# Patent

## Title
Methods of selecting epidermal growth factor receptor (EGFR) binding agents

## Abstract

The present application relates to methods of selecting EGFr binding agents. In certain embodiments, such EGFr binding agents bind to at least a portion of a panitumumab epitope on an EGFr. In certain embodiments, such EGFr binding agents do not bind to a panitumumab epitope on an EGFr.

## Background
This application claims the benefit of U.S. Provisional Application No. 60/999,602, filed Oct. 19, 2007. U.S. Provisional Application No. 60/999,602 is incorporated herein by reference in its entirety for any purpose.


The present application relates to methods of selecting Epidermal Growth Factor Receptor (EGFr) binding agents. In certain embodiments, such EGFr binding agents bind to at least a portion of a panitumumab epitope on an EGFr. In certain embodiments, such EGFr binding agents do not bind to a panitumumab epitope on an EGFr.
BACKGROUND
Certain applications of monoclonal antibodies in cancer therapy use the ability of the antibody to specifically deliver to the cancerous tissues cytotoxic effector functions such as immune-enhancing isotypes, toxins or drugs. An alternative approach is to utilize monoclonal antibodies to directly affect the survival of tumor cells by depriving them of essential extracellular proliferation signals, such as those mediated by growth factors through their cell receptors. One of the attractive targets in this approach is the epidermal growth factor receptor (EGFr), which binds EGF and transforming growth factor α (TGFα) (see, e.g., Ullrich et al., Cell 61:203-212, 1990; Baselga et al., Pharmacol. Ther. 64:127-154, 1994; Mendelsohn et al., in Biologic Therapy of Cancer 607-623, Philadelphia:J. B. Lippincott Co., 1995; Fan et al., Curr. Opin. Oncol. 10:67-73, 1998). Binding of EGF or TGFα to EGFr, a 170 kDa transmembrane cell surface glycoprotein, triggers a cascade of cellular biochemical events, including EGFr autophosphorylation and internalization, which culminates in cell proliferation (see, e.g., Ullrich et al., Cell 61:203-212, 1990).
Several observations implicate EGFr in supporting development and progression of human solid tumors. EGFr has been demonstrated to be overexpressed on many types of human solid tumors (see, e.g., Mendelsohn Cancer Cells 7:359 (1989), Mendelsohn Cancer Biology 1:339-344 (1990), Modjtahedi and Dean Int'l J. Oncology 4:277-296 (1994)). For example, EGF-r overexpression has been observed in certain lung, breast, colon, gastric, brain, bladder, head and neck, ovarian, and prostate carcinomas (see, e.g., Modjtahedi and Dean Int'l J. Oncology 4:277-296 (1994)). The increase in receptor levels has been reported to be associated with a poor clinical prognosis (see, e.g., Baselga et al. Pharmacol. Ther. 64:127-154, 1994; Mendelsohn et al., Biologic Therapy of Cancer pp. 607-623, Philadelphia:J. B. Lippincott Co., 1995; Modjtahedi et al., Intl. J. of Oncology 4:277-296, 1994; Gullick, Br. Medical Bulletin, 47:87-98, 1991; Salomon et al., Crit. Rev. Oncol. Hematol. 19:183-232, 1995). Both epidermal growth factor (EGF) and transforming growth factor-alpha (TGF-α) have been demonstrated to bind to EGF-r and to lead to cellular proliferation and tumor growth. In many cases, increased surface EGFr expression was accompanied by production of TGFα or EGF by tumor cells, suggesting the involvement of an autocrine growth control in the progression of those tumors (see, e.g., Baselga et al. Pharmacol. Ther. 64:127-154, 1994; Mendelsohn et al., Biologic Therapy of Cancer pp. 607-623, Philadelphia:J. B. Lippincott Co., 1995; Modjtahedi et al., Intl. J. of Oncology 4:277-296, 1994; Salomon et al., Crit. Rev. Oncol. Hematol. 19:183-232, 1995).
