervariable regions in each chain are held together in close proximity by the FRs and, with the hypervariable regions from the other chain, contribute to the formation of the antigen-binding site of antibodies (see Kabat et al., Sequences of Proteins of Immunological Interest, 5th Ed. Public Health Service, National Institutes of Health, Bethesda, Md., 1991). The constant domains are not involved directly in binding an antibody to an antigen, but exhibit various effector functions, such as participation of the antibody in antibody dependent cellular cytotoxicity (ADCC).
The term “hypervariable region” or “HVR,” as used herein, refers to each of the regions of an antibody variable domain which are hypervariable in sequence and/or form structurally defined loops (“hypervariable loops”). Generally, native four-chain antibodies comprise six HVRs; three in the VH (H1, H2, H3), and three in the VL (L1, L2, L3). HVRs generally comprise amino acid residues from the hypervariable loops and/or from the “complementarity determining regions” (CDRs), the latter being of highest sequence variability and/or involved in antigen recognition. An HVR as used herein comprise any number of residues located within positions 24-36 (for L1), 46-56 (for L2), 89-97 (for L3), 26-35B (for H1), 47-65 (for H2), and 93-102 (for H3). Therefore, an HVR includes residues in positions described previously in (A), (B), and (C): (A) 24-34 (L1), 50-52 (L2), 91-96 (L3), 26-32 (H1), 53-55 (H2), and 96-101 (H3) (Chothia and Lesk, J. Mol. Biol. 196:901-917 (1987); (B) 24-34 of L1, 50-56 of L2, 89-97 of L3, 31-35B of H1, 50-65 of H2, and 95-102 of H3 (Kabat et al., Sequences of Proteins of Immunological Interest, 5th Ed. Public Health Service, National Institutes of Health, Bethesda, Md. (1991); (C) 30-36 (L1), 46-55 (L2), 89-96 (L3), 30-35 (H1), 47-58 (H2), 93-100a-j (H3) (MacCallum et al. J. Mol. Biol. 262:732-745 (1996). Unless otherwise indicated, HVR residues and other residues in the variable domain (e.g., FR residues) are numbered herein according to Kabat et al., supra.
A number of HVR delineations are in use and are encompassed herein. The Kabat Complementarity Determining Regions (CDRs) are based on sequence variability and are the most commonly used (Kabat et al., Sequences of Proteins of Immunological Interest, 5th Ed. Public Health Service, National Institutes of Health, Bethesda, Md., 1991). Chothia refers instead to the location of the structural loops (Chothia and Lesk J. Mol. Biol. 196:901-917 (1987)). The AbM HVRs represent a compromise between the Kabat HVRs and Chothia structural loops, and are used by Oxford Molecular's AbM antibody modeling software. The “contact” HVRs are based on an analysis of the available complex crystal structures. The residues from each of these HVRs are noted below.














Loop
Kabat
AbM
Chothia
Contact







L1
L24-L34
L24-L34
L26-L32
L30-L36


L2
L50-L56
L50-L56
L50-L52
L46-L55


L3
L89-L97
L89-L97
L91-L96
L89-L96


H1
H31-H35B
H26-H35B
H26-H32
H30-H35B







(Kabat Numbering)











H1
H31-H35
H26-H35
H26-H32
H30-H35







(Chothia Numbering)