Thus, certain groups have proposed that antibodies against EGF, TGF-α, and EGF-r may be useful in the therapy of tumors expressing or overexpressing EGF-r (see, e.g., Mendelsohn Cancer Cells 7:359 (1989), Mendelsohn Cancer Biology 1:339-344 (1990), Modjtahedi and Dean Int'l J. Oncology 4:277-296 (1994), Tosi et al. Int'l J. Cancer 62:643-650 (1995)). Indeed, it has been demonstrated that anti-EGF-r antibodies blocking EGF and TGF-α binding to the receptor appear to inhibit tumor cell proliferation. At the same time, however, anti-EGF-r antibodies have not appeared to inhibit EGF and TGF-α independent cell growth (Modjtahedi and Dean Int'l J. Oncology 4:277-296 (1994)).
Monoclonal antibodies specific to the human EGFr, capable of neutralizing EGF and TGFα binding to tumor cells and of inhibiting ligand-mediated cell proliferation in vitro, have been generated from mice and rats (see, e.g., Baselga et al., Pharmacol. Ther. 64:127-154, 1994; Mendelsohn et al., in Biologic Therapy of Cancer pp. 607-623, Philadelphia:J. B. Lippincott Co., 1995; Fan et al., Curr. Opin. Oncol. 10:67-73, 1998; Modjtahedi et al., Intl. J. Oncology 4:277-296, 1994). Some of those antibodies, such as the mouse 108, 225 (see, e.g., Aboud-Pirak et al., J. Natl. Cancer Inst 80:1605-1611, 1988) and 528 (see, e.g., Baselga et al., Pharmacol. Ther. 64:127-154, 1994; Mendelsohn et al., in Biologic Therapy of Cancer pp. 607-623, Philadelphia:J. B. Lippincott Co., 1995) or the rat ICR16, ICR62 and ICR64 (see, e.g., Modjtajedi et al., Intl. J. Oncology 4:277-296, 1994; Modjtahedi et al., Br. J. Cancer 67:247-253, 1993; Modjtahedi et al., Br. J. Cancer 67:254-261, 1993) monoclonal antibodies, were evaluated extensively for their ability to affect tumor growth in xenograft mouse models. Most of the anti-EGFr monoclonal antibodies were efficacious in preventing tumor formation in athymic mice when administered together with the human tumor cells (Baselga et al. Pharmacol. Ther. 64:127-154, 1994; Modjtahedi et al., Br. J. Cancer 67: 254-261, 1993). When injected into mice bearing established human tumor xenografts, the mouse monoclonal antibodies 225 and 528 caused partial tumor regression and required the co-administration of chemotherapeutic agents, such as doxorubicin or cisplatin, for eradication of the tumors (Baselga et al. Pharmacol. Ther. 64:127-154, 1994; Mendelsohn et al., in Biologic Therapy of Cancer pp. 607-623, Philadelphia:J. B. Lippincott Co., 1995; Fan et al., Cancer Res. 53:4637-4642, 1993; Baselga et al., J. Natl. Cancer Inst. 85: 1327-1333, 1993). A chimeric version of the 225 monoclonal antibody (C225), in which the mouse antibody variable regions are linked to human constant regions, exhibited an improved in vivo anti-tumor activity but only at high doses (see, e.g., Goldstein et al., Clinical Cancer Res. 1:1311-1318, 1995; Prewett et al., J. Immunother. Emphasis Tumor Immunol. 19:419-427, 1996). The rat ICR16, ICR62, and ICR64 antibodies caused regression of established tumors but not their complete eradication (Modjtahedi et al., Br. J. Cancer 67:254-261, 1993). These results established EGFr as a promising target for antibody therapy against EGFr-expressing solid tumors and led to human clinical trials with the C225 monoclonal antibody in multiple human solid cancers (see, e.g., Baselga et al. Pharmacol. Ther. 64:127-154, 1994; Mendelsohn et al., Biologic Therapy of Cancer pp. 607-623, Philadelphia:J. B. Lippincott Co., 1995; Modjtahedi et al., Intl. J. of Oncology 4:277-296, 1994).