H2
H50-H65
H50-H58
H53-H55
H47-H58


H3
H95-H102
H95-H102
H96-H101
H93-H101









HVRs may comprise “extended HVRs” as follows: 24-36 or 24-34 (L1), 46-56 or 50-56 (L2) and 89-97 or 89-96 (L3) in the VL and 26-35 (H1), 50-65 or 49-65 (H2) and 93-102, 94-102, or 95-102 (H3) in the VH. The variable domain residues are numbered according to Kabat et al., supra, for each of these definitions.
“Framework regions” (FR) are those variable domain residues other than the CDR residues. Each variable domain typically has four FRs identified as FR1, FR2, FR3, and FR4. If the CDRs are defined according to Kabat, the light chain FR residues are positioned at about residues 1-23 (LCFR1), 35-49 (LCFR2), 57-88 (LCFR3), and 98-107 (LCFR4) and the heavy chain FR residues are positioned about at residues 1-30 (HCFR1), 36-49 (HCFR2), 66-94 (HCFR3), and 103-113 (HCFR4) in the heavy chain residues. If the CDRs comprise amino acid residues from hypervariable loops, the light chain FR residues are positioned about at residues 1-25 (LCFR1), 33-49 (LCFR2), 53-90 (LCFR3), and 97-107 (LCFR4) in the light chain and the heavy chain FR residues are positioned about at residues 1-25 (HCFR1), 33-52 (HCFR2), 56-95 (HCFR3), and 102-113 (HCFR4) in the heavy chain residues. In some instances, when the CDR comprises amino acids from both a CDR as defined by Kabat and those of a hypervariable loop, the FR residues will be adjusted accordingly. For example, when CDRH1 includes amino acids H26-H35, the heavy chain FR1 residues are at positions 1-25 and the FR2 residues are at positions 36-49.
A “human consensus framework” is a framework that represents the most commonly occurring amino acid residues in a selection of human immunoglobulin VL or VH framework sequences. Generally, the selection of human immunoglobulin VL or VH sequences is from a subgroup of variable domain sequences. Generally, the subgroup of sequences is a subgroup as in Kabat. In one embodiment, for the VL, the subgroup is subgroup kappa I as in Kabat. In one embodiment, for the VH, the subgroup is subgroup III as in Kabat.
One example of an “intact” antibody is one that comprises an antigen-binding site as well as a CL and heavy chain constant domains, CH1, CH2, and CH3. The constant domains can be native sequence constant domains (e.g., human native sequence constant domains) or amino acid sequence variant thereof.
“Antibody fragments” comprise a portion of an intact antibody, preferably the antigen binding or a variable region of the intact antibody. Examples of antibody fragments include Fab, Fab′, F(ab′)2, and Fv fragments; diabodies (Db); tandem diabodies (taDb), linear antibodies (e.g., U.S. Pat. No. 5,641,870, Example 2; Zapata et al., Protein Eng. 8(10): 1057-1062 (1995)); one-armed antibodies, single variable domain antibodies, minibodies, single-chain antibody molecules; and multispecific antibodies formed from antibody fragments (e.g., including but not limited to, Db-Fc, taDb-Fc, taDb-CH3 and (scFV)4-Fc).
A “Fab” fragment is an antigen-binding fragment generated by papain digestion of antibodies and consists of an entire L chain along with the variable region domain of the H chain (VH), and the first constant domain of one heavy chain (CH1). Papain digestion of antibodies produces two identical Fab fragments. Pepsin treatment of an antibody yields a single large F(ab′)2 fragment which roughly corresponds to two disulfide linked Fab fragments having divalent antigen-binding activity and is still capable of cross-linking antigen. Fab′ fragments differ from Fab fragments by having an additional few residues at the carboxy terminus of the CH1 domain including one or more cysteines from the antibody hinge region. Fab′-SH is the designation herein for Fab′ in which the cysteine residue(s) of the constant domains bear a free thiol group. F(ab′)2 antibody fragments originally were produced as pairs of Fab′ fragments which have hinge cysteines between them. Other chemical couplings of antibody fragments are also known.
A “Fc” fragment is a residual antibody fragment generated by papain digestion, the designation reflecting the ability of the fragment to crystallize readily. The Fc fragment comprises the carboxy-terminal portions of both H chains held together by disulfides. The effector functions of antibodies are determined by sequences in the Fc region; this region is also the part recognized by Fc receptors (FcR) found on certain types of cells.
The term “Fc region” herein is used to define a C-terminal region of an immunoglobulin heavy chain, including native sequence Fc regions and variant Fc regions. Although the boundaries of the Fc region of an immunoglobulin heavy chain might vary, the human IgG heavy chain Fc region is usually defined to stretch from an amino acid residue at position Cys226, or from Pro230, to the carboxyl-terminus thereof. The C-terminal lysine (residue 447 according to the EU numbering system) of the Fc region may be removed, for example, during production or purification of the antibody, or by recombinantly engineering the nucleic acid encoding a heavy chain of the antibody. Accordingly, a composition of intact antibodies may comprise antibody populations with all K447 residues removed, antibody populations with no K447 residues removed, and antibody populations having a mixture of antibodies with and without the K447 residue.
A “functional Fc region” possesses an “effector function” of a native sequence Fc region. Exemplary “effector functions” include C1q binding; CDC; Fc receptor binding; ADCC; phagocytosis; down regulation of cell surface receptors (e.g., B cell receptor; BCR), etc. Such effector functions generally require the Fc region to be combined with a binding domain (e.g., an antibody variable domain) and can be assessed using various assays as disclosed, for example, in definitions herein.
A “native sequence Fc region” comprises an amino acid sequence identical to the amino acid sequence of an Fc region found in nature. Native sequence human Fc regions include a native sequence human IgG 1 Fc region (non-A and A allotypes); native sequence human IgG2 Fc region; native sequence human IgG3 Fc region; and native sequence human IgG4 Fc region as well as naturally occurring variants thereof.
A “variant Fc region” comprises an amino acid sequence which differs from that of a native sequence Fc region by virtue of at least one amino acid modification, preferably one or more amino acid substitution(s). Preferably, the variant Fc region has at least one amino acid substitution compared to a native sequence Fc region or to the Fc region of a parent polypeptide, e.g., from about one to about ten amino acid substitutions, and preferably from about one to about five amino acid substitutions in a native sequence Fc region or in the Fc region of the parent polypeptide. The variant Fc region herein will preferably possess at least about 80% homology with a native sequence Fc region and/or with an Fc region of a parent polypeptide, and most preferably at least about 90% homology therewith, more preferably at least about 95% homology therewith.
“Fc complex” as used herein refers to two CH2 domains of an Fc region interacting together and/or two CH3 domains of an Fc region interacting together, wherein the CH2 domains and/or the CH3 domains interact through bonds and/or forces (e.g., Van der Waals, hydrophobic, hydrophilic forces) that are not peptide bonds.
“Fc component” as used herein refers to a hinge region, a CH2 domain or a CH3 domain of an Fc region.
“Fc CH component” or “FcCH” as used herein refers to a polypeptide comprising a CH2 domain, a CH3 domain, or CH2 and CH3 domains of an Fc region.
“Fv” consists of a dimer of one heavy- and one light-chain variable region domain in tight, non-covalent association. From the folding of these two domains emanate six hypervariable loops (3 loops each from the H and L chain) that contribute the amino acid residues for antigen binding and confer antigen binding specificity to the antibody. However, even a single variable domain (or half of an Fv comprising only three CDRs specific for an antigen) has the ability to recognize and bind antigen, although often at a lower affinity than the entire binding site.
As used herein, the term “immunoadhesin” designates molecules which combine the binding specificity of a heterologous protein (an “adhesin”) with the effector functions of immunoglobulin constant domains. Structurally, the immunoadhesins comprise a fusion of an amino acid sequence with a desired binding specificity, which amino acid sequence is other than the antigen recognition and binding site of an antibody (i.e., is “heterologous” compared to a constant region of an antibody), and an immunoglobulin constant domain sequence (e.g., CH2 and/or CH3 sequence of an IgG). The adhesin and immunoglobulin constant domains may optionally be separated by an amino acid spacer. Exemplary adhesin sequences include contiguous amino acid sequences that comprise a portion of a receptor or a ligand that binds to a protein of interest. Adhesin sequences can also be sequences that bind a protein of interest, but are not receptor or ligand sequences (e.g., adhesin sequences in peptibodies). Such polypeptide sequences can be selected or identified by various methods, include phage display techniques and high throughput sorting methods. The immunoglobulin constant domain sequence in the immunoadhesin can be obtained from any immunoglobulin, such as IgG1, IgG2, IgG3, or IgG4 subtypes, IgA (including IgA1 and IgA2), IgE, IgD, or IgM.
By amino acid “spacer” as used herein is meant an amino acid sequence of two or more amino acids in length that is not cleavable, for example, by auto-cleavage, enzymatic, or chemical cleavage. The spacer can consist of neutral, polar, or nonpolar amino acids. An amino acid spacer can be, for example, 2 to 100 amino acids in length, such as between 10-80 amino acids or 20-40 amino acids in length, for example, 3, 5, 10, 15, 20, 25, 30, 35, or 40 amino acids in length. In some embodiments, an amino acid spacer may include glycine (G) and serine (S) residues, for example, as GGS repeats. In some embodiments, an amino acid spacer may include threonine (T) and histidine (H) residues. Exemplary spacers are THT (SEQ ID NO: 1), GGGSTHT (SEQ ID NO: 2), and GGGSGGGSTHT (SEQ ID NO: 3).
“Single-chain Fv” also abbreviated as “sFv” or “scFv” are antibody fragments that comprise the VH and VL antibody domains connected into a single polypeptide chain. Preferably, the sFv polypeptide further comprises a polypeptide linker between the VH and VL domains, which enables the sFv to form the desired structure for antigen binding. For a review of sFv, see Pluckthun, The Pharmacology of Monoclonal Antibodies, vol. 113, Rosenburg and Moore eds., Springer-Verlag, New York, pp. 269-315 (1994); Malmborg et al., J. Immunol. Methods 183:7-13, 1995.
The term “diabodies” refers to small antibody fragments prepared by constructing sFv fragments (see preceding paragraph) with short linkers (about 5-10 residues) between the VH and VL domains such that inter-chain but not intra-chain pairing of the V domains is achieved, resulting in a bivalent fragment, i.e., fragment having two antigen-binding sites. Bispecific diabodies are heterodimers of two “crossover” sFv fragments in which the VH and VL domains of the two antibodies are present on different polypeptide chains. Diabodies are described more fully in, for example, EP 404,097; WO 93/11161; and Hollinger et al., Proc. Natl. Acad. Sci. USA 90:6444-6448 (1993).
The expression “single domain antibodies” (sdAbs) or “single variable domain (SVD) antibodies” generally refers to antibodies in which a single variable domain (VH or VL) can confer antigen binding. In other words, the single variable domain does not need to interact with another variable domain in order to recognize the target antigen. Examples of single domain antibodies include those derived from camelids (llamas and camels) and cartilaginous fish (e.g., nurse sharks) and those derived from recombinant methods from humans and mouse antibodies (Nature (1989) 341:544-546; Dev Comp Immunol (2006) 30:43-56; Trend Biochem Sci (2001) 26:230-235; Trends Biotechnol (2003) 21:484-490; WO 2005/035572; WO 03/035694; Febs Lett (1994) 339:285-290; WO00/29004; WO 02/051870).
The term “half-antibody” as used herein refers to one arm of an antibody and includes at least a VH domain and one CH domain. In some embodiments, a half-antibody may associate with an immunoadhesin to form a heteromultimer of the invention. In other embodiments, a first half-antibody may associate with a second half-antibody of identical or different amino acid sequence (e.g., differing by at least one amino acid residue) to form a symmetric or an asymmetric heteromultimer, respectively.
The term “single-chain antibody” is used herein in the broadest sense and specifically covers an antibody with monospecifity or multispecificity (e.g., bispecificity) that is initially generated as a single continuous polypeptide chain. Such single-chain antibodies include, but are not limited to, an antibody having two linked HCs, which can be different from or identical to one another and include two different or identical VH domains, an HD tether linking the two HCs, and at least one heavy chain constant domain selected from two different or identical CH2 domains and two different or identical CH3 domains. The single-chain antibodies may additionally include one or two, different or identical, CH1 domains. In some embodiments, the single-chain antibodies include one or two hinge domains, which link one HC domain (e.g., VH or CH1) with a second contiguously located domain (e.g., CH2). In other embodiments, the single-chain antibodies may include one or two linked LCs that can be different from or identical to one another and which may each include two different or identical VL and CL domains, each linked to a particular HC by a CLH tether. As described herein, the single-chain antibodies may additionally use knob-into-hole technology to support HC/HC or HC/LC heterodimerization and may include cleavable tethers. Single-chain antibodies are heteromultimers of the invention.
As used herein, the term “multi-chain antibody” refers to an antibody comprised of two LCs and two HCs, wherein the two HCs are expressed as a single polypeptide and at least one LC is expressed as a separate polypeptide. The independently expressed LCs associate with their cognate HCs to form an antibody with two functional arms. The multi-chain antibodies may be monospecific or multispecific. The multi-chain antibodies may additionally use knob-into-hole technology to support HC/HC or HC/LC heterodimerization and may include cleavable tethers.
The term “knob-into-hole” or “KnH” technology as mentioned herein refers to the technology directing the pairing of two polypeptides together in vitro or in vivo by introducing a protuberance (knob) into one polypeptide and a cavity (hole) into the other polypeptide at an interface in which they interact. For example, KnHs have been introduced in the Fc:Fc binding interfaces, CL:CH1 interfaces or VH/VL interfaces of antibodies (e.g., US2007/0178552, WO 96/027011, WO 98/050431 and Zhu et al. (1997) Protein Science 6:781-788). This is especially useful in driving the pairing of two different heavy chains together during the manufacture of multispecific antibodies. For example, multispecific antibodies having KnH in their Fc regions can further comprise single variable domains linked to each Fc region, or further comprise different heavy chain variable domains that pair with similar or different light chain variable domains. KnH technology can also be used to pair two different receptor extracellular domains together or any other polypeptide sequences that comprise different target recognition sequences.
The term “multispecific antibody” is used in the broadest sense and specifically covers an antibody that has polyepitopic specificity. Such multispecific antibodies include, but are not limited to, an antibody comprising a heavy chain variable domain (VH) and a light chain variable domain (VL), where the VH/VL unit has polyepitopic specificity, antibodies having two or more VL and VH domains with each VH/VL unit binding to a different epitope, antibodies having two or more single variable domains with each single variable domain binding to a different epitope, full-length antibodies, antibody fragments such as Fab, Fv, dsFv, scFv, diabodies, bispecific diabodies and triabodies, antibody fragments that have been linked covalently or non-covalently. “Polyepitopic specificity” refers to the ability to specifically bind to two or more different epitopes on the same or different target(s). “Monospecific” refers to the ability to bind only one antigen. In one embodiment, the monospecific heteromultimer binds two different epitopes on the same target/antigen. According to one embodiment, the multispecific antibody is an IgG antibody that binds to each epitope with an affinity of 5 μM to 0.001 pM, 3 μM to 0.001 pM, 1 μM to 0.001 pM, 0.5 μM to 0.001 pM, or 0.1 μM to 0.001 pM.
Antibodies of the invention can be “chimeric” antibodies in which a portion of the heavy and/or light chain is identical with or homologous to corresponding sequences in antibodies derived from a particular species or belonging to a particular antibody class or subclass, while the remainder of the chain(s) is identical with or homologous to corresponding sequences in antibodies derived from another species or belonging to another antibody class or subclass, as well as fragments of such antibodies, provided that they exhibit the desired biological activity (U.S. Pat. No. 4,816,567; and Morrison et ah, Proc. Natl. Acad. Sci. USA 81:6851-6855 (1984)). Chimeric antibodies of interest herein include primatized antibodies comprising variable domain antigen-binding sequences derived from a non-human primate (e.g., Old World Monkey, Ape, etc.) and human constant region sequences.
“Humanized” forms of non-human (e.g., rodent) antibodies are chimeric antibodies that contain minimal sequence derived from the non-human antibody. For the most part, humanized antibodies are human immunoglobulins (recipient antibody) in which residues from a hypervariable region of the recipient are replaced by residues from a hypervariable region of a non-human species (donor antibody) such as mouse, rat, rabbit or non-human primate having the desired antibody specificity, affinity, and capability. In some instances, framework region (FR) residues of the human immunoglobulin are replaced by corresponding non-human residues. Furthermore, humanized antibodies can comprise residues that are not found in the recipient antibody or in the donor antibody. These modifications are made to further refine antibody performance. In general, the humanized antibody will comprise substantially all or at least one, and typically two, variable domains, in which all or substantially all of the hypervariable loops correspond to those of a non-human immunoglobulin and all, or substantially all, of the FRs are those of a human immunoglobulin sequence. The humanized antibody optionally also will comprise at least a portion of an immunoglobulin constant region (Fc), typically that of a human immunoglobulin. For further details, see Jones et al., Nature 321:522-525 (1986); Riechmann et al, Nature 332:323-329 (1988); and Presta, Curr. Op. Struct. Biol. 2:593-596 (1992).
“Complex” or “complexed” as used herein refers to the association of two or more molecules that interact with each other through bonds and/or forces (e.g., Van der Waals, hydrophobic, hydrophilic forces) that are not peptide bonds. In one embodiment, the complex is heteromultimeric. It should be understood that the term “protein complex” or “polypeptide complex” as used herein includes complexes that have a non-protein entity conjugated to a protein in the protein complex (e.g., including, but not limited to, chemical molecules such as a toxin or a detection agent).
The term “heteromultimer” or “heteromultimeric” as used herein describes two or more polypeptides of different sequence that interact with each other by a non-peptidic, covalent bond (e.g., disulfide bond) and/or a non-covalent interaction (e.g., hydrogen bonds, ionic bonds, Van der Waals forces, or hydrophobic interactions). Also included in this definition are multimeric polypeptides in an initially linked form (e.g., as produced in the form of a single continuous polypeptide chain). As used herein, heteromultimers include, for example, single-chain antibodies and multi-chain antibodies, as well as multimers having one or more half antibodies associated with one or more immunoadhesins. Heteromultimers include polypeptides and/or polypeptide complexes in which an HD tether is present or absent.
An antibody of this invention “which binds” an antigen of interest is one that binds the antigen with sufficient affinity such that the antibody is useful as a diagnostic and/or therapeutic agent in targeting a protein or a cell or tissue expressing the antigen, and does not significantly cross-react with other proteins. In such embodiments, the extent of binding of the antibody to a “non-target” protein will be less than about 10% of the binding of the antibody to its particular target protein as determined by fluorescence activated cell sorting (FACS) analysis or radioimmunoprecipitation (RIA) or ELISA. With regard to the binding of an antibody to a target molecule, the term “specific binding” or “specifically binds to” or is “specific for” a particular polypeptide or an epitope on a particular polypeptide target means binding that is measurably different from a non-specific interaction (e.g., a non-specific interaction may be binding to bovine serum albumin or casein). Specific binding can be measured, for example, by determining binding of a molecule compared to binding of a control molecule. For example, specific binding can be determined by competition with a control molecule that is similar to the target, for example, an excess of non-labeled target. In this case, specific binding is indicated if the binding of the labeled target to a probe is competitively inhibited by excess unlabeled target. The term “specific binding” or “specifically binds to” or is “specific for” a particular polypeptide or an epitope on a particular polypeptide target as used herein can be exhibited, for example, by a molecule having a Kd for the target of about 1 μM to about 1 fM, alternatively about 200 nM to about 1 fM, alternatively about 200 nM to about 1 pM, alternatively about 150 nM to about 1 fM, alternatively about 150 nM to about 1 pM, alternatively about 100 nM to about 1 fM, alternatively about 100 nM to about 1 pM, alternatively about 60 nM to about 1 fM, alternatively about 60 nM to about 1 pM, alternatively about 50 nM to about 1 fM, alternatively about 50 nM to about 1 pM, alternatively about 30 nM to about 1 fM, alternatively about 30 nM to about 1 pM, alternatively about 20 nM to about 1 fM, alternatively about 20 nM to about 1 pM, alternatively about 10 nM to about 1 fM, alternatively about 10 nM to about 1 pM, alternatively about 8 nM to about 1 fM, alternatively about 8 nM to about 1 pM, alternatively about 6 nM to about 1 fM, alternatively about 6 nM to about 1 pM, alternatively about 4 nM to about 1 fM, alternatively about 4 nM to about 1 pM, alternatively about 2 nM to about 1 fM, alternatively about 2 nM to about 1 pM, alternatively about 1 nM to about 1 fM, alternatively about 1 nM to about 1 pM. In one embodiment, the term “specific binding” refers to binding where a molecule binds to a particular polypeptide or epitope on a particular polypeptide without substantially binding to any other polypeptide or polypeptide epitope.
“Binding affinity” generally refers to the strength of the sum total of noncovalent interactions between a single binding site of a molecule (e.g., an antibody) and its binding partner (e.g., an antigen). Unless indicated otherwise, as used herein, “binding affinity” refers to intrinsic binding affinity which reflects a 1:1 interaction between members of a binding pair (e.g., antibody and antigen). The affinity of a molecule X for its partner Y can generally be represented by the dissociation constant (Kd). For example, the Kd can be about 200 nM, 150 nM, 100 nM, 60 nM, 50 nM, 40 nM, 30 nM, 20 nM, 10 nM, 8 nM, 6 nM, 4 nM, 2 nM, 1 nM, or stronger. Affinity can be measured by common methods known in the art, including those described herein. Low-affinity antibodies generally bind antigen slowly and tend to dissociate readily, whereas high-affinity antibodies generally bind antigen faster and tend to remain bound longer. A variety of methods of measuring binding affinity are known in the art, any of which can be used for purposes of the present invention.
In one embodiment, the “Kd” or “Kd value” according to this invention is measured by using surface plasmon resonance assays using a BIAcoreTM-2000 or a BIAcoreTM-3000 (BIAcore, Inc., Piscataway, N.J.) at 25° C. with immobilized antigen CM5 chips at  ̃10 response units (RU). The antibodies of this invention can have affinities for their targets with Kd values of about 1 μM to about 1 fM, alternatively about 200 nM to about 1 fM, alternatively about 200 nM to about 1 pM, alternatively about 150 nM to about 1 fM, alternatively about 150 nM to about 1 pM, alternatively about 100 nM to about 1 fM, alternatively about 100 nM to about 1 pM, alternatively about 60 nM to about 1 fM, alternatively about 60 nM to about 1 pM, alternatively about 50 nM to about 1 fM, alternatively about 50 nM to about 1 pM, alternatively about 30 nM to about 1 fM, alternatively about 30 nM to about 1 pM, alternatively about 20 nM to about 1 fM, alternatively about 20 nM to about 1 pM, alternatively about 10 nM to about 1 fM, alternatively about 10 nM to about 1 pM, alternatively about 8 nM to about 1 fM, alternatively about 8 nM to about 1 pM, alternatively about 6 nM to about 1 fM, alternatively about 6 nM to about 1 pM, alternatively about 4 nM to about 1 fM, alternatively about 4 nM to about 1 pM, alternatively about 2 nM to about 1 fM, alternatively about 2 nM to about 1 pM, alternatively about 1 nM to about 1 fM, alternatively about 1 nM to about 1 pM. To measure Kd values by using surface plasmon resonance assays, carboxymethylated dextran biosensor chips (CMS, BIAcore Inc.) are activated with N-ethyl-N′-(3-dimethylaminopropyl)-carbodiimide hydrochloride (EDC) and N-hydroxysuccinimide (NHS) according to the supplier's instructions. Antigen is diluted with 10 mM sodium acetate, pH 4.8, into 5 μg/ml ( ̃0.2 μM) before injection at a flow rate of 5 μl/minute to achieve approximately 10 response units (RU) of coupled protein. Following the injection of antigen, 1M ethanolamine is injected to block unreacted groups. For kinetics measurements, two-fold serial dilutions of Fab (e.g., 0.78 nM to 500 nM) are injected in PBS with 0.05% Tween 20 (PBST) at 25° C. at a flow rate of approximately 25 μl/min. Association rates (kon) and dissociation rates (koff) are calculated using a simple one-to-one Langmuir binding model (BIAcore Evaluation Software version 3.2) by simultaneous fitting the association and dissociation sensorgram. The equilibrium dissociation constant (Kd) is calculated as the ratio koff/kon. See, e.g., Chen et al., J. Mol. Biol. 293:865-881 (1999). If the on-rate exceeds 106 M−1S−1 by the surface plasmon resonance assay above, then the on-rate can be determined by using a fluorescent quenching technique that measures the increase or decrease in fluorescence emission intensity (excitation=295 nm; emission=340 nm, 16 nm band-pass) at 25° C. of a 20 nM anti-antigen antibody (Fab form) in PBS, pH 7.2, in the presence of increasing concentrations of antigen as measured in a spectrometer, such as a stop-flow equipped spectrophometer (Aviv Instruments) or a 8000-series SLM-Aminco spectrophotometer (ThermoSpectronic) with a stir red cuvette.
An “on-rate” or “rate of association” or “association rate” or “kon” according to this invention can also be determined with the same surface plasmon resonance technique described above using a BIAcoreTM-2000 or a BIAcoreTM-3000 (BIAcore, Inc., Piscataway, N.J.) at 25° C. with immobilized antigen CM5 chips at  ̃10 response units (RU). Briefly, carboxymethylated dextran biosensor chips (CM5, BIAcore Inc.) are activated with N-ethyl-N′-(3-dimethylaminopropyl)-carbodiimide hydrochloride (EDC) and N-hydroxysuccinimide (NHS) according to the supplier's instructions. Antigen is diluted with 10 mM sodium acetate, pH 4.8, into 5 μg/ml ( ̃0.2 μM) before injection at a flow rate of 5 μl/minute to achieve approximately 10 response units (RU) of coupled protein. Following the injection of antigen, 1M ethanolamine is injected to block unreacted groups. For kinetics measurements, two-fold serial dilutions of Fab (e.g., 0.78 nM to 500 nM) are injected in PBS with 0.05% Tween 20 (PBST) at 25° C. at a flow rate of approximately 25 μl/min. Association rates (kon) and dissociation rates (koff) are calculated using a simple one-to-one Langmuir binding model (BIAcore Evaluation Software version 3.2) by simultaneous fitting the association and dissociation sensorgram. The equilibrium dissociation constant (Kd) is calculated as the ratio koff/kon. See, e.g., Chen et al., J. Mol. Biol. 293:865-881 (1999). However, if the on-rate exceeds 106 M−1S−1 by the surface plasmon resonance assay above, then the on-rate is preferably determined by using a fluorescent quenching technique that measures the increase or decrease in fluorescence emission intensity (excitation=295 nm; emission=340 nm, 16 nm band-pass) at 25° C. of a 20 nM anti-antigen antibody (Fab form) in PBS, pH 7.2, in the presence of increasing concentrations of antigen as measured in a spectrometer, such as a stop-flow equipped spectrophotometer (Aviv Instruments) or a 8000-series SLM-Aminco spectrophotometer (ThermoSpectronic) with a stirred cuvette.
“Biologically active” and “biological activity” and “biological characteristics” with respect to a polypeptide of this invention, such as an antibody, fragment, or derivative thereof, means having the ability to bind to a biological molecule, except where specified otherwise.
The heteromultimers of the present invention are generally purified to substantial homogeneity. The phrases “substantially homogeneous,” “substantially homogeneous form” and “substantial homogeneity” are used to indicate that the product is substantially devoid of by-products originated from undesired polypeptide combinations.
Expressed in terms of purity, substantial homogeneity means that the amount of byproducts does not exceed 10%, 9%, 8%, 7%, 6%, 4%, 3%, 2% or 1% by weight or is less than 1% by weight. In one embodiment, the by-product is below 5%.
“Biological molecule” refers to a nucleic acid, a protein, a carbohydrate, a lipid, and combinations thereof. In one embodiment, the biologic molecule exists in nature.
“Isolated,” when used to describe the various heteromultimers disclosed herein, means a heteromultimer that has been identified and separated and/or recovered from a cell or cell culture from which it was expressed. Contaminant components of its natural environment are materials that would typically interfere with diagnostic or therapeutic uses for the polypeptide, and can include enzymes, hormones, and other proteinaceous or nonproteinaceous solutes. In preferred embodiments, the heteromultimer will be purified (1) to a degree sufficient to obtain at least 15 residues of N-terminal or internal amino acid sequence by use of a spinning cup sequenator, or (2) to homogeneity by SDS-PAGE under non-reducing or reducing conditions using Coomassie blue or, preferably, silver stain. Isolated heteromultimers include antibodies in situ within recombinant cells, because at least one component of the polypeptide natural environment will not be present. Ordinarily, however, isolated polypeptides will be prepared by at least one purification step.