Certain advances in the biological arts made it possible to produce a fully human anti-EGFr antibody. Using mice transgenic for human immunoglobulin genes (XenomouseTM technology, Abgenix, Inc.), human antibodies specific for human EGFr were developed (see, e.g., Mendez, Nature Genetics, 15:146-156, 1997; Jakobovits, Adv. Drug Deliv. Rev., 31 (1-2):33-42, 1998; Jakobovits, Expert Opin. Invest. Drugs, 7(4):607-614, 1998; Yang et al., Crit. Rev. Oncol. Hematol. 38(1):17-23, 2001; WO98/24893; WO 98/50433). One such antibody, panitumumab, a human IgG2 monoclonal antibody with an affinity of 5×10−11 M for human EGFr, has been shown to block binding of EGF to the EGFr, to block receptor signaling, and to inhibit tumor cell activation and proliferation in vitro (see, e.g., WO98/50433; U.S. Pat. No. 6,235,883). Studies in athymic mice have demonstrated that panitumumab also has in vivo activity, not only preventing the formation of human epidermoid carcinoma A431 xenografts in athymic mice, but also eradicating already-established large A431 tumor xenografts (see, e.g., Yang et al., Crit. Rev. Oncol. Hematol. 38(1):17-23, 2001; Yang et al., Cancer Res. 59(6):1236-43, 1999). Panitumumab has been considered for the treatment of renal carcinoma, colorectal adenocarcinoma, prostate cancer, and non small cell squamous lung carcinoma, among other cancers (see, e.g., U.S. Patent Publication No. 2004/0033543) Panitumumab has been approved by the Food & Drug Administration to treat patients with metastatic colorectal cancer.
SUMMARY
In certain embodiments, methods of selecting a specific binding agent to an epidermal growth factor receptor (EGFr) polypeptide are provided. In certain embodiments, the method selects a specific binding agent that binds to at least a portion of a panitumumab epitope on an EGFr polypeptide. In certain embodiments, the method comprises a) contacting an EGFr polypeptide with an agent; b) determining the affinity of the agent for the EGFr polypeptide; c) contacting a mutant EGFr polypeptide with the agent, wherein the mutant EGFr polypeptide comprises at least one point mutation at at least one amino acid position selected from P349, D355, F412, I438, K443, K465, and I467; d) determining the affinity of the agent for the mutant EGFr polypeptide; and e) selecting the agent if the affinity for the EGFr polypeptide is greater than the affinity for the mutant EGFr polypeptide.
In certain embodiments, the method comprises a) contacting a first EGFr polypeptide with an agent, wherein the first EGFr polypeptide comprises an L2 domain; b) determining the affinity of the agent for the first EGFr polypeptide; c) contacting a second EGFr polypeptide with the agent, wherein the second EGFr polypeptide lacks an L2 domain; d) determining the affinity of the agent for the second EGFr polypeptide; and e) selecting the agent if the affinity for the first EGFr polypeptide is greater than the affinity for the second EGFr polypeptide.
In certain embodiments, methods of selecting a specific binding agent to an epidermal growth factor receptor (EGFr) polypeptide are provided. In certain embodiments, the method selects a specific binding agent does not bind to a panitumumab epitope on an EGFr polypeptide (EGFr). In certain embodiments, the method comprises a) contacting an EGFr polypeptide with an agent; b) determining the affinity of the agent for the EGFr polypeptide; c) contacting a mutant EGFr polypeptide with the agent, wherein the mutant EGFr polypeptide comprises at least one point mutation at least one amino acid position selected from P349, D355, F412, I438, K443, K465, and I467; d) determining the affinity of the agent for the mutant EGFr polypeptide; and e) selecting the agent if the affinity for the EGFr polypeptide is similar to the affinity for the mutant EGFr polypeptide.
In certain embodiments, the method comprises a) contacting a first EGFr polypeptide with an agent, wherein the first EGFr polypeptide comprises an L2 domain; b) determining the affinity of the agent for the first EGFr polypeptide; c) contacting a second EGFr polypeptide with the agent, wherein the second EGFr polypeptide lacks an L2 domain; d) determining the affinity of the agent for the second EGFr polypeptide; and e) selecting the agent if the affinity for the first EGFr polypeptide is similar to the affinity for the second EGFr polypeptide.



BRIEF DESCRIPTION OF THE FIGURES
FIG. 1 shows the amino acid sequence of human EGFr (SEQ ID NO: 1). The L1, CR1, L2, CR2, and transmembrane domains are indicated on the figure. The amino acid residues P349, D355, F412, I438, K443, K465, and I467 are also indicated on the figure.