By “linked” or “links” as used herein is meant either a direct peptide bond linkage between a first and second amino acid sequence or a linkage that involves a third amino acid sequence that is peptide bonded to and between the first and second amino acid sequences. For example, an amino acid linker bonded to the C-terminal end of one amino acid sequence and to the N-terminal end of the other amino acid sequence.
By “linker” as used herein is meant an amino acid sequence of two or more amino acids in length. The linker can consist of neutral, polar, or nonpolar amino acids. A linker can be, for example, 2 to 100 amino acids in length, such as between 2 and 50 amino acids in length, for example, 3, 5, 10, 15, 20, 25, 30, 35, 40, 45, or 50 amino acids in length. A linker can be “cleavable,” for example, by auto-cleavage, or enzymatic or chemical cleavage. Cleavage sites in amino acid sequences and enzymes and chemicals that cleave at such sites are well known in the art and are also described herein.
By a “HD tether” or “HeteroDimerization tether” as used herein is meant an amino acid linker that joins two different heavy chain constant (CH) domain-containing polypeptides together. Generally, the two CH domain-containing polypeptides are joined together by linking a CH2 or CH3 domain of the first polypeptide to a VL domain, which is itself a component of a second CH-containing polypeptide. In some embodiments, the HD tether links the CH3 domain of a first polypeptide directly to the VH domain of a second CH domain-containing polypeptide. In general, HD tethers of 15-100 amino acids are effective, as are HD tethers of 20-40 amino acids, 25-40 amino acids, and 30-40 amino acids. In particular embodiments, an HD tether is between 30 and 39 amino acids in length (e.g., 30, 31, 32, 33, 34, 35, 36, 37, 38, or 39 amino acids in length). An HD tether may be “cleavable,” for example, by auto-cleavage, or enzymatic or chemical cleavage using methods and reagents standard in the art.
By a “CLH tether” or “Cognate LC-HC tether” as used herein is meant an amino acid linker that joins a light chain with its cognate heavy chain. A CLH tether generally refers to amino acids that link the CL domain of a light chain to the VH domain of a heavy chain. In some embodiments, the CLH tether links the VL domain of a light chain directly to the VH domain of a heavy chain. In general, CLH tethers of 10-80 amino acids are effective, as are CLH tethers of 20-40 amino acids, 25-40 amino acids, 30-40 amino acids, and 30-35 amino acids (e.g., 30, 31, 32, 33, 34, or 35 amino acids). Single-chain antibodies of the invention may have multiple CLH tethers that may or may not differ in sequence and/or length. In preferred embodiments, a single-chain antibody has two tethers (CLH tether1 and CLH tether2) which each join a light chain to its cognate heavy chain. A CLH tether may be “cleavable,” for example, by auto-cleavage, or enzymatic or chemical cleavage using methods and reagents standard in the art.
Enzymatic cleavage of a “linker” or a “tether” may involve the use of an endopeptidase such as, for example, urokinase, Lys-C, Asp-N, Arg-C, V8, Glu-C, chymotrypsin, trypsin, pepsin, papain, thrombin, tissue plasminogen activator (tPa), genenase, Factor Xa, TEV (tobacco etch virus cysteine protease), enterokinase, HRV C3 (human rhinovirus C3 protease), kininogenase, as well as subtilisin-like proprotein convertases (e.g., furin (PC1), PC2, or PC3) or N-arginine dibasic convertase. In a desirable embodiment, enzymatic cleavage involves the endopeptidase furin. Chemical cleavage may also involve use of, for example, hydroxylamine, N-chlorosuccinimide, N-bromosuccinimide, or cyanogen bromide.
A “furin endopeptidase cleavage site” as used herein is an X1-X2-X3-Arginine amino acid sequence (SEQ ID NO:6), where X1 is a basic amino acid residue (natural or unnatural, modified or unmodified) and X2 and X3 can each be any amino acid residue (natural or unnatural, modified or unmodified) that can be cleaved at the C-terminal side by furin endopeptidase. Furin endopeptidase cleaves at the C-terminal side of an Arginine residue. In certain embodiments, the furin cleavage site comprises the amino acid sequence RXRXYR, wherein Y is K or R and X is any amino acid residue (SEQ ID NO:7), and more specifically RXRXRR (SEQ ID NO:8). In certain embodiments, the furin cleavage site comprises the amino acid sequence RKRKRR (SEQ ID NO:9). In certain other embodiments, the furin cleavage site comprises the amino acid sequence of RHRQPR (SEQ ID NO:10). In yet other embodiments, the furin cleavage site comprises the amino acid sequence RSRKRR (SEQ ID NO:11).
A “Lys-C endopeptidase cleavage site” as used herein is a Lysine residue in an amino acid sequence that can be cleaved at the C-terminal side by Lys-C endopeptidase. Lys-C endopeptidase cleaves at the C-terminal side of a Lysine residue.
Enzymatic cleavage of a “linker” or a “tether” may also involve the use of an exopeptidase such as, for example, Carboxypeptidase A, Carboxypeptidase B, Carboxypeptidase D, Carboxypeptidase E (also called Carboxypeptidase H), Carboxypeptidase M, Carboxypeptidase N, or Carboxypeptidase Z to remove the residual endopeptidase recognition sequences following endopeptidase cleavage.
Antibody “effector functions” refer to those biological activities attributable to the Fc region (a native sequence Fc region or amino acid sequence variant Fc region) of an antibody, and vary with the antibody isotype. Examples of antibody effector functions include: C1q binding and complement dependent cytotoxicity; Fc receptor binding; antibody-dependent cell-mediated cytotoxicity (ADCC); phagocytosis; down regulation of cell surface receptors (e.g., B cell receptor); and B cell activation.
“Antibody-dependent cell-mediated cytotoxicity” or “ADCC” refers to a form of cytotoxicity in which secreted Ig bound onto Fc receptors (FcRs) present on certain cytotoxic cells (e.g., Natural Killer (NK) cells, neutrophils, and macrophages) enable these cytotoxic effector cells to bind specifically to an antigen-bearing target cell and subsequently kill the target cell with cytotoxic agents. The antibodies “arm” the cytotoxic cells and are absolutely required for such killing. The primary cells for mediating ADCC, NK cells, express FcγRIII only, whereas monocytes express FcγRI, FcγRII, and FcγRIII. FcR expression on hematopoietic cells is summarized in Table 3 on page 464 of Ravetch and Kinet, Annu. Rev. Immunol. 9:457-92 (1991). To assess ADCC activity of a molecule of interest, an in vitro ADCC assay, such as that described in U.S. Pat. No. 5,500,362 or 5,821,337 can be performed. Useful effector cells for such assays include peripheral blood mononuclear cells (PBMC) and Natural Killer (NK) cells. Alternatively, or additionally, ADCC activity of the molecule of interest can be assessed in vivo, e.g., in a animal model such as that disclosed in Clynes et al., Proc. Natl. Acad. Sci. USA 95:652-656 (1998).
“Fc receptor” or “FcR” describes a receptor that binds to the Fc region of an antibody. The preferred FcR is a native sequence human FcR. Moreover, a preferred FcR is one that binds an IgG antibody (a gamma receptor) and includes receptors of the FcγRI, FcγRII, and FcγRIII subclasses, including allelic variants and alternatively spliced forms of these receptors. FcγRII receptors include FcγRIIA (an “activating receptor”) and FcγRIIB (an “inhibiting receptor”), which have similar amino acid sequences that differ primarily in the cytoplasmic domains thereof. Activating receptor FcγRIIA contains an immunoreceptor tyrosine-based activation motif (ITAM) in its cytoplasmic domain Inhibiting receptor FcγRIIB contains an immunoreceptor tyrosine-based inhibition motif (ITIM) in its cytoplasmic domain (see review M. in Daëron, Annu Rev. Immunol. 15:203-234 (1997)). FcRs are reviewed in Ravetch and Kinet, Annu. Rev. Immunol. 9:457-492 (1991); Capel et al., Immunomethods 4:25-34 (1994); and de Haas et al., J. Lab. Clin. Med. 126:330-41 (1995). Other FcRs, including those to be identified in the future, are encompassed by the term “FcR” herein. The term also includes the neonatal receptor, FcRn, which is responsible for the transfer of maternal IgGs to the fetus (Guyer et al., J. Immunol. 117:587 (1976) and Kim et al., J. Immunol. 24:249 (1994)).
“Human effector cells” are leukocytes that express one or more FcRs and perform effector functions. Preferably, the cells express at least FcγRIII and perform ADCC effector function. Examples of human leukocytes that mediate ADCC include peripheral blood mononuclear cells (PBMC), natural killer (NK) cells, monocytes, cytotoxic T cells, and neutrophils; with PBMCs and NK cells being preferred. The effector cells can be isolated from a native source, e.g., from blood.
“Complement dependent cytotoxicity” or “CDC” refers to the lysis of a target cell in the presence of complement. Activation of the classical complement pathway is initiated by the binding of the first component of the complement system (C1q) to antibodies (of the appropriate subclass) that are bound to their cognate antigen. To assess complement activation, a CDC assay, e.g., as described in Gazzano-Santoro et al., J. Immunol. Methods 202:163 (1996), can be performed.
The term “therapeutically effective amount” refers to an amount of heteromultimer, antibody, antibody fragment, or derivative to treat a disease or disorder in a subject. In the case of tumor (e.g., a cancerous tumor), the therapeutically effective amount of the heteromultimer, antibody, or antibody fragment (e.g., a multispecific antibody or antibody fragment) may reduce the number of cancer cells; reduce the primary tumor size; inhibit (i.e., slow to some extent and preferably stop) cancer cell infiltration into peripheral organs; inhibit (i.e., slow to some extent and preferably stop) tumor metastasis; inhibit, to some extent, tumor growth; and/or relieve to some extent one or more of the symptoms associated with the disorder. To the extent the heteromultimer, antibody, or antibody fragment may prevent growth and/or kill existing cancer cells, it may be cytostatic and/or cytotoxic. For cancer therapy, efficacy in vivo can, for example, be measured by assessing the duration of survival, time to disease progression (TTP), the response rates (RR), duration of response, and/or quality of life.
By “reduce or inhibit” is meant the ability to cause an overall decrease preferably of 20% or greater, more preferably of 50% or greater, and most preferably of 75%, 85%, 90%, 95%, or greater. Reduce or inhibit can refer to the symptoms of the disorder being treated, the presence or size of metastases, the size of the primary tumor, or the size or number of the blood vessels in angiogenic disorders.
The term “cytotoxic agent” as used herein refers to a substance that inhibits or prevents the function of a cell and/or causes destruction of a cell. The term is intended to include radioactive isotopes (e.g., At211, I131, I125, Y90, Re186, Re188, sm153, Bi212, Ra223, P32, and radioactive isotopes of Lu), chemotherapeutic agents, e.g., methotrexate, adriamicin, vinca alkaloids (vincristine, vinblastine, etoposide), doxorubicin, melphalan, mitomycin C, chlorambucil, daunorubicin or other intercalating agents, enzymes and fragments thereof such as nucleolytic enzymes, antibiotics, and toxins such as small molecule toxins or enzymatically active toxins of bacterial, fungal, plant or animal origin, including fragments and/or variants thereof, and the various antitumor, anticancer, and chemotherapeutic agents disclosed herein. Other cytotoxic agents are described herein. A tumoricidal agent causes destruction of tumor cells.
A “chemotherapeutic agent” is a chemical compound useful in the treatment of cancer. Examples of chemotherapeutic agents include alkylating agents such as thiotepa and CYTOXAN® cyclosphosphamide; alkyl sulfonates such as busulfan, improsulfan and piposulfan; aziridines such as benzodopa, carboquone, meturedopa, and uredopa; ethylenimines and methylamelamines including altretamine, triethylenemelamine, trietylenephosphoramide, triethiylenethiophosphoramide and trimethylolomelamine; acetogenins (especially bullatacin and bullatacinone); delta-9-tetrahydrocannabinol (dronabinol, MARTNOL®); beta-lapachone; lapachol; colchicines; betulinic acid; a camptothecin (including the synthetic analogue topotecan (HYCAMTIN®), CPT-11 (irinotecan, CAMPTOSAR®), acetylcamptothecin, scopolectin, and 9-aminocamptothecin); bryostatin; callystatin; CC-1065 (including its adozelesin, carzelesin and bizelesin synthetic analogues); podophyllotoxin; podophyllinic acid; teniposide; cryptophycins (particularly cryptophycin 1 and cryptophycin 8); dolastatin; duocarmycin (including the synthetic analogues, KW-2189 and CB1-TM1); eleutherobin; pancratistatin; a sarcodictyin; spongistatin; nitrogen mustards such as chlorambucil, chlornaphazine, cholophosphamide, estramustine, ifosfamide, mechlorethamine, mechlorethamine oxide hydrochloride, melphalan, novembichin, phenesterine, prednimustine, trofosfamide, uracil mustard; nitrosureas such as carmustine, chlorozotocin, fotemustine, lomustine, nimustine, and ranimnustine; antibiotics such as the enediyne antibiotics (e.g., calicheamicin, especially calicheamicin gamma 1 (see, e.g., Agnew, Chem. Intl. Ed. Engl. 33: 183-186 (1994)); dynemicin, including dynemicin A; an esperamicin; as well as neocarzinostatin chromophore and related chromoprotein enediyne antiobiotic chromophores), aclacinomysins, actinomycin, authramycin, azaserine, bleomycins, cactinomycin, carabicin, carminomycin, carzinophilin, chromomycinis, dactinomycin, daunorubicin, detorubicin, 6-diazo-5-oxo-L-norleucine, ADRIAMYCIN® doxorubicin (including morpholino-doxorubicin, cyanomorpholino-doxorubicin, 2-pyrrolino-doxorubicin and deoxydoxorubicin), epirubicin, esorubicin, idarubicin, marcellomycin, mitomycins such as mitomycin C, mycophenolic acid, nogalamycin, olivomycins, peplomycin, potfiromycin, puromycin, quelamycin, rodorubicin, streptonigrin, streptozocin, tubercidin, ubenimex, zinostatin, zorubicin; anti-metabolites such as methotrexate and 5-fluorouracil (5-FU); folic acid analogues such as denopterin, methotrexate, pteropterin, trimetrexate; purine analogs such as fludarabine, 6-mercaptopurine, thiamiprine, thioguanine; pyrimidine analogs such as ancitabine, azacitidine, 6-azauridine, carmofur, cytarabine, dideoxyuridine, doxifluridine, enocitabine, floxuridine; androgens such as calusterone, dromostanolone propionate, epitiostanol, mepitiostane, testolactone; anti-adrenals such as aminoglutethimide, mitotane, trilostane; folic acid replenisher such as frolinic acid; aceglatone; aldophosphamide glycoside; aminolevulinic acid; eniluracil; amsacrine; bestrabucil; bisantrene; edatraxate; defofamine; demecolcine; diaziquone; elfornithine; elliptinium acetate; an epothilone; etoglucid; gallium nitrate; hydroxyurea; lentinan; lonidainine; maytansinoids such as maytansine and ansamitocins; mitoguazone; mitoxantrone; mopidanmol; nitraerine; pentostatin; phenamet; pirarubicin; losoxantrone; 2-ethylhydrazide; procarbazine; PSK® polysaccharide complex (JHS Natural Products, Eugene, Oreg.); razoxane; rhizoxin; sizofiran; spirogermanium; tenuazonic acid; triaziquone; 2,2′,2′′-trichlorotriethylamine; trichothecenes (especially T-2 toxin, verracurin A, roridin A and anguidine); urethan; vindesine (ELDISINE®, FILDESIN®); dacarbazine; mannomustine; mitobronitol; mitolactol; pipobroman; gacytosine; arabinoside (“Ara-C”); thiotepa; taxoids, e.g., TAXOL® paclitaxel (Bristol-Myers Squibb Oncology, Princeton, N.J.), ABRAXANE® Cremophor-free, albumin-engineered nanoparticle formulation of paclitaxel (American Pharmaceutical Partners, Schaumberg, EL), and TAXOTERE® doxetaxel (Rhone-Poulenc Rorer, Antony, France); chloranbucil; gemcitabine (GEMZAR®); 6-thioguanine; mercaptopurine; methotrexate; platinum analogs such as cisplatin and carboplatin; vinblastine (VELBAN®); platinum; etoposide (VP-16); ifosfamide; mitoxantrone; vincristine (ONCOVIN®); oxaliplatin; leucovovin; vinorelbine (NAVELBINE®); novantrone; edatrexate; daunomycin; aminopterin; ibandronate; topoisomerase inhibitor RFS 2000; difluorometlhylomithine (DMFO); retinoids such as retinoic acid; capecitabine (XELODA®); pharmaceutically acceptable salts, acids or derivatives of any of the above; as well as combinations of two or more of the above such as CHOP, an abbreviation for a combined therapy of cyclophosphamide, doxorubicin, vincristine, and prednisolone, and FOLFOX, an abbreviation for a treatment regimen with oxaliplatin (ELOXATINTM) combined with 5-FU and leucovovin.
Also included in this definition are anti-hormonal agents that act to regulate, reduce, block, or inhibit the effects of hormones that can promote the growth of cancer, and are often in the form of systemic, or whole-body treatment. They may be hormones themselves. Examples include anti-estrogens and selective estrogen receptor modulators (SERMs), including, for example, tamoxifen (including NOLVADEX® tamoxifen), EVISTA® raloxifene, droloxifene, 4-hydroxytamoxifen, trioxifene, keoxifene, LY117018, onapristone, and FARESTON® toremifene; anti-progesterones; estrogen receptor down-regulators (ERDs); agents that function to suppress or shut down the ovaries, for example, leutinizing hormone-releasing hormone (LHRH) agonists such as LUPRON® and ELIGARD® leuprolide acetate, goserelin acetate, buserelin acetate and tripterelin; other anti-androgens such as flutamide, nilutamide and bicalutamide; and aromatase inhibitors that inhibit the enzyme aromatase, which regulates estrogen production in the adrenal glands, such as, for example, 4(5)-imidazoles, aminoglutethimide, MEGASE® megestrol acetate, AROMASIN® exemestane, formestanie, fadrozole, RIVISOR® vorozole, FEMARA® letrozole, and ARIMIDEX® anastrozole. In addition, such definition of chemotherapeutic agents includes bisphosphonates such as clodronate (for example, BONEFOS® or OSTAC®), DIDROCAL® etidronate, NE-58095, ZOMETA® zoledronic acid/zoledronate, FOSAMAX® alendronate, AREDIA® pamidronate, SKELID® tiludronate, or ACTONEL® risedronate; as well as troxacitabine (a 1,3-dioxolane nucleoside cytosine analog); antisense oligonucleotides, particularly those that inhibit expression of genes in signaling pathways implicated in abherant cell proliferation, such as, for example, PKC-alpha, Raf, H-Ras, and epidermal growth factor receptor (EGF-R); vaccines such as THERATOPE® vaccine and gene therapy vaccines, for example, ALLOVECTIN® vaccine, LEUVECTIN® vaccine, and VAXID® vaccine; LURTOTECAN® topoisomerase 1 inhibitor; ABARELIX® GnRH antagonist; lapatinib ditosylate (an ErbB-2 and EGFR dual tyrosine kinase small-molecule inhibitor also known as GW572016); and pharmaceutically acceptable salts, acids or derivatives of any of the above.
A “growth inhibitory agent” when used herein refers to a compound or composition which inhibits growth of a cell either in vitro or in vivo. Thus, the growth inhibitory agent may be one which significantly reduces the percentage of cells in S phase. Examples of growth inhibitory agents include agents that block cell cycle progression (at a place other than S phase), such as agents that induce G1 arrest and M-phase arrest. Classical M-phase blockers include the vincas (e.g., vincristine and vinblastine), taxanes, and topoisomerase II inhibitors such as doxorubicin, epirubicin, daunorubicin, etoposide, and bleomycin. The agents that arrest G1 also spill over into S-phase arrest, for example, DNA alkylating agents such as tamoxifen, prednisone, dacarbazine, mechlorethamine, cisplatin, methotrexate, 5-fluorouracil, and ara-C. Further information can be found in The Molecular Basis of Cancer, Mendelsohn and Israel, eds., Chapter 1, entitled “Cell cycle regulation, oncogenes, and antineoplastic drugs” by Murakami et al. (WB Saunders: Philadelphia, 1995), especially p. 13. The taxanes (paclitaxel and docetaxel) are anticancer drugs both derived from the yew tree. Docetaxel (TAXOTERE®, Rhone-Poulenc Rorer), derived from the European yew, is a semisynthetic analogue of paclitaxel (TAXOL®, Bristol-Myers Squibb). Paclitaxel and docetaxel promote the assembly of microtubules from tubulin dimers and stabilize microtubules by preventing depolymerization, which results in the inhibition of mitosis in cells.
“Anti-cancer therapy” as used herein refers to a treatment that reduces or inhibits cancer in a subject. Examples of anti-cancer therapy include cytotoxic radiotherapy as well as the administration of a therapeutically effective amount of a cytotoxic agent, a chemotherapeutic agent, a growth inhibitory agent, a cancer vaccine, an angiogenesis inhibitor, a prodrug, a cytokine, a cytokine antagonist, a corticosteroid, an immunosuppressive agent, an anti-emetic, an antibody or antibody fragment, or an analgesic to the subject.
“Target molecule” refers to a molecule which can bind to a protein complex of this invention (preferably with affinity higher than 1 μM Kd according to Scatchard analysis). Examples of target molecules include, but are not limited to, serum soluble proteins and their receptors, such as cytokines and cytokine receptors, adhesins, growth factors and their receptors, hormones, viral particles (e.g., RSVF protein, CMV, StaphA, influenza, hepatitis C virus), micoorganisms (e.g., bacterial cell proteins, fungal cells), adhesins, CD proteins and their receptors.
A “subject” is a vertebrate, such as a mammal, e.g., a human. Mammals include, but are not limited to, farm animals (such as cows), sport animals, pets (such as cats, dogs and horses), primates, mice, and rats.
Commercially available reagents referred to in the Examples were used according to manufacturer's instructions unless otherwise indicated. The source of those cells identified in the following Examples, and throughout the specification, by ATCC accession numbers is the American Type Culture Collection, Manassas, Va. Unless otherwise noted, the present invention uses standard procedures of recombinant DNA technology, such as those described hereinabove and in the following textbooks: Sambrook et al., supra; Ausubel et al., Current Protocols in Molecular Biology (Green Publishing Associates and Wiley Interscience, NY, 1989); Innis et al., PCR Protocols: A Guide to Methods and Applications (Academic Press, Inc., NY, 1990); Harlow et al., Antibodies: A Laboratory Manual (Cold Spring Harbor Press, Cold Spring Harbor, 1988); Gait, Oligonucleotide Synthesis (IRL Press, Oxford, 1984); Freshney, Animal Cell Culture, 1987; Coligan et al., Current Protocols in Immunology, 1991.
Throughout this specification and claims, the word “comprise,” or variations such as “comprises” or “comprising,” will be understood to imply the inclusion of a stated integer or group of integers but not the exclusion of any other integer or group of integers.
The term “prodrug” as used in this application refers to a precursor or derivative form of a pharmaceutically active substance that may optionally be less cytotoxic to tumor cells compared to the parent drug and is capable of being enzymatically activated or converted into the more active parent form. See, e.g., Wilman, “Prodrugs in Cancer Chemotherapy” Biochemical Society Transactions, 14, pp. 375-382, 615th Meeting Belfast (1986) and Stella et al., “Prodrugs: A Chemical Approach to Targeted Drug Delivery,” Directed Drug Delivery, Borchardt et al., (ed.), pp. 247-267, Humana Press (1985). Prodrugs include, but are not limited to, phosphate-containing prodrugs, thiophosphate-containing prodrugs, sulfate-containing prodrugs, peptide-containing prodrugs, D-amino acid-modified prodrugs, glycosylated prodrugs, beta-lactam-containing prodrugs, optionally substituted phenoxyacetamide-containing prodrugs or optionally substituted phenylacetamide-containing prodrugs, 5-fluorocytosine and other 5-fluorouridine prodrugs which can be converted into the more active cytotoxic free drug. Examples of cytotoxic drugs that can be derivatized into a prodrug form for use in this invention include, but are not limited to, those chemotherapeutic agents described above.
The term “cytokine” is a generic term for proteins released by one cell population which act on another cell as intercellular mediators. Examples of such cytokines are lymphokines, monokines, and traditional polypeptide hormones. Included among the cytokines are growth hormone such as human growth hormone (HGH), N-methionyl human growth hormone, and bovine growth hormone; parathyroid hormone; thyroxine; insulin; proinsulin; relaxin; prorelaxin; glycoprotein hormones such as follicle stimulating hormone (FSH), thyroid stimulating hormone (TSH), and luteinizing hormone (LH); epidermal growth factor (EGF); hepatic growth factor; fibroblast growth factor (FGF); prolactin; placental lactogen; tumor necrosis factor-alpha and -beta; mullerian-inhibiting substance; mouse gonadotropin-associated peptide; inhibin; activin; vascular endothelial growth factor; integrin; thrombopoietin (TPO); nerve growth factors such as NGF-α; platelet-growth factor; transforming growth factors (TGFs) such as TGF-alpha and TGF-β; insulin-like growth factor-I and -II; erythropoietin (EPO); osteoinductive factors; interferons such as interferon-alpha, -beta and -gamma colony stimulating factors (CSFs) such as macrophage-CSF (M-CSF); granulocyte-macrophage-CSF (GM-CSF); and granulocyte-CSF (G-CSF); interleukins (ILs) such as IL-1, IL-1α, IL-1β, IL-2, IL-3, IL-4, IL-5, IL-6, IL-7, IL-8, IL-9, IL-10, IL-11, IL-12; IL-18 a tumor necrosis factor such as TNF-α or TNF-β; and other polypeptide factors including LIF and kit ligand (KL). As used herein, the term cytokine includes proteins from natural sources or from recombinant cell culture and biologically active equivalents of the native sequence cytokines.
By “cytokine antagonist” is meant a molecule that partially or fully blocks, inhibits, or neutralizes a biological activity of at least one cytokine. For example, the cytokine antagonists may inhibit cytokine activity by inhibiting cytokine expression and/or secretion, or by binding to a cytokine or to a cytokine receptor. Cytokine antagonists include antibodies, heteromultimers, synthetic or native-sequence peptides, immunoadhesins, and small-molecule antagonists that bind to a cytokine or cytokine receptor. The cytokine antagonist is optionally conjugated with or fused to a cytotoxic agent.
The term “immunosuppressive agent” as used herein refers to substances that act to suppress or mask the immune system of the subject being treated. This includes substances that suppress cytokine production, downregulate or suppress self-antigen expression, or mask the MHC antigens. Examples of immunosuppressive agents include 2-amino-6-aryl-5-substituted pyrimidines (see U.S. Pat. No. 4,665,077); mycophenolate mofetil such as CELLCEPT®; azathioprine (IMURAN®, AZASAN®/6-mercaptopurine; bromocryptine; danazol; dapsone; glutaraldehyde (which masks the MHC antigens, as described in U.S. Pat. No. 4,120,649); anti-idiotypic antibodies for MHC antigens and MHC fragments; cyclosporin A; steroids such as corticosteroids and glucocorticosteroids, e.g., prednisone, prednisolone such as PEDIAPRED® (prednisolone sodium phosphate) or ORAPRED® (prednisolone sodium phosphate oral solution), methylprednisolone, and dexamethasone; methotrexate (oral or subcutaneous) (RHEUMATREX®, TREXALLTM); hydroxycloroquine/chloroquine; sulfasalazine; leflunomide; cytokine or cytokine receptor antagonists including anti-interferon-γ, -β, or -α antibodies, anti-tumor necrosis factor-α antibodies (infliximab or adalimumab), anti-TNFα immunoadhesin (ENBREL®, etanercept), anti-tumor necrosis factor-β antibodies, anti-interleukin-2 antibodies and anti-IL-2 receptor antibodies; anti-LFA-1 antibodies, including anti-CD11a and anti-CD18 antibodies; anti-L3T4 antibodies; heterologous anti-lymphocyte globulin; polyclonal or pan-T antibodies, or monoclonal anti-CD3 or anti-CD4/CD4a antibodies; soluble peptide containing a LFA-3 binding domain (WO 90/08187); streptokinase; TGF-β; streptodornase; RNA or DNA from the host; FK506; RS-61443; deoxyspergualin; rapamycin; T-cell receptor (Cohen et al., U.S. Pat. No. 5,114,721); T-cell receptor fragments (Offner et al. Science 251: 430-432 (1991); WO 90/11294; Ianeway, Nature 341:482 (1989); and WO 91/01133); T cell receptor antibodies (EP 340,109) such as T10B9; cyclophosphamide (CYTOXAN®); dapsone; penicillamine (CUPRIMINE®); plasma exchange; or intravenous immunoglobulin (IVIG). These may be used alone or in combination with each other, particularly combinations of steroid and another immunosuppressive agent or such combinations followed by a maintenance dose with a non-steroid agent to reduce the need for steroids.
An “analgesic” refers to a drug that acts to inhibit or suppress pain in a subject. Exemplary analgesics include non-steroidal anti-inflammatory drugs (NSAIDs) including ibuprofen (MOTRIN®), naproxen (NAPROSYN®), acetylsalicylic acid, indomethacin, sulindac, and tolmetin, including salts and derivatives thereof, as well as various other medications used to reduce the stabbing pains that may occur, including anticonvulsants (gabapentin, phenyloin, carbamazepine) or tricyclic antidepressants. Specific examples include acetaminophen, aspirin, amitriptyline (ELAVIL®), carbamazepine (TEGRETOL®), phenyltoin (DILANTIN®), gabapentin (NEURONTIN®), (E)-N-Vanillyl-8-methyl-6-noneamid (CAPSAICIN®), or a nerve blocker.
“Corticosteroid” refers to any one of several synthetic or naturally occurring substances with the general chemical structure of steroids that mimic or augment the effects of the naturally occurring corticosteroids. Examples of synthetic corticosteroids include prednisone, prednisolone (including methylprednisolone), dexamethasone triamcinolone, and betamethasone.
A “cancer vaccine,” as used herein is a composition that stimulates an immune response in a subject against a cancer. Cancer vaccines typically consist of a source of cancer-associated material or cells (antigen) that may be autologous (from self) or allogenic (from others) to the subject, along with other components (e.g., adjuvants) to further stimulate and boost the immune response against the antigen. Cancer vaccines can result in stimulating the immune system of the subject to produce antibodies to one or several specific antigens, and/or to produce killer T cells to attack cancer cells that have those antigens.
An “anti-emetic” is a compound that reduces or prevents nausea in a subject. Anti-emetic compounds include, for example, neurokinin-1 receptor antagonists, 5HT3 receptor antagonists (such as ondansetron, granisetron, tropisetron, and zatisetron), GABAB receptor agonists, such as baclofen, a corticosteroid such as dexamethasone, KENALOG®, ARISTOCORT®, or NASALIDE®, an antidopaminergic, phenothiazines (for example prochlorperazine, fluphenazine, thioridazine and mesoridazine), dronabinol, metroclopramide, domperidone, haloperidol, cyclizine, lorazepam, prochlorperazine, and levomepromazine.
II. Construction of Single-Chain and Multi-Chain Tethered Antibodies and Other Heteromultimers
Heteromultimers, including monospecific and multispecific (e.g., bispecific) antibodies, described herein may be constructed by using one or more tethers.