FIGS. 2A and 2B show binding of panitumumab to certain EGFr protein fragments, as described in Example 1.
FIG. 3 shows a bar graph summarizing the binding of panitumumab to certain EGFr L2 domain point mutations, as described in Example 2.
FIG. 4 shows a bar graph indicating panitumumab inhibition of EGFr activation by certain ligands, as described in Example 3.



DETAILED DESCRIPTION OF CERTAIN EMBODIMENTS
The section headings used herein are for organizational purposes only and are not to be construed as limiting the subject matter described. All documents or portions of documents cited in this application, including but not limited to patents, patent applications, articles, books, and treatises, are expressly incorporated by reference herein in their entirety for any purpose. In the event that one or more of the documents, or portions of documents, incorporated by reference defines a term that contradicts that term's definition in this application, this application controls.
Standard techniques may be used for recombinant DNA, oligonucleotide synthesis, and tissue culture and transformation (e.g., electroporation, lipofection). Enzymatic reactions and purification techniques may be performed according to manufacturer's specifications or as commonly accomplished in the art or as described herein. The foregoing techniques and procedures may be generally performed according to conventional methods well known in the art and as described in various general and more specific references that are cited and discussed throughout the present specification. See e.g., Sambrook et al. Molecular Cloning:A Laboratory Manual (2d ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (1989)). Unless specific definitions are provided, the nomenclatures utilized in connection with, and the laboratory procedures and techniques of, analytical chemistry, synthetic organic chemistry, and medicinal and pharmaceutical chemistry described herein are those well known and commonly used in the art. Standard techniques may be used for chemical syntheses, chemical analyses, pharmaceutical preparation, formulation, delivery, and treatment of patients.
In this application, the use of the singular includes the plural unless specifically stated otherwise. In this application, the word “a” or “an” means “at least one” unless specifically stated otherwise. In this application, the use of “or” means “and/or” unless specifically stated otherwise. In the context of a multiple dependent claim, the use of “or” refers back to more than one preceding independent or dependent claim in the alternative only. Furthermore, the use of the term “including,” as well as other forms, such as “includes” and “included,” is not limiting. Also, terms such as “element” or “component” encompass both elements or components comprising one unit and elements or components that comprise more than one unit unless specifically stated otherwise.
DEFINITIONS
Unless otherwise defined, scientific and technical terms used in connection with the present invention shall have the meanings that are commonly understood by those of ordinary skill in the art. As utilized in accordance with the present disclosure, the following terms, unless otherwise indicated, shall be understood to have the following meanings:
The terms “isolated polynucleotide” and “isolated nucleic acid” are used interchangeably, and refer to a polynucleotide of genomic, cDNA, or synthetic origin or some combination thereof, which by virtue of its origin the “isolated polynucleotide” (1) is not associated with all or a portion of a polynucleotide in which the “isolated polynucleotide” is found in nature, (2) is linked to a polynucleotide which it is not linked to in nature, or (3) does not occur in nature as part of a larger sequence.
The terms “isolated protein” and “isolated polypeptide” and “isolated peptide” are used interchangeably, and refer to any polypeptide that (1) is free of at least some proteins with which it would normally be found, (2) is essentially free of other proteins from the same source, e.g., from the same species, (3) is expressed by a cell from a different species, or (4) does not occur in nature.
The terms “polypeptide” and “protein” are used interchangeably and are used herein as a generic term to refer to native protein, fragments, peptides, or analogs of a polypeptide sequence. Hence, native protein, fragments, and analogs are species of the polypeptide genus.
The terminology “X#Y” in the context of a mutation in a polypeptide sequence is art-recognized, where “#” indicates the location of the mutation in terms of the amino acid number of the polypeptide, “X” indicates the amino acid found at that position in the wild-type amino acid sequence, and “Y” indicates the mutant amino acid at that position. For example, the notation “D355T” with reference to the EGFr polypeptide indicates that there is an aspartic acid at amino acid number 355 of the wild-type EGFr sequence, and that aspartic acid is replaced with a threonine in the mutant EGFr sequence.
The terms “EGFr polypeptide” and “EGFr protein” are used interchangeably, and refer to a human EGFr polypeptide or fragment thereof, wherein the fragment thereof comprises at least one domain selected from an L1 domain, a CR1 domain, an L2 domain, and a CR2 domain. The amino acid sequence of an exemplary human EGFr polypeptide, without the 24 amino acid leader sequence, is shown in SEQ ID NO: 1 and in FIG. 1. In certain embodiments, an EGFr polypeptide comprises an L2 domain. In certain embodiments, an EGFr polypeptide lacks an L2 domain. An EGFr extracellular domain (“ECD”) polypeptide is an EGFr polypeptide that lacks the cytoplasmic and transmembrane domains. The amino acid sequence of an exemplary human EGFr ECD is shown in SEQ ID NO: 2. In certain embodiments, an EGFr ECD polypeptide comprises an L1 domain, a CR1 domain, an L2 domain, and a CR2 domain. In certain embodiments, an EGFr ECD polypeptide comprises an L2 domain. In certain embodiments, an EGFr ECD polypeptide lacks an L2 domain. The amino acid sequences for an exemplary L1 domain, an exemplary CR1 domain, an exemplary L2 domain, and an exemplary CR2 domain are shown in SEQ ID NOs:4, 5, 3, and 6, respectively. In certain instances, epidermal growth factor (EGF) binds to the L2 domain of an EGFr polypeptide.
A “binding fragment” of an EGFr polypeptide, as used herein, refers to a fragment of an EGFr polypeptide that is capable of binding to panitumumab. In certain embodiments, a binding fragment comprises the extracellular domain (“ECD”) of EGFr. In certain embodiments, a binding fragment comprises the L2 domain of EGFr. In certain embodiments, a binding fragment comprises the amino acid sequence of SEQ ID NO: 3.
The terms “mutant EGFr polypeptide” and “mutant EGFr protein” are used interchangeably, and refer to a human EGFr polypeptide comprising at least one point mutation in the extracellular domain. In certain embodiments, a mutant EGFr polypeptide comprises at least one point mutation at least one amino acid position selected from P349, D355, F412, I438, K443, K465, and I467. In certain embodiments, a mutant EGFr polypeptide comprises at least one point mutation selected from P349A, D355T, F412A, I438A, K443A, K465A, and I467A.
A mutant EGFr extracellular domain (“ECD”) polypeptide is a mutant EGFr polypeptide that lacks the cytoplasmic and transmembrane domains. In certain embodiments, a mutant EGFr ECD polypeptide comprises at least one point mutation at least one amino acid position selected from P349, D355, F412, I438, K443, K465, and I467. In certain embodiments, a mutant EGFr ECD polypeptide comprises at least one point mutation selected from P349A, D355T, F412A, I438A, K443A, K465A, and I467A.
The term “naturally-occurring” as used herein as applied to an object refers to the fact that an object can be found in nature. For example, a polypeptide or polynucleotide sequence that is present in an organism (including viruses) that can be isolated from a source in nature and which has not been intentionally modified by man in the laboratory or otherwise is naturally-occurring.
The term “operably linked” refers to components that are in a relationship permitting them to function in their intended manner. For example, in the context of a polynucleotide sequence, a control sequence may be “operably linked” to a coding sequence when the control sequence and coding sequence are in association with each other in such a way that expression of the coding sequence is achieved under conditions compatible with the functioning of the control sequence.
The term “control sequence” refers to polynucleotide sequences which may effect the expression and processing of coding sequences with which they are in association. The nature of such control sequences may differ depending upon the host organism. Certain exemplary control sequences for prokaryotes include, but are not limited to, promoters, ribosomal binding sites, and transcription termination sequences. Certain exemplary control sequences for eukaryotes include, but are not limited to, promoters, enhancers, and transcription termination sequences. In certain embodiments, “control sequences” can include leader sequences and/or fusion partner sequences.
The terms “polynucleotide” and “oligonucleotide” are used interchangeably, and as referred to herein means a polymeric form of nucleotides of at least 10 bases in length. In certain embodiments, the bases may comprise at least one of ribonucleotides, deoxyribonucleotides, and a modified form of either type of nucleotide. The term includes single and double stranded forms of DNA.