Use of tethers enables the construction of a relatively pure population of heteromultimers that have different heavy and/or light chains within a single heteromultimer. In particular, as described above, antibodies typically include two identical heavy chains, each of which is paired with one of two identical light chains. Use of the tether technology of the invention enables different antibody heavy chains to dimerize with each other in the formation of a single heteromultimeric antibody formed by a single polypeptide chain. The tethers can connect a first heavy chain to a second heavy chain, typically by linking a CH3 domain of a first heavy chain to a VL domain of a light chain, which itself is linked to a second heavy chain by a second tether. In a heteromultimeric single-chain antibody, a third tether may link a second light chain directly to the first heavy chain, thus resulting in a heteromultimer that includes two different heavy chains, which may each be paired with its cognate light chain. In other embodiments, the tethers can connect a first heavy chain to a second heavy chain directly by linking the C-terminus of a first heavy chain constant domain with the N-terminus of a second heavy chain variable domain. Each pair of heavy and light chains within such a heteromultimer may have different binding specificity due to the presence of the different heavy and light chain cognate pairs, and thus the heteromultimer can be considered as a multispecific antibody. Use of the tether technology of the invention also enables the formation of a heteromultimer (e.g., a multi-chain antibody) that may include the association of three polypeptide chains, wherein one polypeptide chain includes two HCs connected directly together by an HD tether as described above, and the other two polypeptide chains are identical and form LCs which associate with the two HCs to form two functional HC/LC cognate pairs. In other embodiments, use of an HD and CLH tether enable the formation of a multi-specific antibody by two polypeptide chains, wherein one polypeptide chain forms a first LC and the other polypeptide chain includes two HCs and a second LC, which associates with the first HC via an HD tether and with the second HC via a CLH tether. In other embodiments, use of an HD and CLH tether enable the formation of a multi-specific antibody with two polypeptide chains, wherein the first polypeptide chain includes a first LC and two HCs, where one HC interacts with the first LC directly via a CLH tether and with the second HC directly via an HD tether, and the second polypeptide forms a second LC which associates with the HC that is not linked to the first LC. In other embodiments, use of the tether technology of the invention enables the formation of a heteromultimer in which an immunoadhesin associates with a half-antibody via an HD tether. The tether technology can be exploited alone or in combination with knob-into-hole (“KnH”) technology to engineer the heteromultimers of the invention. Heteromultimers including tethers, with or without KnH technology, as well as recombinant heteromultimer production are described in detail below.
A. Heteromultimer Tethers
The invention provides heteromultimers constructed using tethers. For example, a heteromultimer can have a tether that links the C-terminus of an immunoglobulin heavy chain constant domain with the N-terminus of an immunoglobulin heavy chain variable domain. In other embodiments, the heteromultimer further includes one or more (e.g., two) additional tethers to aid in proper association of the heavy chain with its cognate light chain (i.e., association of the heavy chain with the light chain to which it is tethered). Such a heteromultimer can be constructed with or without an additional heterodimerizing domain, such as one created with KnH technology.
As depicted in the schematic diagram in FIG. 1, an exemplary heteromultimer is a multispecific single-chain antibody that contains two different heavy chains (HC1 and HC2) and two different light chains (LC1 and LC2), where HC1 and LC1 form a first cognate pair and HC2 and LC2 form a second cognate pair. In the exemplary heteromultimer, three tethers exist. A first tether (HD tether) links HC1 with LC2, and a second tether (CLH tether1) and third tether (CLH tether2) link LC1 with HC1 and LC2 with HC2, respectively. The tethers aid in bringing the two different heavy chains and their cognate light chains together, thereby generating a heteromultimeric single-chain antibody with multispecificity.
In a particular embodiment, the HD tether is long enough to span the distance between the C-terminus of HC1 and the N-terminus of LC2 (or, in the absence of LC2, HC2) in the assembled heteromultimer (FIG. 1) to allow for proper association of the first and second heavy chains, but is short enough to prevent intermolecular homodimerization of HC1 and/or HC2. The distances between the C-terminus of HC1 and the N-terminus of LC2 (or, in the absence of LC2, HC2) can differ between assembled heteromultimers, and thus the length of HD tethers can also vary between heteromultimers. In general, HD tethers of 15-100 amino acids are effective, as are HD tethers of 20-40 amino acids, 25-40 amino acids, and 30-40 amino acids. In particular embodiments, an HD tether is between 36 and 39 amino acids in length (e.g., 36, 37, 38, or 39 amino acids in length).
In a particular embodiment, the CLH tethers are each long enough to span the distance between the N-terminus of a heavy chain and the C-terminus of its cognate light chain in the assembled heteromultimer (FIG. 1) to allow for the proper light chain/heavy chain association, but are short enough to prevent unwanted intrachain association (i.e., the association of a light chain with a non-cognate heavy chain to which it is not directly tethered). The distances between the N-terminus of a heavy chain and the C-terminus of its cognate light chain can differ between antibodies, or even within the antibody itself (i.e., the distance between the N-terminus of a heavy chain and the C-terminus of a cognate light chain of the first cognate pair is different from that of the second cognate pair). Accordingly, the lengths of the HD tethers can vary between heteromultimers of the invention, and the length of CLH tether1 may not equal the length of CLH tether2 within the same heteromultimer. In general, CLH tethers of 10-80 amino acids are effective, as are CLH tethers of 20-40 amino acids, 25-40 amino acids, 30-40 amino acids, and 30-35 amino acids (e.g., 30, 31, 32, 33, 34, or 35 amino acids). Heteromultimers of the invention may have two tethers (CLH tether1 and CLH tether2) joining a first light chain with a first heavy chain and a second light chain with a second heavy chain.
An HD or CLH tether may remain flexible and not form secondary structures, and for this purpose tethers containing glycine (G) and serine (S) residues can be used. Tethers may consist solely of G and S residues, but also may include other residues, as long as the tethers remain flexible to allow for the intrachain associations described above. In particular embodiments, the HD or CLH tethers contain GGS repeats (FIG. 2). In some embodiments, the HD tether contains at least 1 GGS repeat. An exemplary HD tether described herein contains 8-9 GGS repeats (SEQ ID NO: 19) and endopeptidase cleavage sites (e.g., furin and Lys-C cleavage sites) at its N- and C-termini (FIG. 2). In another embodiment, the CLH tethers contain at least 1 GGS repeat. An exemplary CLH tether described herein contains 6 GGS repeats (SEQ ID NO: 20) and endopeptidase cleavage sites (e.g., furin cleavage sites) at its N- and C-termini (FIG. 2).
B. Cleavage of Heteromultimer Tethers
Once heteromultimers of the invention are assembled, the tethers may no longer be required and can, in some embodiments, be cleaved from the heteromultimers. Cleavage sites found in or immediately adjacent to the tethers, but either not present in the non-tether heteromultimer component sequences or not accessible for cleavage under the conditions used, can be used to remove the tethers.
FIG. 2 illustrates the location of exemplary cleavage sites in the three tethers that can exist within an exemplary heteromultimeric single-chain antibody. In general, cleavage sites in the tethers are located at or close to the C- and N-termini of the tether sequences or within the antibody sequence at or close to the site where the antibody and tether are joined. If one or more of the tethers are cleaved using Lys-C endopeptidase (e.g., at a Lysine residue at the C-terminus of the constant heavy chain), the sequence of the heteromultimer may need to be modified to remove Lys-C endopeptidase cleavage sites. An example of such a modification is the mutation of a lysine in the hinge region to an alanine (e.g., K222A, Kabat numbering system; K222A, EU numbering system in exemplary heteromultimers described herein). Modifications of other cleavage sites may be required and made in a similar manner when different cleavage agents are selected for use in the invention.
Cleavage of amino acid sequences at particular sites is standard in the art and can involve enzymatic cleavage, chemical cleavage, or auto-processing. For example, a tether may be cleaved from a protein using an endopeptidase. Exemplary endopeptidases include, without limitation, furin, urokinase, Lys-C, Asp-N, Arg-C, V8, Glu-C, thrombin, tissue plasminogen activator (tPa), genenase (a variant of subtilisin BPN′ protease), Factor Xa, TEV (tobacco etch virus cysteine protease), enterokinase, HRV C3 (human rhinovirus C3 protease), kininogenase, chymotrypsin, trypsin, pepsin, and papain, all of which are commercially available (e.g., from Boehringer Mannheim, Thermo Scientific, or New England Biolabs). Subtilisin-like proprotein convertases such as furin (PC1), PC2, and PC3, (Steiner (1991) in Peptide Biosynthesis and Processing (Fricker ed.) pp. 1-16, CRC Press, Boca Raton, Fla.; Muller et al., JBC 275:39213-39222, (2000)) and N-arginine dibasic convertases (Chow et al., JBC 275:19545-19551 (2000)) cleave at dibasic sites. Lys-C cleaves at the carboxyl side of lysine residues, V8 and Glu-C cleave at the carboxyl side of Glutamate residues, Arg-C cleaves at the carboxyl side of arginine residues, Asp-N cleaves at the amino side of aspartate residues, chymotropsin cleaves at the carboxyl side of tyrosine, phenylalanine, tryptophan, and leucine residues, and trypsin cleaves at the carboxyl side of arginine and lysine residues. TEV cleaves the amino acid sequence GluAsnLeuTyrPheGlnGly (SEQ ID NO: 4) between the “Gln” and “Gly” residues. Use of such enzymes is standard in the art and protocols are available from the manufacturers. FIG. 3A shows an exemplary heteromultimeric single-chain antibody after cleavage with furin.
Alternatively a tether may be cleaved from a protein using a chemical, such as hydroxylamine. Hydroxylamine cleaves asparagine-glycine peptide bonds. If hydroxylamine is used to cleave the tether from a protein, several glycine or asparagine residues in the protein may need to be mutated to avoid fragmenting the protein.
Numerous other chemicals that cleave peptide bonds are known in the art. For example, N-chlorosuccinimide cleaves at the C-terminal side of tryptophan residues (Shechter et al., Biochemistry 15:5071-5075 (1976)). N-bromosuccinimide and cyanogen bromide also cleave at the C-terminal side of tryptophan residues. In addition, 2-nitrothiocyanobenzoic acid or organophosphines may be used to cleave a protein at the N-terminal side of a Cysteine residue (see, e.g., EP 0339217).
Proteins are also known to auto-process. For example, the Hedgehog protein is processed at a GlyAspTrpAsnAlaArgTrpCysPhe cleavage site (SEQ ID NO: 5) by a proteolytic activity within the protein. An autoproteolytic cleavage site may also be included in a linker or tether sequence.
Following endopeptidase cleavage, the heteromultimers of the invention can be further processed by one or more exopeptidases either before or after purification of the heteromultimer. FIG. 3B shows a heteromultimeric single-chain antibody after purification and furin, Lys-C, and exopeptidase (e.g., Carboxypeptidase B) treatment. Following furin treatment, the HD tether still attached to the CH31 domain of the heteromultimer is removed by Lys-C treatment. The residual furin recognition sequences attached to the CL1 and CL2 domains are removed by treatment with an exopeptidase (e.g., Carboxypeptidase B).
C. Knob-into-Hole Technology
The heteromultimers of the invention may additionally include a heterodimerization domain using knob-into-hole (KnH) technology (see, e.g., U.S. Pat. No. 5,731,168, which is incorporated herein by reference in its entirety), which would engineer an interface between the two different antibody heavy chains to promote their association. In general, the method involves introducing a “protuberance” at the interface of a first heavy chain and a corresponding “cavity” in the interface of a second heavy chain, such that the protuberance can be positioned in the cavity so as to further promote heterodimerization of the heavy chains.
A first preferred interface includes at least part of the CH3 domain of a first heavy chain (CH3′) constant domain and at least part of the CH3 domain of a second heavy chain (CH32) constant domain. Protuberances can be constructed by replacing small amino acid side chains from the interface of a first domain (e.g., CH31) with larger side chains (e.g., tyrosine or tryptophan). Compensatory cavities of identical or similar size to the protuberances are optionally created on the interface of a second domain (e.g., CH32) by replacing large amino acid side chains with smaller ones (e.g., alanine or threonine). A second preferred interface includes at least part of the CL domain of a light chain and at the CH1 domain of a heavy chain, at which a protuberance-cavity interaction can be constructed as described above. Where a suitably positioned and dimensioned protuberance or cavity exists at the interface of either the first or second domain, it is only necessary to engineer a corresponding cavity or protuberance, respectively, at the adjacent interface.
D. Monospecific or Multispecific Heteromultimers Having Different Binding Properties
It should be understood that the variable domains of such heteromultimers can be derived from several methods. For example, the variable domains of the heteromultimers of this invention can be the same as existing antibodies known in the art.
As described above, an HD tether of the invention may be used to generate a heteromultimer having varied binding properties. In some embodiments, the invention may be used to generate a single-chain monospecific antibody that includes two half-antibodies with different binding affinities for the same target epitope. In another embodiment, the invention may be used to generate a single-chain multispecific antibody (an antibody that binds to at least two antigens or to at least two epitopes on the same antigen). Typically, in naturally occurring IgG antibodies, the variable regions of each pair of heavy and light chains in the antibody are identical. Use of tethers according to the present invention enables the two heavy chains within an antibody to be different, resulting in antibodies having antigen-binding domains with different binding specificities (e.g., epitope targets) or antigen-binding domains with the same binding specificities but different binding affinities. In some embodiments, the HD tether promotes association between two different heavy chains encoded within a single polypeptide chain to yield heavy-chain only, single-chain antibodies. In other embodiments, CLH tethers promote the association between a heavy chain and its cognate light chain. In some embodiments, the association between one of the heavy chains and its cognate light chain is established without a CLH tether to generate a heteromultimer of the invention. Optionally, one or more of the tethers include endopeptidase cleavage sites (e.g., furin and Lys-C cleavage sites), which can be cleaved so that the one or more tethers are removed from the heteromultimer after assembly. Optionally, the heteromultimer of this invention further includes one or more protuberance-cavity interfaces generated using KnH technology.
As depicted in FIG. 1, the exemplary bispecific heteromultimer (in this case, bispecific antibody) described above contains an HD tether and two CLH tethers, which may each include two furin cleavage sites at their N- and C-termini. Optionally, the exemplary heteromultimer can use KnH technology to further promote the association of HC1 and HC2.
Heteromultimers for which cleavage of tethers is anticipated should contain within its sequence no cleavage sites for the endopeptidase(s) used to cleave tethers or, if there are cleavage sites within the non-tether sequence of the heteromultimer, the cleavage sites should not be cleaved under the conditions used, unless cleavage of the heteromultimer is also intended. The sequence of a heteromultimer can be scanned to determine whether there are any cleavage sites (e.g., a furin or a Lys-C endopeptidase cleavage site) in the heavy or light chain sequences of the heteromultimer that would need to be removed to avoid cleavage of the heteromultimer itself upon removal of the tethers.
Single-chain monospecific or multispecific heteromultimers (e.g., antibodies) may be constructed using the methods described herein where the two different heavy chains of the heteromultimer are connected directly to one another by the HD tether. In one embodiment, the single-chain, heavy chain-only monospecific or multispecific heteromultimer may additionally lack CH1 domains (the VH domains are directly connected to at least one CH domain, optionally by hinges). In another embodiment, the single-chain monospecific or multispecific heteromultimer heavy chains lack CH1 domains, but associate with their corresponding light chains, which lack CL domains, via CLH tethers. Such heteromultimers can be used to bring two different antigens together or to associate B and T cells. In yet another embodiment, tethers may be utilized to associate a half-antibody with an immunoadhesin.
Further, the invention includes heteromultimers with monospecificity or multispecificity. In one embodiment, a first heavy chain, linked to its cognate light chain by a CLH tether, associates with a second heavy chain, whose cognate light chain associates with it independently of a tether.
E. Heteromultimers Having Different Effector Functions
In some embodiments, heteromultimers (e.g., single-chain or multi-chain antibodies, or antibody-immunoadhesin complexes) of the invention constructed using the methods described herein may include a CH2 domain mutation, allowing for altered effector function. Typically, the CH2 domain mutation is a mutation at N297 that may result in the heteromultimer having an altered glycosylation state. In certain embodiments, the N297 mutation is an N297A substitution. Altered effector functions include, but are not limited to, C1q binding and complement dependent cytotoxicity, Fc receptor binding, antibody-dependent cell-mediated cytotoxicity, phagocytosis, down regulation of cell surface receptors (e.g., B cell receptor), and B cell activation.
F. Conjugated Protein Complexes
As described in detail below, the HD tether of the invention may also be used to generate protein complexes such heteromultimers (e.g., monospecific, bispecific, multispecific, single- or multi-chain antibodies) in which a constant region is modified by conjugation to a cytotoxic agent. For instance, the HD tether enables the construction of heteromultimers where one of the heavy chain constant regions (HC1 or HC2) contains a modification that allows for conjugation to a cytotoxic agent, while the other heavy chain constant region does not. In one example, HC1 is conjugated to a cytotoxic agent while HC2 is not. A schematic diagram illustrating an example of a conjugated heteromultimer of the invention is shown in FIG. 4. The exemplary heteromultimeric single-chain antibody includes two full-length heavy chains and cognate light chains, as well as the HD and CLH tethers described above. As indicated in FIG. 4, one of the heavy chains has been conjugated to a cytotoxic agent (e.g., a toxin or an antibiotic). Similarly, in an alternative heteromultimer construct, one of the light chain constant regions may be conjugated to a cytotoxic agent, while the other light chain constant region is not (e.g., LC1 is conjugated to a cytotoxic agent and LC2 is not). As depicted in FIG. 5A, the conjugated protein complex may be a multi-chain antibody of the invention. Conjugation of a cytotoxic agent is not limited to the specific multi-chain antibody depicted in FIG. 5A. Multi-chain antibodies, such as those depicted in FIG. 5B and FIG. 5C, as well as immunoadhesin-antibody heteromultimers may also be conjugated at a constant region.
In one particular example, a constant region of the heteromultimer may be modified to introduce electrophilic moieties which can react with nucleophilic substituents on a linker reagent used to conjugate the cytotoxic agent to the heteromultimer or on the cytotoxic agent itself. The sugars of glycosylated antibodies may be oxidized, e.g., with periodate oxidizing reagents, to form aldehyde or ketone groups which may react with the amine group of linker reagents or a cytotoxic agent. The resulting imine Schiff base groups may form a stable linkage, or may be reduced, e.g., by borohydride reagents, to form stable amine linkages. Nucleophilic groups on a cytotoxic agent include, but are not limited to, amine, thiol, hydroxyl, hydrazide, oxime, hydrazine, thiosemicarbazone, hydrazine carboxylate, and arylhydrazide groups capable of reacting to form covalent bonds with electrophilic groups on antibody regions and linker reagents including: (i) active esters such as NHS esters, HOBt esters, haloformates, and acid halides; (ii) alkyl and benzyl halides such as haloacetamides; and (iii) aldehydes, ketones, carboxyl, and maleimide groups.
G. Other Protein Features
Heteromultimers according to the invention can include sequences from any source, including human or murine sources, or combinations thereof. The sequences of certain portions of the proteins (e.g., the hypervariable regions) can also be artificial sequences, such as sequences identified by screening a library (e.g., a phage display library) including random sequences.
In the case of heteromultimers including sequences from different sources, the heteromultimers can be “chimeric” heteromultimers in which a portion of the heavy and/or light chain is identical with or homologous to corresponding sequences in antibodies derived from a particular species or belonging to a particular antibody class or subclass, while the remainder of the chain(s) is identical with or homologous to corresponding sequences in antibodies derived from another species or belonging to another antibody class or subclass, as well as fragments of such antibodies, provided that they exhibit the desired biological activity (U.S. Pat. No. 4,816,567; and Morrison et al., Proc. Natl. Acad. Sci. USA 81:6851-6855 (1984)). Such chimeric heteromultimers may, for example, include murine variable regions (or portions thereof) and human constant regions.
The chimeric single-chain heteromultimers can optionally also be “humanized” single-chain heteromultimers (e.g., single-chain antibodies), which contain minimal sequence derived from the non-human antibody. Humanized heteromultimers typically are derived from human antibodies (recipient antibody) in which residues from a hypervariable region of the recipient are replaced by residues from a hypervariable region of a non-human species (donor antibody) such as mouse, rat, rabbit or non-human primate having the desired specificity, affinity, and capability. In some instances, framework region (FR) residues of the human immunoglobulin are replaced by corresponding non-human residues. Furthermore, humanized heteromultimers can comprise residues that are not found in the recipient antibody or in the donor antibody. These modifications are made to further refine heteromultimer performance. In general, the humanized heteromultimer will comprise substantially all of at least one, and typically two, variable domains, in which all or substantially all of the hypervariable loops correspond to those of a non-human immunoglobulin, and all or substantially all of the FRs are those of a human immunoglobulin sequence. The humanized heteromultimer optionally also will comprise at least a portion of an immunoglobulin constant region (Fc), typically that of a human immunoglobulin. For further details, see Jones et al., Nature 321:522-525 (1986); Riechmann et al., Nature 332:323-329 (1988); and Presta, Curr. Op. Struct. Biol. 2:593-596 (1992).
In more detail, a humanized heteromultimer can have one or more amino acid residues introduced into it from a source that is non-human. These non-human amino acid residues are often referred to as “import” residues, which are typically taken from an “import” variable domain. Humanization can be essentially performed following the method of Winter and co-workers (Jones et al., Nature 321:522-525 (1986); Riechmann et al., Nature 332:323-327 (1988); Verhoeyen et al., Science 239:1534-1536 (1988)), by substituting rodent CDRs or CDR sequences for the corresponding sequences of a human antibody. Accordingly, such “humanized” heteromultimers are chimeric antibodies (U.S. Pat. No. 4,816,567) wherein substantially less than an intact human variable domain has been substituted by the corresponding sequence from a non-human species. In practice, humanized heteromultimers are typically human antibodies in which some CDR residues and possibly some FR residues are substituted by residues from analogous sites in rodent antibodies.
The choice of human variable domains, both light and heavy, to be used in making the humanized heteromultimers is very important to reduce antigenicity. According to the so-called “best-fit” method, the sequence of the variable domain of a rodent antibody is screened against the entire library of known human variable-domain sequences. The human sequence that is closest to that of the rodent is then accepted as the human framework (FR) for the humanized heteromultimer (Sims et al., J. Immunol. 151:2296 (1993); Chothia et al., J. Mol. Biol. 196:901 (1987)). Another method uses a particular framework derived from the consensus sequence of all human antibodies of a particular subgroup of light or heavy chains. The same framework may be used for several different humanized heteromultimers (Carter et al., Proc. Natl. Acad. Sci. USA 89:4285 (1992); Presta et al., J. Immnol. 151:2623 (1993)).
It is further important that heteromultimers be humanized with retention of high affinity for the one or more target antigens and other favorable biological properties. To achieve this goal, according to an exemplary method, humanized heteromultimers are prepared by a process of analysis of the parental sequences and various conceptual humanized products using three-dimensional models of the parental and humanized sequences. Three-dimensional immunoglobulin models are commonly available and are familiar to those skilled in the art. Computer programs are available that illustrate and display probable three-dimensional conformational structures of selected candidate immunoglobulin sequences. Inspection of these displays permits analysis of the likely role of the residues in the functioning of the candidate immunoglobulin sequence, i.e., the analysis of residues that influence the ability of the candidate immunoglobulin to bind its antigen. In this way, FR residues can be selected and combined from the recipient and import sequences so that the desired heteromultimer characteristic, such as increased affinity for the target antigen(s), is achieved. In general, the CDR residues are directly and most substantially involved in influencing antigen binding.
III. Vectors, Host Cells, and Recombinant Methods
For recombinant production of a heteromultimer of the invention, the nucleic acid encoding it is isolated and inserted into a replicable vector for further cloning (amplification of the DNA) or for expression. DNA encoding the heteromultimer is readily isolated and sequenced using conventional procedures (e.g., by using oligonucleotide probes that are capable of binding specifically to genes encoding the heavy and light chains of the heteromultimer). Many vectors are available. The choice of vector depends in part on the host cell to be used. Generally, preferred host cells are of either prokaryotic or eukaryotic (generally mammalian, but also including fungi (e.g., yeast), insect, plant, and nucleated cells from other multicellular organisms) origin. It will be appreciated that constant regions of any isotype can be used for this purpose, including IgG, IgM, IgA, IgD, and IgE constant regions, and that such constant regions can be obtained from any human or animal species.
A. Generating Heteromultimers Using Prokaryotic Host Cells
i. Vector Construction
Polynucleotide sequences encoding polypeptide components of the heteromultimer of the invention can be obtained using standard recombinant techniques. Desired polynucleotide sequences may be isolated and sequenced from antibody producing cells such as hybridoma cells. Alternatively, polynucleotides can be synthesized using nucleotide synthesizer or PCR techniques. Once obtained, sequences encoding the polypeptides are inserted into a recombinant vector capable of replicating and expressing heterologous polynucleotides in prokaryotic hosts. Many vectors that are available and known in the art can be used for the purpose of the present invention. Selection of an appropriate vector will depend mainly on the size of the nucleic acids to be inserted into the vector and the particular host cell to be transformed with the vector. Each vector contains various components, depending on its function (amplification or expression of heterologous polynucleotide, or both) and its compatibility with the particular host cell in which it resides. The vector components generally include, but are not limited to: an origin of replication, a selection marker gene, a promoter, a ribosome binding site (RBS), a signal sequence, the heterologous nucleic acid insert and a transcription termination sequence.
In general, plasmid vectors containing replicon and control sequences which are derived from species compatible with the host cell are used in connection with these hosts. The vector ordinarily carries a replication site, as well as marking sequences which are capable of providing phenotypic selection in transformed cells. For example, E. coli is typically transformed using pBR322, a plasmid derived from an E. coli species. pBR322 contains genes encoding ampicillin (Amp) and tetracycline (Tet) resistance and thus provides easy means for identifying transformed cells. pBR322, its derivatives, or other microbial plasmids or bacteriophage may also contain, or be modified to contain, promoters which can be used by the microbial organism for expression of endogenous proteins. Examples of pBR322 derivatives used for expression of particular heteromultimeric antibodies are described in detail in Carter et al., U.S. Pat. No. 5,648,237.
In addition, phage vectors containing replicon and control sequences that are compatible with the host microorganism can be used as transforming vectors in connection with these hosts. For example, bacteriophage such as λGEM-11TM may be utilized in making a recombinant vector which can be used to transform susceptible host cells such as E. coli LE392.
The expression vector of the invention may comprise two or more promoter-cistron pairs, encoding each of the polypeptide components. A promoter is an untranslated regulatory sequence located upstream (5′) to a cistron that modulates its expression. Prokaryotic promoters typically fall into two classes, inducible and constitutive. An inducible promoter is a promoter that initiates increased levels of transcription of the cistron under its control in response to changes in the culture condition, e.g., the presence or absence of a nutrient or a change in temperature.
A large number of promoters recognized by a variety of potential host cells are well known. The selected promoter can be operably linked to cistron DNA encoding the light or heavy chain by removing the promoter from the source DNA via restriction enzyme digestion and inserting the isolated promoter sequence into the vector of the invention. Both the native promoter sequence and many heterologous promoters may be used to direct amplification and/or expression of the target genes. In some embodiments, heterologous promoters are utilized, as they generally permit greater transcription and higher yields of expressed target gene as compared to the native target polypeptide promoter.