Similarly, unless specified otherwise, the lefthand end of single-stranded polynucleotide sequences is the 5′ end; the lefthand direction of double-stranded polynucleotide sequences is referred to as the 5′ direction. The direction of 5′ to 3′ addition of nascent RNA transcripts is referred to as the transcription direction. Sequence regions on the DNA strand having the same sequence as the RNA and which are 5′ to the 5′ end of the RNA transcript are referred to as “upstream sequences”. Sequence regions on the DNA strand having the same sequence as the RNA and which are 3′ to the 3′ end of the RNA transcript are referred to as “downstream sequences”.
The terms “mutant EGFr polynucleotide”, “mutant EGFr oligonucleotide,” and “mutant EGFr nucleic acid” are used interchangeably, and refer to a polynucleotide encoding a mutant EGFr polypeptide.
The terms “mutant EGFr ECD polynucleotide”, “mutant EGFr ECD oligonucleotide,” and “mutant EGFr ECD nucleic acid” are used interchangeably, and refer to a polynucleotide encoding a mutant EGFr ECD polypeptide.
As used herein, the twenty conventional amino acids and their abbreviations follow conventional usage. See Immunology—A Synthesis (2nd Edition, E. S. Golub and D. R. Gren, Eds., Sinauer Associates, Sunderland, Mass. (1991)), which is incorporated herein by reference. The term “amino acid” or “amino acid residue,” as used herein, refers to naturally occurring L amino acids or to D amino acids. The commonly used one- and three-letter abbreviations for amino acids are used herein (Bruce Alberts et al., Molecular Biology of the Cell, Garland Publishing, Inc., New York (4th ed. 2002)). Stereoisomers (e.g., D-amino acids) of the twenty conventional amino acids, unnatural amino acids such as α-, α-disubstituted amino acids, N-alkyl amino acids, lactic acid, and other unconventional amino acids may also be suitable components for polypeptides of the present invention. Examples of unconventional amino acids include, but are not limited to:4-hydroxyproline, γ-carboxyglutamate, ε-N,N,N-trimethyllysine, ε-N-acetyllysine, O-phosphoserine, N-acetylserine, N-formylmethionine, 3-methylhistidine, 5-hydroxylysine, σ-N-methylarginine, and other similar amino acids and imino acids (e.g., 4-hydroxyproline). In the polypeptide notation used herein, the lefthand direction is the amino terminal direction and the righthand direction is the carboxy-terminal direction, in accordance with standard usage and convention.
In certain embodiments, conservative amino acid substitutions include substitution with one or more unconventional amino acid residues. In certain embodiments, unconventional amino acid residues are incorporated by chemical peptide synthesis rather than by synthesis in biological systems.
The term “acidic residue” refers to an amino acid residue in D- or L-form that comprises at least one acidic group when incorporated into a polypeptide between two other amino acid residues that are the same or different. In certain embodiments, an acidic residue comprises a sidechain that comprises at least one acidic group. Exemplary acidic residues include, but are not limited to, aspartic acid (D) and glutamic acid (E). In certain embodiments, an acidic residue may be an unconventional amino acid.
The term “aromatic residue” refers to an amino acid residue in D- or L-form that comprises at least one aromatic group. In certain embodiments, an aromatic residue comprises a sidechain that comprises at least one aromatic group. Exemplary aromatic residues include, but are not limited to, phenylalanine (F), tyrosine (Y), and tryptophan (W). In certain embodiments, an aromatic residue may be an unconventional amino acid.
The term “basic residue” refers to an amino acid residue in F- or L-form that may comprise at least one basic group when incorporated into a polypeptide next to one or more amino acid residues that are the same or different. In certain embodiments, a basic residue comprises a sidechain that comprises at least one basic group. Exemplary basic residues include, but are not limited to, histidine (H), lysine (K), and arginine (R). In certain embodiments, a basic residue may be an unconventional amino acid.
The term “neutral hydrophilic residue” refers to an amino acid residue in D- or L-form that comprises at least one hydrophilic and/or polar group, but does not comprise an acidic or basic group when incorporated into a polypeptide next to one or more amino acid residues that are the same or different. Exemplary neutral hydrophilic residues include, but are not limited to, alanine (A), cysteine (C), serine (S), threonine (T), asparagine (N), and glutamine (Q). In certain embodiments, a neutral hydrophilic residue may be an unconventional amino acid.