Promoters suitable for use with prokaryotic hosts include the PhoA promoter, the β-galactamase and lactose promoter systems, a tryptophan (trp) promoter system and hybrid promoters such as the tac or the trc promoter. However, other promoters that are functional in bacteria (such as other known bacterial or phage promoters) are suitable as well. Their nucleotide sequences have been published, thereby enabling a skilled worker to ligate them to cistrons encoding the target light and heavy chains (Siebenlist et al., (1980) Cell 20:269) using linkers or adaptors to supply any required restriction sites.
In one aspect of the invention, each cistron within the recombinant vector comprises a secretion signal sequence component that directs translocation of the expressed polypeptides across a membrane. In general, the signal sequence may be a component of the vector, or it may be a part of the target polypeptide DNA that is inserted into the vector. The signal sequence selected for the purpose of this invention should be one that is recognized and processed (i.e., cleaved by a signal peptidase) by the host cell. For prokaryotic host cells that do not recognize and process the signal sequences native to the heterologous polypeptides, the signal sequence is substituted by a prokaryotic signal sequence selected, for example, from the group consisting of the alkaline phosphatase, penicillinase, Ipp, or heat-stable enterotoxin II (STII) leaders, LamB, PhoE, PelB, OmpA, and MBP. In one embodiment of the invention, the signal sequences used in both cistrons of the expression system are STII signal sequences or variants thereof.
In another aspect, the production of the heteromultimers according to the invention can occur in the cytoplasm of the host cell, and therefore does not require the presence of secretion signal sequences within each cistron. In that regard, heteromultimer light and heavy chains are expressed, folded and assembled to form functional heteromultimers within the cytoplasm. Certain host strains (e.g., the E. coli trxB-strains) provide cytoplasm conditions that are favorable for disulfide bond formation, thereby permitting proper folding and assembly of expressed protein subunits (Proba and Pluckthun, Gene, 159:203 (1995)).
Prokaryotic host cells suitable for expressing heteromultimers of the invention include Archaebacteria and Eubacteria, such as Gram-negative or Gram-positive organisms. Examples of useful bacteria include Escherichia (e.g., E. coli), Bacilli (e.g., B. subtilis), Enterobacteria, Pseudomonas species (e.g., P. aeruginosa), Salmonella typhimurium, Serratia marcescans, Klebsiella, Proteus, Shigella, Rhizobia, Vitreoscilla, or Paracoccus. In one embodiment, gram-negative cells are used. In one embodiment, E. coli cells are used as hosts for the invention. Examples of E. coli strains include strain W3110 (Bachmann, Cellular and Molecular Biology, vol. 2 (Washington, D.C.: American Society for Microbiology, 1987), pp. 1190-1219; ATCC Deposit No. 27,325) and derivatives thereof, including strain 33D3 having genotype W3110 ΔfhuA (ΔtonΔ) ptr3 lac Iq lacL8 ΔompTΔ(nmpc-fepE) degP41 kanR (U.S. Pat. No. 5,639,635). Other strains and derivatives thereof, such as E. coli 294 (ATCC 31,446), E. coli B, E. coli λ 1776 (ATCC 31,537) and E. coli RV308 (ATCC 31,608) are also suitable. These examples are illustrative rather than limiting. Methods for constructing derivatives of any of the above-mentioned bacteria having defined genotypes are known in the art and described in, for example, Bass et al., Proteins 8:309-314 (1990). It is generally necessary to select the appropriate bacteria taking into consideration replicability of the replicon in the cells of a bacterium. For example, E. coli, Serratia, or Salmonella species can be suitably used as the host when well-known plasmids such as pBR322, pBR325, pACYC 177, or pKN410 are used to supply the replicon. Typically the host cell should secrete minimal amounts of proteolytic enzymes, and additional protease inhibitors may desirably be incorporated in the cell culture.
ii. Heteromultimer Production
Host cells are transformed with the above-described expression vectors and cultured in conventional nutrient media modified as appropriate for inducing promoters, selecting transformants, or amplifying the genes encoding the desired sequences.
Transformation means introducing DNA into the prokaryotic host so that the DNA is replicable, either as an extrachromosomal element or as a chromosomal integrant. Depending on the host cell used, transformation is done using standard techniques appropriate to such cells. The calcium treatment employing calcium chloride is generally used for bacterial cells that contain substantial cell-wall barriers. Another method for transformation employs polyethylene glycol/DMSO. Yet another technique used is electroporation.
Prokaryotic cells used to produce the heteromultimers of the invention are grown in media known in the art and suitable for culture of the selected host cells. Examples of suitable media include Luria broth (LB) plus necessary nutrient supplements. In some embodiments, the media also contains a selection agent, chosen based on the construction of the expression vector, to selectively permit growth of prokaryotic cells containing the expression vector. For example, ampicillin is added to media for growth of cells expressing ampicillin resistant gene.
Any necessary supplements besides carbon, nitrogen, and inorganic phosphate sources may also be included at appropriate concentrations introduced alone or as a mixture with another supplement or medium such as a complex nitrogen source. Optionally the culture medium may contain one or more reducing agents selected from the group consisting of glutathione, cysteine, cystamine, thioglycollate, dithioerythritol, and dithiothreitol.
The prokaryotic host cells are cultured at suitable temperatures. For E. coli growth, for example, the preferred temperature ranges from about 20° C. to about 39° C., more preferably from about 25° C. to about 37° C., even more preferably at about 30° C. The pH of the medium may be any pH ranging from about 5 to about 9, depending mainly on the host organism. For E. coli, the pH is preferably from about 6.8 to about 7.4, and more preferably about 7.0.
If an inducible promoter is used in the expression vector of the invention, protein expression is induced under conditions suitable for the activation of the promoter. In one aspect of the invention, PhoA promoters are used for controlling transcription of the polypeptides. Accordingly, the transformed host cells are cultured in a phosphate-limiting medium for induction. Preferably, the phosphate-limiting medium is the C.R.A.P medium (see, e.g., Simmons et al., J. Immunol. Methods (2002), 263:133-147). A variety of other inducers may be used, according to the vector construct employed, as is known in the art.
In one embodiment, the expressed heteromultimers of the present invention are secreted into and recovered from the periplasm of the host cells. Protein recovery typically involves disrupting the microorganism, generally by such means as osmotic shock, sonication or lysis. Once cells are disrupted, cell debris or whole cells may be removed by centrifugation or filtration. The heteromultimers may be further purified, for example, by affinity resin chromatography. Alternatively, proteins can be transported into the culture media and isolated therein. Cells may be removed from the culture and the culture supernatant being filtered and concentrated for further purification of the proteins produced. The expressed polypeptides can be further isolated and identified using commonly known methods such as polyacrylamide gel electrophoresis (PAGE) and Western blot assay.
In one aspect of the invention, heteromultimer production is conducted in large quantity by a fermentation process. Various large-scale fed-batch fermentation procedures are available for production of recombinant proteins. Large-scale fermentations have at least 1000 liters of capacity, preferably about 1,000 to 100,000 liters of capacity. These fermentors use agitator impellers to distribute oxygen and nutrients, especially glucose (the preferred carbon/energy source). Small-scale fermentation refers generally to fermentation in a fermentor that is no more than approximately 100 liters in volumetric capacity, and can range from about 1 liter to about 100 liters.
In a fermentation process, induction of protein expression is typically initiated after the cells have been grown under suitable conditions to a desired density, e.g., an OD550 of about 180-220, at which stage the cells are in the early stationary phase. A variety of inducers may be used, according to the vector construct employed, as is known in the art and described above. Cells may be grown for shorter periods prior to induction. Cells are usually induced for about 12-50 hours, although longer or shorter induction time may be used.
To improve the production yield and quality of the heteromultimers of the invention, various fermentation conditions can be modified. For example, to improve the proper assembly and folding of the secreted heteromultimers, additional vectors overexpressing chaperone proteins, such as Dsb proteins (DsbA, DsbB, DsbC, DsbD, and/or DsbG) or FkpA (a peptidylprolyl cis,trans-isomerase with chaperone activity) can be used to co-transform the host prokaryotic cells. The chaperone proteins have been demonstrated to facilitate the proper folding and solubility of heterologous proteins produced in bacterial host cells (Chen et al., (1999) J. Biol. Chem. 274:19601-19605; Georgiou et al., U.S. Pat. No. 6,083,715; Georgiou et al., U.S. Pat. No. 6,027,888; Bothmann and Pluckthun (2000) J. Biol. Chem. 275:17100-17105; Ramm and Pluckthun, (2000) J. Biol. Chem. 275:17106-17113; Arie et al., (2001) Mol. Microbiol. 39:199-210).
To minimize proteolysis of expressed heterologous proteins (especially those that are proteolytically sensitive), certain host strains deficient for proteolytic enzymes can be used for the present invention. For example, host cell strains may be modified to effect genetic mutation(s) in the genes encoding known bacterial proteases such as Protease III, OmpT, DegP, Tsp, Protease I, Protease Mi, Protease V, Protease VI, and combinations thereof. Some E. coli protease-deficient strains are available and described in, for example, Joly et al., (1998), Proc. Natl. Acad. Sci. USA 95:2773-2777; Georgiou et al., U.S. Pat. No. 5,264,365; Georgiou et al., U.S. Pat. No. 5,508,192; Hara et al., Microbial Drug Resistance, 2:63-72 (1996).
In one embodiment, E. coli strains deficient for proteolytic enzymes and transformed with plasmids overexpressing one or more chaperone proteins are used as host cells in the expression system of the invention.
In another embodiment, the E. coli cell additionally expresses an endopeptidase (e.g., furin) to cleave the one or more tethers of the heteromultimer of interest prior to purification. In yet another embodiment, the eukaryotic host cell may express an endopeptidase (e.g., furin) and an exopeptidase (e.g., Carboxypeptidase B), where the endopeptidase cleaves the one or more tethers of the heteromultimer and the exopeptidase degrades the residual endopeptidase cleavage sites prior to purification.
iii. Heteromultimer Purification
Standard protein purification methods known in the art can be employed. The following procedures are exemplary of suitable purification procedures: fractionation on immunoaffinity or ion-exchange columns, ethanol precipitation, reverse phase HPLC, chromatography on silica or on a cation-exchange resin such as DEAE, chromatofocusing, SDS-PAGE, hydrophobic interaction columns (HIC), ammonium sulfate precipitation, and gel filtration using, for example, Sephadex G-75.
In one aspect, Protein A immobilized on a solid phase is used for immunoaffinity purification of the full-length heteromultimer products of the invention. Protein A is a 41-kD cell wall protein from Staphylococcus aureus which binds with a high affinity to the Fc region of antibodies. Lindmark et al., (1983) J. Immunol. Meth. 62:1-13. The solid phase to which Protein A is immobilized is preferably a column comprising a glass or silica surface, more preferably a controlled pore glass column or a silicic acid column. In some applications, the column has been coated with a reagent, such as glycerol, in an attempt to prevent nonspecific adherence of contaminants.
As the first step of purification, the preparation derived from the cell culture as described above is applied onto the Protein A immobilized solid phase to allow specific binding of the heteromultimer of interest to Protein A. The solid phase is then washed to remove contaminants non-specifically bound to the solid phase. The heteromultimer of interest may be recovered from the solid phase by elution into a solution containing a chaotropic agent or mild detergent. Exemplary chaotropic agents include, but are not limited to, urea, Guanidine-HCl, lithium perchlorate, Histidine, and Arginine. Exemplary mild detergents include, but are not limited to, Tween (e.g., Tween-20), Triton (e.g., Triton X-100), NP-40 (nonylphenoxylpolyethoxylethanol), Nonidet P-40 (octyl phenoxylpolyethoxylethanol), and Sodium Dodecyl Sulfate (SDS). Diluting the heteromultimer into a solution containing a chaotropic agent or mild detergent after elution from the column (e.g., mAbSure column) maintains the stability of the heteromultimer post-elution. In some embodiments, the one or more residual endopeptidase cleavage sites of the endopeptidase-treated heteromultimers of the invention can be processed and degraded post-purification by addition of exopeptidases (e.g., Carboxypeptidase B). In other embodiments, the one or more tethers of the heteromultimers of the invention can be cleaved and processed by endopeptidases (e.g., furin) and exopeptidases (e.g., Carboxypeptidase B) post-purification instead of pre-purification.
B. Generating Heteromultimers Using Eukaryotic Host Cells
The vector components generally include, but are not limited to, one or more of the following: a signal sequence, an origin of replication, one or more marker genes, an enhancer element, a promoter, and a transcription termination sequence.
i. Signal Sequence Component
A vector for use in a eukaryotic host cell may contain a signal sequence or other polypeptide having a specific cleavage site at the N-terminus of the mature protein or polypeptide of interest. The heterologous signal sequence selected can be one that is recognized and processed (i.e., cleaved by a signal peptidase) by the host cell. In mammalian cell expression, mammalian signal sequences as well as viral secretory leaders, for example, the herpes simplex gD signal, are available. The DNA for such precursor region is ligated in reading frame to DNA encoding the antibody.
ii. Origin of Replication
Generally, an origin of replication component is not needed for mammalian expression vectors. For example, the SV40 origin may typically be used, but only because it contains the early promoter.
iii. Selection Gene Component
Expression and cloning vectors may contain a selection gene, also termed a selectable marker. Typical selection genes encode proteins that (a) confer resistance to antibiotics or other toxins, e.g., ampicillin, neomycin, methotrexate, or tetracycline, (b) complement auxotrophic deficiencies, where relevant, or (c) supply critical nutrients not available from complex media.
One example of a selection scheme utilizes a drug to arrest growth of a host cell. Those cells that are successfully transformed with a heterologous gene produce a protein conferring drug resistance and thus survive the selection regimen. Examples of such dominant selection use the drugs neomycin, mycophenolic acid, and hygromycin.
Another example of suitable selectable markers for mammalian cells are those that enable the identification of cells competent to take up the heteromultimer nucleic acid, such as DHFR, thymidine kinase, metallothionein-I and -II, preferably primate metallothionein genes, adenosine deaminase, ornithine decarboxylase, etc.
For example, cells transformed with the DHFR selection gene are first identified by culturing all of the transformants in a culture medium that contains methotrexate (Mtx), a competitive antagonist of DHFR. An appropriate host cell when wild-type DHFR is employed is the Chinese hamster ovary (CHO) cell line deficient in DHFR activity (e.g., ATCC CRL-9096).
Alternatively, host cells (particularly wild-type hosts that contain endogenous DHFR) transformed or co-transformed with DNA sequences encoding an heteromultimer, wild-type DHFR protein, and another selectable marker such as aminoglycoside 3′-phosphotransferase (APH) can be selected by cell growth in medium containing a selection agent for the selectable marker such as an aminoglycosidic antibiotic, e.g., kanamycin, neomycin, or G418. See, for example, U.S. Pat. No. 4,965,199.
iv. Promoter Component
Expression and cloning vectors usually contain a promoter that is recognized by the host organism and is operably linked to the nucleic acid sequence(s) encoding the heteromultimer. Promoter sequences are known for eukaryotes. Virtually all eukaryotic genes have an AT-rich region located approximately 25 to 30 bases upstream from the site where transcription is initiated. Another sequence found 70 to 80 bases upstream from the start of transcription of many genes is a CNCAAT region (SEQ ID NO:12) where N may be any nucleotide. At the 3′ end of most eukaryotic genes is an AATAAA sequence (SEQ ID NO:13) that may be the signal for addition of the poly A tail to the 3′ end of the coding sequence. All of these sequences are suitably inserted into eukaryotic expression vectors.
Transcription from vectors encoding the heteromultimers in mammalian host cells is controlled, for example, by promoters obtained from the genomes of viruses such as, for example, polyoma virus, fowlpox virus, adenovirus (such as Adenovirus 2), bovine papilloma virus, avian sarcoma virus, cytomegalovirus, a retrovirus, hepatitis-B virus, and Simian Virus 40 (SV40), from heterologous mammalian promoters, e.g., the actin promoter or an immunoglobulin promoter, or from heat-shock promoters, provided such promoters are compatible with the host cell systems.
The early and late promoters of the SV40 virus are conveniently obtained as an SV40 restriction fragment that also contains the SV40 viral origin of replication. The immediate early promoter of the human cytomegalovirus is conveniently obtained as a HindIII E restriction fragment. A system for expressing DNA in mammalian hosts using the bovine papillomavirus as a vector is disclosed in U.S. Pat. No. 4,419,446. A modification of this system is described in U.S. Pat. No. 4,601,978. Alternatively, the Rous Sarcoma Virus long terminal repeat can be used as the promoter.
v. Enhancer Element Component
Transcription of DNA encoding heteromultimer polypeptide(s) by higher eukaryotes can be increased by inserting an enhancer sequence into the vector. Many enhancer sequences are now known from mammalian genes (e.g., globin, elastase, albumin, α-fetoprotein, and insulin genes). Also, one may use an enhancer from a eukaryotic cell virus. Examples include the SV40 enhancer on the late side of the replication origin (bp 100-270), the cytomegalovirus early promoter enhancer, the polyoma enhancer on the late side of the replication origin, and adenovirus enhancers. See also Yaniv, Nature 297:17-18 (1982) for a description of elements for enhancing activation of eukaryotic promoters. The enhancer may be spliced into the vector at a position 5′ or 3′ to the heteromultimer polypeptide-encoding sequence, provided that enhancement is achieved, but is generally located at a site 5′ from the promoter.
vi. Transcription Termination Component
Expression vectors used in eukaryotic host cells will typically also contain sequences necessary for the termination of transcription and for stabilizing the mRNA. Such sequences are commonly available from the 5′ and, occasionally 3′, untranslated regions of eukaryotic or viral DNAs or cDNAs. These regions contain nucleotide segments transcribed as polyadenylated fragments in the untranslated portion of the mRNA encoding a heteromultimer. One useful transcription termination component is the bovine growth hormone polyadenylation region. See WO 94/11026 and the expression vector disclosed therein.
vii. Selection and Transformation of Host Cells
Suitable host cells for cloning or expressing the DNA in the vectors herein include higher eukaryote cells described herein, including vertebrate host cells. Propagation of vertebrate cells in culture (tissue culture) has become a routine procedure. Examples of useful mammalian host cell lines are monkey kidney CV1 line transformed by SV40 (COS-7, ATCC CRL 1651); human embryonic kidney line (293 or 293 cells subcloned for growth in suspension culture, Graham et al., J. Gen. Virol. 36:59 (1977)); baby hamster kidney cells (BHK, ATCC CCL 10); Chinese hamster ovary cells/−DHFR (CHO, Urlaub et al., Proc. Natl. Acad. Sci. USA 77:4216 (1980)); mouse sertoli cells (TM4, Mather, Biol. Reprod. 23:243-251 (1980)); monkey kidney cells (CV1 ATCC CCL 70); African green monkey kidney cells (VERO-76, ATCC CRL-1587); human cervical carcinoma cells (HELA, ATCC CCL 2); canine kidney cells (MDCK, ATCC CCL 34); buffalo rat liver cells (BRL 3A, ATCC CRL 1442); human lung cells (W138, ATCC CCL 75); human liver cells (Hep G2, HB 8065); mouse mammary tumor (MMT 060562, ATCC CCL51); TRI cells (Mather et al., Annals N.Y. Acad. Sci. 383:44-68 (1982)); MRC 5 cells; FS4 cells; and a human hepatoma line (Hep G2).
Host cells are transformed with the above-described expression or cloning vectors for heteromultimer production and cultured in conventional nutrient media modified as appropriate for inducing promoters, selecting transformants, or amplifying the genes encoding the desired sequences.
viii. Culturing the Host Cells
The host cells used to produce a heteromultimer of this invention may be cultured in a variety of media. Commercially available media such as Ham's F10 (Sigma), Minimal Essential Medium ((MEM), (Sigma), RPMI-1640 (Sigma), and Dulbecco's Modified Eagle's Medium ((DMEM), Sigma) are suitable for culturing the host cells. In addition, any of the media described in Ham et al., Meth. Enz. 58:44 (1979), Barnes et al., Anal. Biochem. 102:255 (1980), U.S. Pat. Nos. 4,767,704; 4,657,866; 4,927,762; 4,560,655; or 5,122,469; WO 90/03430; WO 87/00195; or U.S. Pat. Re. 30,985 may be used as culture media for the host cells. Any of these media may be supplemented as necessary with hormones and/or other growth factors (such as insulin, transferrin, or epidermal growth factor), salts (such as sodium chloride, calcium, magnesium, and phosphate), buffers (such as HEPES), nucleotides (such as adenosine and thymidine), antibiotics (such as GENTAMYCINTM drug), trace elements (defined as inorganic compounds usually present at final concentrations in the micromolar range), and glucose or an equivalent energy source. Any other necessary supplements may also be included at appropriate concentrations that would be known to those skilled in the art. The culture conditions, such as temperature, pH, and the like, are those previously used with the host cell selected for expression, and will be apparent to the ordinarily skilled artisan.
ix. Purification of Heteromultimer
When using recombinant techniques, the heteromultimer can be produced intracellularly, or directly secreted into the medium. If the heteromultimer is produced intracellularly, as a first step, the particulate debris, either host cells or lysed fragments, are removed, for example, by centrifugation or ultrafiltration. Where the heteromultimer is secreted into the medium, supernatants from such expression systems are generally first concentrated using a commercially available protein concentration filter, for example, an Amicon or Millipore Pellicon ultrafiltration unit. A protease inhibitor such as PMSF may be included in any of the foregoing steps to inhibit proteolysis and antibiotics may be included to prevent the growth of adventitious contaminants.
The heteromultimer composition prepared from the cells can be purified using, for example, hydroxylapatite chromatography, gel electrophoresis, dialysis, and affinity chromatography, with affinity chromatography being the preferred purification technique. The suitability of protein A as an affinity ligand depends on the species and isotype of any immunoglobulin Fc domain that is present in the heteromultimer. Protein A can be used to purify heteromultimers that are based on human γ1, γ2, or γ4 heavy chains (Lindmark et al., J. Immunol. Meth. 62:1-13 (1983)). Protein G is recommended for all mouse isotypes and for human γ3 (Guss et al., EMBO J. 5:15671575 (1986)). The matrix to which the affinity ligand is attached is most often agarose, but other matrices are available. Mechanically stable matrices such as controlled pore glass or poly(styrenedivinyl)benzene allow for faster flow rates and shorter processing times than can be achieved with agarose. Where the heteromultimer comprises a CH3 domain, the Bakerbond ABXTM resin (J. T. Baker, Phillipsburg, N.J.) is useful for purification. Other techniques for protein purification such as fractionation on an ion-exchange column, ethanol precipitation, Reverse Phase HPLC, chromatography on silica, chromatography on heparin SEPHAROSETM chromatography on an anion or cation exchange resin (such as a polyaspartic acid column), chromatofocusing, SDS-PAGE, and ammonium sulfate precipitation are also available depending on the antibody to be recovered.
In one embodiment, the eukaryotic host cell additionally expresses an endopeptidase (e.g., furin) to cleave the one or more tethers of the heteromultimer of interest prior to purification (e.g., during trans-Golgi transport). In another embodiment, the eukaryotic host cell may express an endopeptidase (e.g., furin or Lys-C) and an exopeptidase (e.g., Carboxypeptidase B), where the endopeptidase cleaves the one or more tethers of the heteromultimer and the exopeptidase degrades the residual endopeptidase cleavage sites prior to purification.
The heteromultimer of interest is recovered from the solid phase of a column by elution into a solution containing a chaotropic agent or mild detergent. By a “chaotropic agent” is meant a water-soluble substance which disrupts the three-dimensional structure of a protein (e.g., an antibody) by interfering with stabilizing intramolecular interactions (e.g., hydrogen bonds, Van der Waals forces, or hydrophobic effects). Exemplary chaotropic agents include, but are not limited to, urea, Guanidine-HCl, lithium perchlorate, Histidine, and Arginine. By a “mild detergent” is meant a water-soluble substance which disrupts the three-dimensional structure of a protein or protein complex (e.g., a heteromultimer) by interfering with stabilizing intramolecular interactions (e.g., hydrogen bonds, Van der Waals forces, or hydrophobic effects), but which does not permanently disrupt the protein structure as to cause a loss of biological activity (i.e., does not denature the protein). Exemplary mild detergents include, but are not limited to, Tween (e.g., Tween-20), Triton (e.g., Triton X-100), NP-40 (nonylphenoxylpolyethoxylethanol), Nonidet P-40 (octyl phenoxylpolyethoxylethanol), and Sodium Dodecyl Sulfate (SDS).
Following any preliminary purification step(s), the mixture comprising the heteromultimer of interest and contaminants may be subjected to low pH hydrophobic interaction chromatography using an elution buffer at a pH between about 2.5-4.5, preferably performed at low salt concentrations (e.g., from about 0-0.25 M salt).
In some embodiments, the one or more residual endopeptidase cleavage sites of the endopeptidase-treated heteromultimers of the invention can be processed and degraded post-purification by exopeptidases (e.g., Carboxypeptidase B). In other embodiments, the one or more tethers of the heteromultimers of the invention can be cleaved and processed by endopeptidases (e.g., furin) and exopeptidases (e.g., Carboxypeptidase B) post-purification instead of pre-purification.
x. Heteromultimer Production Using Baculovirus
Recombinant baculovirus may be generated by co-transfecting a plasmid encoding heteromultimer or heteromultimer fragment and BaculoGoldTM virus DNA (Pharmingen) into an insect cell such as a Spodoptera frugiperda cell (e.g., Sf9 cells; ATCC CRL 1711) or a Drosophila melanogaster S2 cell using, for example, lipofectin (commercially available from GIBCO-BRL). In a particular example, a heteromultimer sequence is fused upstream of an epitope tag contained within a baculovirus expression vector. Such epitope tags include poly-His tags. A variety of plasmids may be employed, including plasmids derived from commercially available plasmids such as pVL1393 (Novagen) or pAcGP67B (Pharmingen). Briefly, the sequence encoding antibody heteromultimer or a fragment thereof may be amplified by PCR with primers complementary to the 5′ and 3′ regions. The 5′ primer may incorporate flanking (selected) restriction enzyme sites. The product may then be digested with the selected restriction enzymes and subcloned into the expression vector.
After tranfection with the expression vector, the host cells (e.g., Sf9 cells) are incubated for 4-5 days at 28° C. and the released virus is harvested and used for further amplifications. Viral infection and protein expression may be performed as described, for example, by O'Reilley et al. (Baculovirus expression vectors: A Laboratory Manual. Oxford: Oxford University Press (1994)).
Expressed poly-His tagged heteromultimer can then be purified, for example, by Ni2+-chelate affinity chromatography as follows. Extracts can be prepared from recombinant virus-infected Sf9 cells as described by Rupert et al. (Nature 362:175-179 (1993)). Briefly, Sf9 cells are washed, resuspended in sonication buffer (25 mL HEPES pH 7.9; 12.5 mM MgCl2; 0.1 mM EDTA; 10% glycerol; 0.1% NP-40; 0.4 M KCl), and sonicated twice for 20 seconds on ice. The sonicates are cleared by centrifugation, and the supernatant is diluted 50-fold in loading buffer (50 mM phosphate; 300 mM NaCl; 10% glycerol pH 7.8) and filtered through a 0.45 μm filter. A Ni2+-NTA agarose column (commercially available from Qiagen) is prepared with a bed volume of 5 mL, washed with 25 mL of water, and equilibrated with 25 mL of loading buffer. The filtered cell extract is loaded onto the column at 0.5 mL per minute. The column is washed to baseline A280 with loading buffer, at which point fraction collection is started. Next, the column is washed with a secondary wash buffer (50 mM phosphate; 300 mM NaCl; 10% glycerol pH 6.0), which elutes nonspecifically bound protein. After reaching A280 baseline again, the column is developed with a 0 to 500 mM Imidazole gradient in the secondary wash buffer. One mL fractions are collected and analyzed by SDS-PAGE and silver staining or Western blot with Ni2+-NTA-conjugated to alkaline phosphatase (Qiagen). Fractions containing the eluted His10-tagged (SEQ ID NO: 21) heteromultimer are pooled and dialyzed against loading buffer.
Purification of the heteromultimer can also be performed using known chromatography techniques, including for instance, Protein A or protein G column chromatography. The heteromultimer of interest may be recovered from the solid phase of the column by elution into a solution containing a chaotropic agent or mild detergent. Exemplary chaotropic agents and mild detergents include, but are not limited to, Guanidine-HCl, urea, lithium perclorate, Arginine, Histidine, SDS (sodium dodecyl sulfate), Tween, Triton, and NP-40, all of which are commercially available. As described above, the one or more tethers of the heteromultimer may be cleaved and processed post-purification by addition of endopeptidase (e.g., furin or Lys-C) and exopeptidase (e.g., Carboxypeptidase B).
C. Purification Technique
One particular purification approach that may be used for HD tether-containing heteromultimers is shown below.




In addition to arginine, other chaotropic agents or mild detergents that can be used in the above purification protocol after the initial Protein A column step include, but are not limited to, Guanidine-HCl, urea, lithium perclorate, histidine, SDS (sodium dodecyl sulfate), Tween, Triton, and NP-40, all of which are commercially available. In some embodiments, the one or more residual endopeptidase cleavage sites of the endopeptidase-treated heteromultimers of the invention can be processed and degraded post-purification by exopeptidases (e.g., Carboxypeptidase B). In other embodiments, the one or more tethers of the heteromultimers of the invention can be cleaved and processed by endopeptidases (e.g., furin or Lys-C) and exopeptidases (e.g., Carboxypeptidase B) post-purification instead of pre-purification.
IV. Conjugated Proteins
The invention also provides conjugated proteins such as conjugated heteromultimers or immunoconjugates (for example, “antibody-drug conjugates” or “ADC”), comprising any of the heteromultimers described herein (e.g., an HD tether-containing single-chain monospecific or multispecific antibody, an HD tether-containing multi-chain monospecific or multispecific heteromultimer) where one of the constant regions of the light chain or the heavy chain is conjugated to a chemical molecule such as a dye or cytotoxic agent such as a chemotherapeutic agent, a drug, a growth inhibitory agent, a toxin (e.g., an enzymatically active toxin of bacterial, fungal, plant, or animal origin, or fragments thereof), or a radioactive isotope (i.e., a radioconjugate). In particular, as described herein, the use of an HD tether enables the construction of heteromultimers containing two different heavy chains (HC1 and HC2) as well as two different light chains (LC1 and LC2). An immunoconjugate constructed using the methods described herein may contain the cytotoxic agent conjugated to a constant region of only one of the heavy chains (HC1 or HC2) or only one of the light chains (LC1 or LC2). Also, because the immunoconjugate can have the cytotoxic agent attached to only one heavy or light chain, the amount of the cytotoxic agent being administered to a subject is reduced relative to administration of a heteromultimer having the cytotoxic agent attached to both heavy or light chains. Reducing the amount of cytotoxic agent being administered to a subject limits adverse side effects associated with the cytotoxic agent.
The use of antibody-drug conjugates for the local delivery of cytotoxic or cytostatic agents, i.e., drugs to kill or inhibit tumor cells in the treatment of cancer (Syrigos and Epenetos, Anticancer Research 19:605-614 (1999); Niculescu-Duvaz and Springer, Adv. Drg. Del. Rev. 26:151-172 (1997); U.S. Pat. No. 4,975,278) allows targeted delivery of the drug moiety to tumors, and intracellular accumulation therein, where systemic administration of these unconjugated drug agents may result in unacceptable levels of toxicity to normal cells as well as the tumor cells sought to be eliminated (Baldwin et al., Lancet (Mar. 15, 1986):603-605 (1986); Thorpe, (1985) “Antibody Carriers Of Cytotoxic Agents In Cancer Therapy: A Review,” in Monoclonal Antibodies'84: Biological And Clinical Applications, A. Pinchera et al. (ed.s), pp. 475-506). Maximal efficacy with minimal toxicity is sought thereby. Both polyclonal antibodies and monoclonal antibodies have been reported as useful in these strategies (Rowland et al., Cancer Immunol. Immunother. 21:183-187 (1986)). Drugs used in these methods include daunomycin, doxorubicin, methotrexate, and vindesine (Rowland et al., (1986) supra). Toxins used in heteromultimer-toxin conjugates include bacterial toxins such as diphtheria toxin, plant toxins such as ricin, small molecule toxins such as geldanamycin (Mandler et al., Jour. of the Nat. Cancer Inst. 92(19):1573-1581 (2000); Mandler et al., Bioorganic & Med. Chem. Letters 10:1025-1028 (2000); Mandler et al., Bioconjugate Chem. 13:786-791 (2002)), maytansinoids (EP 1391213; Liu et al., Proc. Natl. Acad. Sci. USA 93:8618-8623 (1996)), and calicheamicin (Lode et al., Cancer Res. 58:2928 (1998); Hinman et al., Cancer Res. 53:3336-3342 (1993)). The toxins may effect their cytotoxic and cytostatic effects by mechanisms including tubulin binding, DNA binding, or topoisomerase inhibition. Some cytotoxic drugs tend to be inactive or less active when conjugated to large heteromultimeric antibodies or protein receptor ligands.
Chemotherapeutic agents useful in the generation of immunoconjugates are described herein (e.g., above). Enzymatically active toxins and fragments thereof that can be used include diphtheria A chain, nonbinding active fragments of diphtheria toxin, exotoxin A chain (from Pseudomonas aeruginosa), ricin A chain, abrin A chain, modeccin A chain, alpha-sarcin, Aleurites fordii proteins, dianthin proteins, Phytolaca americana proteins (PAPI, PAPII, and PAP-S), momordica charantia inhibitor, curcin, crotin, sapaonaria officinalis inhibitor, gelonin, mitogellin, restrictocin, phenomycin, enomycin, and the tricothecenes. See, e.g., WO 93/21232 published Oct. 28, 1993. A variety of radionuclides are available for the production of radioconjugated antibodies. Examples include 212Bi, 131I, 131In, 90Y, and 186Re. Conjugates of the antibody and cytotoxic agent are made using a variety of bifunctional protein-coupling agents such as N-succinimidyl-3-(2-pyridyldithiol) propionate (SPDP), iminothiolane (IT), bifunctional derivatives of imidoesters (such as dimethyl adipimidate HCl), active esters (such as disuccinimidyl suberate), aldehydes (such as glutaraldehyde), bis-azido compounds (such as bis (p-azidobenzoyl) hexanediamine), bis-diazonium derivatives (such as bis-(p-diazoniumbenzoyl)-ethylenediamine), diisocyanates (such as toluene 2,6-diisocyanate), and bis-active fluorine compounds (such as 1,5-difluoro-2,4-dinitrobenzene). For example, a ricin immunotoxin can be prepared as described in Vitetta et al., Science 238:1098 (1987). Carbon-14-labeled 1-isothiocyanatobenzyl-3-methyldiethylene triaminepentaacetic acid (MX-DTPA) is an exemplary chelating agent for conjugation of radionucleotide to the antibody. See, e.g., WO94/11026.
Conjugates of a heteromultimer and one or more small molecule toxins, such as a calicheamicin, maytansinoids, dolastatins, aurostatins, a trichothecene, and CC 1065, and the derivatives of these toxins that have toxin activity, are also contemplated herein.
A. Maytansine and Maytansinoids
In some embodiments, the immunoconjugate comprises a heteromultimer of the invention conjugated to one or more maytansinoid molecules.
Maytansinoids are mitototic inhibitors which act by inhibiting tubulin polymerization. Maytansine was first isolated from the east African shrub Maytenus serrata (U.S. Pat. No. 3,896,111). Subsequently, it was discovered that certain microbes also produce maytansinoids, such as maytansinol and C-3 maytansinol esters (U.S. Pat. No. 4,151,042). Synthetic maytansinol and derivatives and analogues thereof are disclosed, for example, in U.S. Pat. Nos. 4,137,230; 4,248,870; 4,256,746; 4,260,608; 4,265,814; 4,294,757; 4,307,016; 4,308,268; 4,308,269; 4,309,428; 4,313,946; 4,315,929; 4,317,821; 4,322,348; 4,331,598; 4,361,650; 4,364,866; 4,424,219; 4,450,254; 4,362,663; and 4,371,533.
Maytansinoid drug moieties are attractive drug moieties in heteromultimeric antibody drug conjugates because they are: (i) relatively accessible to prepare by fermentation or chemical modification, derivatization of fermentation products, (ii) amenable to derivatization with functional groups suitable for conjugation through the non-disulfide linkers to antibodies, (iii) stable in plasma, and (iv) effective against a variety of tumor cell lines.
Immunoconjugates containing maytansinoids, methods of making same, and their therapeutic use are disclosed, for example, in U.S. Pat. Nos. 5,208,020, 5,416,064 and European Patent EP 0 425 235 B1, the disclosures of which are hereby expressly incorporated by reference. Liu et al., Proc. Natl. Acad. Sci. USA 93:8618-8623 (1996) described immunoconjugates comprising a maytansinoid designated DM1 linked to the monoclonal antibody C242 directed against human colorectal cancer. The conjugate was found to be highly cytotoxic towards cultured colon cancer cells, and showed antitumor activity in an in vivo tumor growth assay. Chari et al., Cancer Research 52:127-131 (1992) describe immunoconjugates in which a maytansinoid was conjugated via a disulfide linker to the murine antibody A7 binding to an antigen on human colon cancer cell lines, or to another murine monoclonal antibody TA.1 that binds the HER-2/neu oncogene. The cytotoxicity of the TA.1-maytansinoid conjugate was tested in vitro on the human breast cancer cell line SK-BR-3, which expresses 3×105 HER-2 surface antigens per cell. The drug conjugate achieved a degree of cytotoxicity similar to the free maytansinoid drug, which could be increased by increasing the number of maytansinoid molecules per antibody molecule. The A7-maytansinoid conjugate showed low systemic cytotoxicity in mice.
Maytansinoid conjugates are prepared by chemically linking a heteromultimer to a maytansinoid molecule without significantly diminishing the biological activity of either the heteromultimer, or the maytansinoid molecule. See, e.g., U.S. Pat. No. 5,208,020 (the disclosure of which is hereby expressly incorporated by reference). An average of 3-4 maytansinoid molecules conjugated per heteromultimeric antibody molecule has shown efficacy in enhancing cytotoxicity of target cells without negatively affecting the function or solubility of the antibody, although even one molecule of toxin/antibody would be expected to enhance cytotoxicity over the use of naked antibody. Maytansinoids are well known in the art and can be synthesized by known techniques or isolated from natural sources. Suitable maytansinoids are disclosed, for example, in U.S. Pat. No. 5,208,020 and in the other patents and nonpatent publications referred to hereinabove. Preferred maytansinoids are maytansinol and maytansinol analogues modified in the aromatic ring or at other positions of the maytansinol molecule, such as various maytansinol esters.
There are many linking groups known in the art for making maytansinoid conjugates, including, for example, those disclosed in U.S. Pat. No. 5,208,020 or EP Patent 0 425 235 B1, Chari et al., Cancer Research 52:127-131 (1992), and U.S. Patent Application Publication No. 2005/0169933, the disclosures of which are hereby expressly incorporated by reference. Maytansinoid conjugates comprising the linker component SMCC may be prepared as disclosed in U.S. Patent Application Publication No. 2005/0169933. The linking groups include disulfide groups, thioether groups, acid labile groups, photolabile groups, peptidase labile groups, or esterase labile groups, as disclosed in the above-identified patents, disulfide and thioether groups being preferred. Additional linking groups are described and exemplified herein.
Conjugates of heteromultimer and maytansinoid may be made using a variety of bifunctional protein coupling agents such as N-succinimidyl-3-(2-pyridyldithio) propionate (SPDP), succinimidyl-4-(N-maleimidomethyl) cyclohexane-1-carboxylate (SMCC), iminothiolane (IT), bifunctional derivatives of imidoesters (such as dimethyl adipimidate HCl), active esters (such as disuccinimidyl suberate), aldehydes (such as glutaraldehyde), bis-azido compounds (such as bis (p-azidobenzoyl) hexanediamine), bis-diazonium derivatives (such as bis-(p-diazoniumbenzoyl)-ethylenediamine), diisocyanates (such as toluene 2,6-diisocyanate), and bis-active fluorine compounds (such as 1,5-difluoro-2,4-dinitrobenzene). Particularly preferred coupling agents include N-succinimidyl-3-(2-pyridyldithio) propionate (SPDP) (Carlsson et al., Biochem. J. 173:723-737 (1978)) and N-succinimidyl-4-(2-pyridylthio)pentanoate (SPP) to provide for a disulfide linkage.
The linker may be attached to the maytansinoid molecule at various positions, depending on the type of the link. For example, an ester linkage may be formed by reaction with a hydroxyl group using conventional coupling techniques. The reaction may occur at the C-3 position having a hydroxyl group, the C-14 position modified with hydroxymethyl, the C-15 position modified with a hydroxyl group, and the C-20 position having a hydroxyl group. In a preferred embodiment, the linkage is formed at the C-3 position of maytansinol or a maytansinol analogue.
B. Auristatins and Dolastatins
In some embodiments, the immunoconjugate comprises a heteromultimer of the invention conjugated to dolastatins or dolostatin peptidic analogs and derivatives, the auristatins (U.S. Pat. Nos. 5,635,483 and 5,780,588). Dolastatins and auristatins have been shown to interfere with microtubule dynamics, GTP hydrolysis, and nuclear and cellular division (Woyke et al., Antimicrob. Agents and Chemother. 45(12):3580-3584 (2001)) and have anticancer (U.S. Pat. No. 5,663,149) and antifungal activity (Pettit et al., Antimicrob. Agents Chemother. 42:2961-2965 (1998)). The dolastatin or auristatin drug moiety may be attached to the heteromultimer through the N-(amino) terminus or the C-(carboxyl) terminus of the peptidic drug moiety (WO 02/088172).
Exemplary auristatin embodiments include the N-terminus linked monomethylauristatin drug moieties DE and DF, disclosed in “Monomethylvaline Compounds Capable of Conjugation to Ligands,” U.S. Application Publication No. 2005/0238649, the disclosure of which is expressly incorporated by reference in its entirety.
Typically, peptide-based drug moieties can be prepared by forming a peptide bond between two or more amino acids and/or peptide fragments. Such peptide bonds can be prepared, for example, according to the liquid phase synthesis method (see E. Schröder and K. Lübke, “The Peptides,” volume 1, pp. 76-136, 1965, Academic Press) that is well known in the field of peptide chemistry. The auristatin/dolastatin drug moieties may be prepared according to the methods of: U.S. Pat. Nos. 5,635,483 and 5,780,588; Pettit et al., J. Nat. Prod. 44:482-485 (1981); Pettit et al., Anti-Cancer Drug Design 13:47-66 (1998); Poncet, Curr. Pharm. Des. 5:139-162 (1999); and Pettit, Fortschr. Chem. Org. Naturst. 70:1-79 (1997). See also Doronina, Nat. Biotechnol. 21(7):778-784 (2003); and “Monomethylvaline Compounds Capable of Conjugation to Ligands,” U.S. Application Publication No. 2005/0238649, hereby incorporated by reference in its entirety (disclosing, e.g., linkers and methods of preparing monomethylvaline compounds such as MMAE and MMAF conjugated to linkers).
C. Calicheamicin
In other embodiments, the immunoconjugate comprises a heteromultimer of the invention conjugated to one or more calicheamicin molecules. The calicheamicin family of antibiotics are capable of producing double-stranded DNA breaks at sub-picomolar concentrations. For the preparation of conjugates of the calicheamicin family, see U.S. Pat. Nos. 5,712,374, 5,714,586, 5,739,116, 5,767,285, 5,770,701, 5,770,710, 5,773,001, and 5,877,296 (all to American Cyanamid Company). Structural analogues of calicheamicin which may be used include, but are not limited to, γ11, α21, α31, N-acetyl-γ11, PSAG and θ11 (Hinman et al., Cancer Research 53:3336-3342 (1993), Lode et al., Cancer Research 58:2925-2928 (1998) and the aforementioned U.S. patents to American Cyanamid). Another anti-tumor drug that the antibody can be conjugated is QFA, which is an antifolate. Both calicheamicin and QFA have intracellular sites of action and do not readily cross the plasma membrane. Therefore, cellular uptake of these agents through antibody-mediated internalization greatly enhances their cytotoxic effects.
D. Other Cytotoxic Agents
Other antitumor agents that can be conjugated to the heteromultimers of the invention or made according to the methods described herein include BCNU, streptozoicin, vincristine and 5-fluorouracil, the family of agents known collectively LL-E33288 complex described in U.S. Pat. Nos. 5,053,394 and 5,770,710, as well as esperamicins (U.S. Pat. No. 5,877,296).
Enzymatically active toxins and fragments thereof which can be used include diphtheria A chain, nonbinding active fragments of diphtheria toxin, exotoxin A chain (from Pseudomonas aeruginosa), ricin A chain, abrin A chain, modeccin A chain, alpha-sarcin, Aleurites fordii proteins, dianthin proteins, Phytolaca americana proteins (PAPI, PAPII, and PAP-S), momordica charantia inhibitor, curcin, crotin, sapaonaria officinalis inhibitor, gelonin, mitogellin, restrictocin, phenomycin, enomycin and the tricothecenes (see, for example, WO 93/21232, published Oct. 28, 1993).
The present invention further contemplates an immunoconjugate formed between a heteromultimer and a compound with nucleolytic activity (e.g., a ribonuclease or a DNA endonuclease such as a deoxyribonuclease; DNase).
For selective destruction of a tumor, the heteromultimer may comprise a highly radioactive atom. A variety of radioactive isotopes are available for the production of radioconjugated heteromultimers. Examples include At211, I131, I125, Y90, Re186, Re188, Sm153, Bi212, P32, Pb212 and radioactive isotopes of Lu. When the conjugate is used for detection, it may comprise a radioactive atom for scintigraphic studies, for example Tc99m or I123, or a spin label for nuclear magnetic resonance (NMR) imaging (also known as magnetic resonance imaging, mri), such as iodine-123 again, iodine-131, indium-111, fluorine-19, carbon-13, nitrogen-15, oxygen-17, gadolinium, manganese or iron.
The radio- or other labels may be incorporated in the conjugate in known ways. For example, the peptide may be biosynthesized or may be synthesized by chemical amino acid synthesis using suitable amino acid precursors involving, for example, fluorine-19 in place of hydrogen. Labels such as tc99m or I123, Re186, Re188 and In111 can be attached via a cysteine residue in the peptide. Yttrium-90 can be attached via a lysine residue. The IODOGEN method (Fraker et al., Biochem. Biophys. Res. Commun. 80:49-57 (1978)) can be used to incorporate iodine-123. “Monoclonal Antibodies in Immunoscintigraphy” (Chatal, CRC Press 1989) describes other methods in detail.
Conjugates of the heteromultimer and cytotoxic agent may be made using a variety of bifunctional protein coupling agents such as N-succinimidyl-3-(2-pyridyldithio) propionate (SPDP), succinimidyl-4-(N-maleimidomethyl) cyclohexane-1-carboxylate (SMCC), iminothiolane (IT), bifunctional derivatives of imidoesters (such as dimethyl adipimidate HCl), active esters (such as disuccinimidyl suberate), aldehydes (such as glutaraldehyde), bis-azido compounds (such as bis (p-azidobenzoyl) hexanediamine), bis-diazonium derivatives (such as bis-(p-diazoniumbenzoyl)-ethylenediamine), diisocyanates (such as toluene 2,6-diisocyanate), and bis-active fluorine compounds (such as 1,5-difluoro-2,4-dinitrobenzene). For example, a ricin immunotoxin can be prepared as described in Vitetta et al., Science 238:1098 (1987). Carbon-14-labeled 1-isothiocyanatobenzyl-3-methyldiethylene triaminepentaacetic acid (MX-DTPA) is an exemplary chelating agent for conjugation of radionucleotide to the heteromultimer. See, e.g., WO94/11026. The linker may be a “cleavable linker” facilitating release of the cytotoxic drug in the cell. For example, an acid-labile linker, peptidase-sensitive linker, photolabile linker, dimethyl linker or disulfide-containing linker (Chari et al., Cancer Research 52:127-131 (1992); U.S. Pat. No. 5,208,020) may be used.
The compounds of the invention expressly contemplate, but are not limited to, ADC prepared with cross-linker reagents: BMPS, EMCS, GMBS, HBVS, LC-SMCC, MBS, MPBH, SBAP, SIA, SIAB, SMCC, SMPB, SMPH, sulfo-EMCS, sulfo-GMBS, sulfo-KMUS, sulfo-MBS, sulfo-SIAB, sulfo-SMCC, and sulfo-SMPB, and SVSB (succinimidyl-(4-vinylsulfone)benzoate) which are commercially available (e.g., from Pierce Biotechnology, Inc., Rockford, Ill., U.S.A). See pages 467-498, 2003-2004 Applications Handbook and Catalog.
E. Preparation of Conjugated Heteromultimers
In the conjugated heteromultimers of the invention, a heteromultimer is conjugated to one or more moieties (for example, drug moieties), e.g., about 1 to about 20 moieties per antibody, optionally through a linker. The conjugated heteromultimers may be prepared by several routes, employing organic chemistry reactions, conditions, and reagents known to those skilled in the art, including: (1) reaction of a nucleophilic group of antibody heteromultimer with a bivalent linker reagent via a covalent bond, followed by reaction with a moiety of interest; and (2) reaction of a nucleophilic group of a moiety with a bivalent linker reagent via a covalent bond, followed by reaction with the nucleophilic group of antibody heteromultimer. Additional methods for preparing conjugated heteromultimers are described herein.
The linker reagent may be composed of one or more linker components. Exemplary linker components include 6-maleimidocaproyl (“MC”), maleimidopropanoyl (“MP”), valine-citrulline (“val-cit”), alanine-phenylalanine (“ala-phe”), p-aminobenzyloxycarbonyl (“PAB”), N-Succinimidyl 4-(2-pyridylthio) pentanoate (“SPP”), N-Succinimidyl 4-(N-maleimidomethyl) cyclohexane-1 carboxylate (“SMCC”), and N-Succinimidyl (4-iodo-acetyl) aminobenzoate (“SIAB”). Additional linker components are known in the art and some are described herein. See also “Monomethylvaline Compounds Capable of Conjugation to Ligands,” U.S. Application Publication No. 2005/0238649, the contents of which are hereby incorporated by reference in its entirety.
In some embodiments, the linker may comprise amino acid residues. Exemplary amino acid linker components include a dipeptide, a tripeptide, a tetrapeptide or a pentapeptide. Exemplary dipeptides include: valine-citrulline (vc or val-cit), alanine-phenylalanine (af or ala-phe). Exemplary tripeptides include: glycine-valine-citrulline (gly-val-cit) and glycine-glycine-glycine (gly-gly-gly). Amino acid residues which comprise an amino acid linker component include those occurring naturally, as well as minor amino acids and non-naturally occurring amino acid analogs, such as citrulline. Amino acid linker components can be designed and optimized in their selectivity for enzymatic cleavage by a particular enzymes, for example, a tumor-associated protease, cathepsin B, C and D, or a plasmin protease.
Nucleophilic groups on heteromultimers of the invention include, but are not limited to: (i) N-terminal amine groups, (ii) side chain amine groups, e.g. lysine, (iii) side chain thiol groups, e.g. cysteine, and (iv) sugar hydroxyl or amino groups where the heteromultimer is glycosylated. Amine, thiol, and hydroxyl groups are nucleophilic and capable of reacting to form covalent bonds with electrophilic groups on linker moieties and linker reagents including: (i) active esters such as NHS esters, HOBt esters, haloformates, and acid halides; (ii) alkyl and benzyl halides such as haloacetamides; (iii) aldehydes, ketones, carboxyl, and maleimide groups. Certain heteromultimers have reducible interchain disulfides, i.e., cysteine bridges. Heteromultimers of the invention may be made reactive for conjugation with linker reagents by treatment with a reducing agent such as DTT (dithiothreitol). Each cysteine bridge will thus form, theoretically, two reactive thiol nucleophiles. Additional nucleophilic groups can be introduced into antibodies through the reaction of lysines with 2-iminothiolane (Traut's reagent) resulting in conversion of an amine into a thiol. Reactive thiol groups may be introduced into the heteromultimer (or fragment thereof) by introducing one, two, three, four, or more cysteine residues (e.g., preparing mutant heteromultimers comprising one or more non-native cysteine amino acid residues).
Conjugated heteromultimers of the invention may also be produced by modification of the heteromultimer to introduce electrophilic moieties, which can react with nucleophilic substituents on the linker reagent or drug or other moiety. The sugars of glycosylated heteromultimers of the invention may be oxidized, e.g., with periodate oxidizing reagents, to form aldehyde or ketone groups which may react with the amine group of linker reagents or drug or other moieties. The resulting imine Schiff base groups may form a stable linkage, or may be reduced, e.g., by borohydride reagents to form stable amine linkages. In one embodiment, reaction of the carbohydrate portion of a glycosylated antibody with either glactose oxidase or sodium meta-periodate may yield carbonyl (aldehyde and ketone) groups in the protein that can react with appropriate groups on the drug or other moiety (Hermanson, Bioconjugate Techniques). In another embodiment, proteins containing N-terminal serine or threonine residues can react with sodium meta-periodate, resulting in production of an aldehyde in place of the first amino acid (Geoghegan and Stroh, Bioconjugate Chem. 3:138-146 (1992); U.S. Pat. No. 5,362,852). Such aldehyde can be reacted with a drug moiety or linker nucleophile.
Likewise, nucleophilic groups on a moiety (such as a drug moiety) include, but are not limited to: amine, thiol, hydroxyl, hydrazide, oxime, hydrazine, thiosemicarbazone, hydrazine carboxylate, and arylhydrazide groups capable of reacting to form covalent bonds with electrophilic groups on linker moieties and linker reagents including: (i) active esters such as NHS esters, HOBt esters, haloformates, and acid halides; (ii) alkyl and benzyl halides such as haloacetamides; and (iii) aldehydes, ketones, carboxyl, and maleimide groups.
Alternatively, a fusion protein comprising the heteromultimer and cytotoxic agent may be made, e.g., by recombinant techniques or peptide synthesis. The length of DNA may comprise respective regions encoding the two portions of the conjugate either adjacent one another or separated by a region encoding a linker peptide which does not destroy the desired properties of the conjugate. In yet another embodiment, the heteromultimer may be conjugated to a “receptor” (such streptavidin) for utilization in tumor pre-targeting wherein the heteromultimer-receptor conjugate is administered to the individual, followed by removal of unbound conjugate from the circulation using a clearing agent and then administration of a “ligand” (e.g., avidin) which is conjugated to a cytotoxic agent (e.g., a radionucleotide).
V. Therapeutic Uses
The heteromultimers described herein (e.g., an HD tether-containing single-chain monospecific or multispecific antibody, an HD tether-containing monospecific or multispecific antibody, an immunoadhesin-antibody complex) may be used for therapeutic applications. For example, such heteromultimers can be used for the treatment of any disease for which there is a suitable candidate target for heteromultimer generation, including proliferative diseases, cancer, angiogenic disorders, inflammatory disorders, autoimmune diseases, and immune disorders.
In addition to therapeutic uses, the heteromultimers of the invention can be used for other purposes, including diagnostic methods, such as diagnostic methods for any disease or condition for which there is a suitable candidate target for antibody generation, such as the above diseases or conditions.
VI. Dosages, Formulations, and Duration
The heteromultimers of this invention will be formulated, dosed, and administered in a fashion consistent with good medical practice. Factors for consideration in this context include the particular disorder being treated, the particular mammal being treated, the clinical condition of the individual subject, the cause of the disorder, the site of delivery of the agent, the method of administration, the scheduling of administration, and other factors known to medical practitioners. The “therapeutically effective amount” of the proteins to be administered will be governed by such considerations, and is the minimum amount necessary to prevent, ameliorate, or treat a particular disorder (e.g., a proliferative disease, cancer, an angiogenic disorder, an inflammatory disorder, an autoimmune disease, or an immune disorder). The proteins need not be, but are optionally, formulated with one or more agents currently used to prevent or treat the disorder. The effective amount of such other agents depends on the amount of proteins present in the formulation, the type of disorder or treatment, and other factors discussed above. These are generally used in the same dosages and with administration routes as used hereinbefore or about from 1 to 99% of the heretofore employed dosages.
In one embodiment, the present invention can be used for increasing the duration of survival of a human subject susceptible to or diagnosed with a particular disorder for which there is a suitable candidate target for heteromultimer generation. Duration of survival is defined as the time from first administration of the drug to death. Duration of survival can also be measured by stratified hazard ratio (HR) of the treatment group versus control group, which represents the risk of death for a subject during the treatment.
In yet another embodiment, the methods of the present invention significantly increases the response rate in a group of human subjects susceptible to or diagnosed with a disorder and whom are being treated with one or more therapies directed to the disorder. Response rate is defined as the percentage of treated subjects who responded to the treatment. In one aspect, the combination treatment of the invention using proteins of this invention and surgery or another form of therapy (e.g., radiation therapy or chemotherapeutic agents) significantly increases response rate in the treated subject group compared to the group treated with surgery or another form of therapy alone, the increase having a Chi-square p-value of less than 0.005. Additional measurements of therapeutic efficacy in the treatment of cancers are described in U.S. Patent Application Publication No. 20050186208.
Therapeutic formulations are prepared using standard methods known in the art by mixing the active ingredient having the desired degree of purity with optional physiologically acceptable carriers, excipients or stabilizers (Remington's Pharmaceutical Sciences (20th edition), ed. A. Gennaro, 2000, Lippincott, Williams & Wilkins, Philadelphia, Pa.). Acceptable carriers, include saline, or buffers such as phosphate, citrate and other organic acids; antioxidants including ascorbic acid; low molecular weight (less than about 10 residues) polypeptides; proteins, such as serum albumin, gelatin or immunoglobulins; hydrophilic polymers such as polyvinylpyrrolidone, amino acids such as glycine, glutamine, asparagines, arginine or lysine; monosaccharides, disaccharides, and other carbohydrates including glucose, mannose, or dextrins; chelating agents such as EDTA; sugar alcohols such as mannitol or sorbitol; salt-forming counterions such as sodium; and/or nonionic surfactants such as TWEENTM, PLURONICSTM, or PEG.
Optionally, but preferably, the formulation contains a pharmaceutically acceptable salt, preferably sodium chloride, and preferably at about physiological concentrations. Optionally, the formulations of the invention can contain a pharmaceutically acceptable preservative. In some embodiments the preservative concentration ranges from 0.1 to 2.0%, typically v/v. Suitable preservatives include those known in the pharmaceutical arts. Benzyl alcohol, phenol, m-cresol, methylparaben, and propylparaben are preferred preservatives. Optionally, the formulations of the invention can include a pharmaceutically acceptable surfactant at a concentration of 0.005 to 0.02%.
The formulation herein may also contain more than one active compound as necessary for the particular indication being treated, preferably those with complementary activities that do not adversely affect each other. Such molecules are suitably present in combination in amounts that are effective for the purpose intended.
The active ingredients may also be entrapped in microcapsules prepared, for example, by coacervation techniques or by interfacial polymerization, for example, hydroxymethylcellulose or gelatin-microcapsule and poly-(methylmethacylate) microcapsule, respectively, in colloidal drug delivery systems (for example, liposomes, albumin microspheres, microemulsions, nano-particles and nanocapsules) or in macroemulsions. Such techniques are disclosed in Remington's Pharmaceutical Sciences, supra.
Sustained-release preparations may be prepared. Suitable examples of sustained-release preparations include semipermeable matrices of solid hydrophobic polymers containing the heteromultimer, which matrices are in the form of shaped articles, e.g., films, or microcapsule. Examples of sustained-release matrices include polyesters, hydrogels (for example, poly(2-hydroxyethyl-methacrylate), or poly(vinylalcohol)), polylactides (U.S. Pat. No. 3,773,919), copolymers of L-glutamic acid and γ ethyl-L-glutamate, non-degradable ethylene-vinyl acetate, degradable lactic acid-glycolic acid copolymers such as the LUPRON DEPOTTM (injectable microspheres composed of lactic acid-glycolic acid copolymer and leuprolide acetate), and poly-D-(−)-3-hydroxybutyric acid. While polymers such as ethylene-vinyl acetate and lactic acid-glycolic acid enable release of molecules for over 100 days, certain hydrogels release proteins for shorter time periods. When encapsulated heteromultimers of the invention remain in the body for a long time, they may denature or aggregate as a result of exposure to moisture at 37° C., resulting in a loss of biological activity and possible changes in immunogenicity. Rational strategies can be devised for stabilization depending on the mechanism involved. For example, if the aggregation mechanism is discovered to be intermolecular S—S bond formation through thio-disulfide interchange, stabilization may be achieved by modifying sulfhydryl residues, lyophilizing from acidic solutions, controlling moisture content, using appropriate additives, and developing specific polymer matrix compositions.
The proteins described herein (e.g., an HD tether-containing single-chain monospecific or multispecific antibody, an HD tether-containing multi-chain monospecific or multispecific heteromultimer, an immunoadhesin-antibody complex) are administered to a human subject, in accord with known methods, such as intravenous administration as a bolus or by continuous infusion over a period of time, by intramuscular, intraperitoneal, intracerobrospinal, subcutaneous, intra-articular, intrasynovial, intrathecal, oral, topical, or inhalation routes. Local administration may be particularly desired if extensive side effects or toxicity is associated with antagonism to the target molecule recognized by the proteins. An ex vivo strategy can also be used for therapeutic applications. Ex vivo strategies involve transfecting or transducing cells obtained from the subject with a polynucleotide encoding a heteromultimer of this invention. The transfected or transduced cells are then returned to the subject. The cells can be any of a wide range of types including, without limitation, hemopoietic cells (e.g., bone marrow cells, macrophages, monocytes, dendritic cells, T cells, or B cells), fibroblasts, epithelial cells, endothelial cells, keratinocytes, or muscle cells.
In one example, the heteromultimer of the invention is administered locally, e.g., by direct injections, when the disorder or location of the tumor permits, and the injections can be repeated periodically. The protein complex can also be delivered systemically to the subject or directly to the tumor cells, e.g., to a tumor or a tumor bed following surgical excision of the tumor, in order to prevent or reduce local recurrence or metastasis.
VII. Articles of Manufacture
Another embodiment of the invention is an article of manufacture containing one or more heteromultimer described herein, and materials useful for the treatment or diagnosis of any disorder for which there is a suitable target for heteromultimer generation. 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, etc. The containers may be formed from a variety of materials such as glass or plastic. The container holds a composition that is effective for treating 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 pierceable by a hypodermic injection needle). At least one active agent in the composition is a heteromultimer of the invention. The label or package insert indicates that the composition is used for treating the particular condition. The label or package insert will further comprise instructions for administering the heteromultimer composition to the subject. Articles of manufacture and kits comprising combinatorial therapies described herein are also contemplated.
Package insert refers to instructions customarily included in commercial packages of therapeutic products that contain information about the indications, usage, dosage, administration, contraindications and/or warnings concerning the use of such therapeutic products.
Additionally, the article of manufacture may further comprise a second 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 considered from a commercial and user standpoint, including other buffers, diluents, filters, needles, and syringes.
Kits are also provided that are useful for various purposes, e.g., for purification or immunoprecipitation of an antigen from cells. For isolation and purification of an antigen the kit can contain a heteromultimer coupled to beads (e.g., sepharose beads). Kits can be provided which contain the heteromultimers for detection and quantitation of the antigen in vitro, e.g., in an ELISA or a Western blot. As with the article of manufacture, the kit comprises a container and a label or package insert on or associated with the container. The container holds a composition comprising at least one heteromultimer of the invention. Additional containers may be included that contain, e.g., diluents and buffers or control heteromultimers. The label or package insert may provide a description of the composition as well as instructions for the intended in vitro or diagnostic use.
VIII. Target Molecules
Examples of molecules that may be targeted by a heteromultimer (e.g., a single-chain or multi-chain antibody, or an immunoadhesin-antibody complex) of this invention include, but are not limited to, soluble serum proteins, receptor proteins, membrane-bound proteins (e.g., adhesins), cytokines, chemokines, growth factors, and hormones.
Soluble antigens or fragments thereof, optionally conjugated to other molecules, can be used as immunogens for generating heteromultimers. For transmembrane molecules, such as receptors, fragments of these (e.g., the extracellular domain of a receptor) can be used as the immunogen. Alternatively, cells expressing the transmembrane molecule can be used as the immunogen. Such cells can be derived from a natural source (e.g., cancer cell lines) or may be cells which have been transformed by recombinant techniques to express the transmembrane molecule. Other antigens and forms thereof useful for preparing heteromultimers will be apparent to those in the art.
The foregoing written description is considered to be sufficient to enable one skilled in the art to practice the invention. The following Examples are offered for illustrative purposes only, and are not intended to limit the scope of the present invention in any way. Indeed, various modifications of the invention in addition to those shown and described herein will become apparent to those skilled in the art from the foregoing description and fall within the scope of the appended claims. The description provided in the Examples is intended to be considered generally as a part of the invention.
EXAMPLES
Example 1. Construction of Vectors for the Expression of HD Tether-Containing Heteromultimers
All HD tether-containing heteromultimeric single-chain antibody constructs were made from existing IgG1 monoclonal antibody constructs already available in-house. LCs were prepared using PCR wherein the 3′ primer of the LC extended beyond the LC C-terminus, encoding for the N-terminal portion of the CLH-tether and terminating in a BamHI site. The 5′ LC primer terminated in a ClaI site. The PCR fragment was then digested and cloned into a similarly digested and dephosphorylated pRK vector (Genentech Inc.; Eaton et al., Biochemistry 25:8343-8347 (1986)). The cognate HC was then prepared using PCR wherein the 5′ primer extended beyond the HC N-terminus (minus the signal sequence), encoding for the C-terminal portion of the CLH-tether and terminating in a BamHI site. The 3′ HC primer terminated in an XbaI site. The HC PCR fragment was digested and cloned into a similarly prepared plasmid containing the cognate LC described above and thus forming a tethered half-antibody. The BamHI site is positioned such that it encodes for the amino acid residues “GS” and maintains the integrity of the tether's GGS repeats. The lysine residue at position K222 (Kabat numbering scheme) was next mutated into an alanine residue using Stratagene's Quikchange II XL site-directed mutagenesis kit.
Two of the above-described CLH-tethered half-antibodies were then joined together via another round of PCR wherein the half-antibody destined for the N-terminus of the single-chain antibody was amplified using the same 5′ LC primer used above and a 3′ primer which extended beyond the C-terminus of the HC, encoding for the N-terminus of the HD tether and terminating in a BspEI site. The PCR fragment was digested and cloned into a similarly digested and dephosphorylated pRK vector. The half-antibody destined for the C-terminus of the heteromultimeric single-chain antibody was amplified using the same 3′ HC primer used in constructing the half-antibodies and a 5′ primer which extended beyond the LC N-terminus (minus the signal sequence), encoding for the C-terminal portion of the HD tether and terminating in a BspEI site. The PCR product was digested and cloned into a similarly digested and dephosphorylated N-terminal construct vector. As with BamHI, BspEI can be positioned such that it maintains the integrity of the tether's GGS repeats.
The construction of HD tether-containing heteromultimeric multi-chain antibodies was similar, differing only in that the N-terminal “half-antibody” began with the HC signal sequence and its cognate LC was expressed separately from a second pRK plasmid.
Example 2. Cleavage and Purification of HD Tether-Containing Heteromultimers
An exemplary schema that can be used to purify heteromultimers of the invention is shown below.




In particular, heteromultimers were purified from conditioned media using mAbSure Select resin from GE Healthcare (Sweden) overnight at 4° C. The column was washed with two column volumes (CV) of PBS (phosphate buffered saline), followed by 10 CV of PBS+0.1% Triton X114 detergent, followed by 10 CV potassium phosphate buffer. The columns were eluted with 100 mM Acetic Acid (pH 2.9) and immediately adjusted to pH 8.0 with Tris (200 mM final concentration), pH 8.0. HD tethers were removed from heteromultimers upon treatment with a 1:500 (wt:wt) ratio of Lys-C endopeptidase (Wako Pure Chemical Laboratories) at 37° C. for 1-5 hours. Sample then loaded onto column to remove enzyme. Residual furin recognition sites are subsequently removed using 1:5 (wt:wt) porcine Carboxypeptidase B (Roche Applied Sciences, Cat #10103233001) for 1-5 hours. Cleaved samples were loaded onto a cation exchange column to remove enzyme. Peak fractions were pooled and dialyzed against PBS overnight prior to mass spectrum analysis to ensure identity and purity.
Example 3. Characterization of Engineered Heteromultimers
To determine whether the exemplary heteromultimers constructed using HD tether heterodimerization technology of the invention retained the binding properties of the antibodies or adhesins from which their sequences were derived, binding assays were conducted (FIGS. 6A-6D). These binding assays were run using the kinetics wizard program on the ForteBio Octet system. All samples tested were at a concentration of 25 μg/ml, a concentration that indicates saturation of the anti-human IgG probes in repeat experiments and among varying samples. The probes were loaded with the first sample for 10 minutes and washed for 30 seconds in PBS. All associations for the second and third samples were carried out for 15 minutes with 30-second PBS washes between associations.
Other Embodiments
All patents, patent applications, patent application publications, and other publications cited or referred to in this specification are herein incorporated by reference to the same extent as if each independent patent, patent application, patent application publication or publication was specifically and individually indicated to be incorporated by reference.

## Claims

1. A single-chain antibody comprising a single polypeptide, wherein said a single polypeptide comprises the following domains positioned relative to each other in an N-terminal to C-terminal direction: VL1-CL1-CLH tether1-VH1-CH11-hinge1-CH21-CH31-HD tether-VL2-CL2-CLH tether2-VH2-CH12-hinge2-CH22-CH32.

2. The single-chain antibody of claim 1, wherein said HD tether is between 15-100 amino acids in length.

3. The single-chain antibody of claim 2, wherein said HD tether is between 30-39 amino acids in length.

4. The single-chain antibody of claim 2, wherein said HD tether comprises glycine (G) and serine (S) residues.

5. The single-chain antibody of claim 4, wherein said HD tether comprises GGS repeats.

6. The single-chain antibody of claim 5, wherein said HD tether comprises 8 to 9 GGS repeats (SEQ ID NO: 19).

7. The single-chain antibody of claim 1, wherein said HD tether comprises an amino acid sequence cleavable by an endopeptidase.

8. The single-chain antibody of claim 7, wherein said amino acid sequence is cleaved in situ by said endopeptidase.

9. The single-chain antibody of claim 7, wherein said amino acid sequence is cleaved upon addition of said endopeptidase following purification.

10. The single-chain antibody of claim 7, wherein said HD tether comprises two amino acid sequences cleavable by an endopeptidase located at the N- and C-termini of said HD tether.

11. The single-chain antibody of claim 7, wherein said endopeptidase is selected from the group consisting of furin, urokinase, thrombin, tissue plasminogen activator (tPa), genenase, Lys-C, Arg-C, Asp-N, Glu-C, Factor Xa, tobacco etch virus protease (TEV), enterokinase, human rhinovirus C3 protease (HRV C3), and kininogenase.

12. The single-chain antibody of claim 11, wherein said endopeptidase is furin.

13. The single-chain antibody of claim 12, wherein said HD tether comprises two endopeptidase cleavage sites located at the N- and C-termini of said HD tether, wherein one of said endopeptidase cleavage sites is a furin cleavage site.

14. The single-chain antibody of claim 12, wherein the amino acid sequence cleavable by furin comprises the amino acid sequence RKRKRR (SEQ ID NO:9).

15. The single-chain antibody of claim 12, wherein the amino acid sequence cleavable by furin comprises the amino acid sequence RHRQPR (SEQ ID NO:10).

16. The single-chain antibody of claim 13, wherein one of said endopeptidase cleavage sites is a Lys-C cleavage site.

17. The single-chain antibody of claim 1, wherein said CLH tether1 or said CLH tether2 comprises glycine (G) and serine (S) residues.

18. The single-chain antibody of claim 17, wherein said CLH tether1 or said CLH tether2 comprises GGS repeats.

19. The single-chain antibody of claim 17, wherein said CLH tether1 and said CLH tether2 are each between 10-80 amino acids in length.

20. The single-chain antibody of claim 19, wherein said CLH tether1 and said CLH tether2 are each between 20-40 amino acids in length.

21. The single-chain antibody of claim 1, wherein said CLH tether1 or said CLH tether2 comprises an amino acid sequence cleavable by an endopeptidase.

22. The single-chain antibody of claim 21, wherein said amino acid sequence is cleaved in situ by said endopeptidase.

23. The single-chain antibody of claim 21, wherein said amino acid sequence is cleaved upon addition of said endopeptidase following purification.

24. The single-chain antibody of claim 21, wherein said endopeptidase is selected from the group consisting of furin, urokinase, thrombin, tissue plasminogen activator (tPa), genenase, Lys-C, Arg-C, Asp-N, Glu-C, Factor Xa, tobacco etch virus protease (TEV), enterokinase, human rhinovirus C3 protease (HRV C3), and kininogenase.

25. The single-chain antibody of claim 24, wherein said endopeptidase is furin.

26. The single-chain antibody of claim 25, wherein said CLH tether1 or said CLH tether2 comprises two endopeptidase cleavage sites located at the N- and C-termini of said CLH tether1 or said CLH tether2, wherein said endopeptidase cleavage sites are both furin cleavage sites.

27. The single-chain antibody of claim 25, wherein the amino acid sequence cleavable by furin comprises the amino acid sequence RKRKRR (SEQ ID NO:9).

28. The single-chain antibody of claim 25, wherein the amino acid sequence cleavable by furin comprises the amino acid sequence RHRQPR (SEQ ID NO:10).

29. The single-chain antibody of claim 1, wherein said first hinge domain or said second hinge domain comprises Glu216 to Pro230 of human IgG1.

30. The single-chain antibody of claim 29, wherein said first hinge domain or said second hinge domain comprises a Lys-C endopeptidase cleavage site.

31. The single-chain antibody of claim 30, wherein said Lys-C endopeptidase cleavage site comprises an inactivating mutation.

32. The single-chain antibody of claim 31, wherein said inactivating mutation is a K222A substitution (EU numbering system).

33. The single-chain antibody of claim 1, wherein said single-chain antibody is a bispecific or a multispecific single-chain antibody.

34. The single-chain antibody of claim 33, wherein said single-chain antibody is capable of binding at least two antigens.

35. The single-chain antibody of claim 33, wherein said single-chain antibody is capable of binding at least two epitopes on the same antigen.

36. The single-chain antibody of claim 1, wherein said single-chain antibody comprises a constant region conjugated to a functional moiety on at least one Fc component.

37. The single-chain antibody of claim 1, wherein said single-chain antibody comprises one or more cleavage sites for an exopeptidase following cleavage of one or more of said HD or CLH tethers.

38. The single-chain antibody of claim 37, wherein said one or more cleavage sites are cleaved in situ by said exopeptidase.

39. The single-chain antibody of claim 37, wherein said one or more cleavage sites are cleaved upon addition of said exopeptidase following purification.

40. The single-chain antibody of claim 37, wherein said exopeptidase is selected from the group consisting of Carboxypeptidase A, Carboxypeptidase B, plasma Carboxypeptidase B, Carboxypeptidase D, Carboxypeptidase E, Carboxypeptidase M, Carboxypeptidase N, and Carboxypeptidase Z.

41. The single-chain antibody of claim 40, wherein said exopeptidase cleaves at a basic residue.

42. The single-chain antibody of claim 41, wherein said exopeptidase is a Carboxypeptidase B.

43. The single-chain antibody of claim 1, wherein said CH31 and CH32 domains each comprise a protuberance or cavity, and wherein said protuberance or cavity in said CH31 domain is positionable in said cavity or protuberance, respectively, in said CH32 domain.

44. The single-chain antibody of claim 43, wherein said CH31 and CH32 domains meet at an interface between said protuberance and cavity.

45. The single-chain antibody of claim 1, wherein said polypeptide further comprises:
(a) a protuberance or cavity in said CH11 domain or said CH12 domain or both, and
(b) a protuberance or cavity in said CL1 domain or said CL2 domain or both; and wherein:
(c) said protuberance or cavity in said CH11 domain is positionable in said cavity or protuberance, respectively, in said CL1 domain,
(d) said protuberance or cavity in said CH12 domain is positionable in said cavity or protuberance, respectively, in said CL2 domain; or
(e) both (c) and (d).

46. The single-chain antibody of claim 45, wherein said CH11 and CL1 domains, said CH12 and CL2 domains, or all four of said domains meet at an interface between said protuberance and cavity.

47. The single-chain antibody of claim 1, wherein one or more of said CH21 or CH22 domains comprises a CH2 domain mutation that affects antibody effector function.

48. The single-chain antibody of claim 47, wherein said CH2 domain mutation that affects antibody effector function is an N297 mutation.

49. The single-chain antibody of claim 24, wherein said CLH tether1 or said CLH tether2 comprises two endopeptidase cleavage sites located at the N- and C-termini of said CLH tether1 or said CLH tether2, wherein one of said endopeptidase sites is a furin cleavage site and one of said endopeptidase sites is a Lys-C cleavage site.

50. The single-chain antibody of claim 12, wherein the amino acid sequence cleavable by furin comprises the amino acid sequence of RXRXRR (SEQ ID NO:8), wherein X is any amino acid residue.

51. The single-chain antibody of claim 25, wherein the amino acid sequence cleavable by furin comprises the amino acid sequence of RXRXRR (SEQ ID NO:8), wherein X is any amino acid residue.

52. The single chain antibody of claim 12, wherein the amino acid sequence cleavable by furin comprises the amino acid sequence of RXRXYR (SEQ ID NO: 7), wherein Y is K or R and X is any amino acid residue.

53. The single chain antibody of claim 25, wherein the amino acid sequence cleavable by furin comprises the amino acid sequence of RXRXYR (SEQ ID NO: 7), wherein Y is K or R and X is any amino acid residue.