The terms “lipophilic residue” and “Laa” refer to an amino acid residue in D- or L-form having at least one uncharged, aliphatic and/or aromatic group. In certain embodiments, a lipophilic residue comprises a side chain that comprises at least one uncharged, aliphatic, and/or aromatic group. Exemplary lipophilic sidechains include, but are not limited to, alanine (A), phenylalanine (F), isoleucine (I), leucine (L), norleucine (Nile), methionine (M), valine (V), tryptophan (W), and tyrosine (Y). In certain embodiments, a lipophilic residue may be an unconventional amino acid.
The term “amphiphilic residue” refers to an amino acid residue in D- or L-form that is capable of being either a hydrophilic or lipophilic residue. An exemplary amphiphilic residue includes, but is not limited to, alanine (A). In certain embodiments, an amphiphilic residue may be an unconventional amino acid.
The term “nonfunctional residue” refers to an amino acid residue in D- or L-form that lacks acidic, basic, and aromatic groups when incorporated into a polypeptide next to one or more amino acid residues that are the same or different. Exemplary nonfunctional amino acid residues include, but are not limited to, methionine (M), glycine (G), alanine (A), valine (V), isoleucine (I), leucine (L), and norleucine (Nle). In certain embodiments, a nonfunctional residue may be an unconventional amino acid.
In certain embodiments, glycine (G) and proline (P) are considered amino acid residues that can influence polypeptide chain orientation.
In certain embodiments, a conservative substitution may involve replacing a member of one residue type with a member of the same residue type. As a non-limiting example, in certain embodiments, a conservative substitution may involve replacing an acidic residue, such as D, with a different acidic residue, such as E. In certain embodiments, a non-conservative substitution may involve replacing a member of one residue type with a member of a different residue type. As a non-limiting example, in certain embodiments, a non-conservative substitution may involve replacing an acidic residue, such as D, with a basic residue, such as K. In certain embodiments, a cysteine residue is substituted with another amino acid residue to prevent disulfide bond formation with that position in the polypeptide.
In making conservative or non-conservative substitutions, according to certain embodiments, the hydropathic index of amino acids may be considered. Each amino acid has been assigned a hydropathic index on the basis of its hydrophobicity and charge characteristics. The hydropathic indices of the 20 naturally-occurring amino acids are:isoleucine (+4.5); valine (+4.2); leucine (+3.8); phenylalanine (+2.8); cysteine/cystine (+2.5); methionine (+1.9); alanine (+1.8); glycine (−0.4); threonine (−0.7); serine (−0.8); tryptophan (−0.9); tyrosine (−1.3); proline (−1.6); histidine (−3.2); glutamate (−3.5); glutamine (−3.5); aspartate (−3.5); asparagine (−3.5); lysine (−3.9); and arginine (−4.5).
The importance of the hydropathic amino acid index in conferring interactive biological function on a protein is understood in the art. Kyte et al., J. Mol. Biol., 157:105-131 (1982). It is known in certain instances that certain amino acids may be substituted for other amino acids having a similar hydropathic index or score and still retain a similar biological activity. In making changes based upon the hydropathic index, in certain embodiments, the substitution of amino acids whose hydropathic indices are within ±2 is included. In certain embodiments, those which are within ±1 are included, and in certain embodiments, those within ±0.5 are included.
It is also understood in the art that the substitution of like amino acids can be made, effectively on the basis of hydrophilicity, particularly where the biologically functional protein or peptide thereby created is intended for use in immunological embodiments, as in the present case. In certain embodiments, the greatest local average hydrophilicity of a protein, as governed by the hydrophilicity of its adjacent amino acids, correlates with its immunogenicity and antigenicity, i.e., with a biological property of the polypeptide.
The following hydrophilicity values have been assigned to these amino acid residues:arginine (+3.0); lysine (+3.0); aspartate (+3.0±1); glutamate (+3.0±1); serine (+0.3); asparagine (+0.2); glutamine (+0.2); glycine (0); threonine (−0.4); proline (−0.5±1); alanine (−0.5); histidine (−0.5); cysteine (−1.0); methionine (−1.3); valine (−1.5); leucine (−1.8); isoleucine (−1.8); tyrosine (−2.3); phenylalanine (−2.5) and tryptophan (−3.4). In making changes based upon similar hydrophilicity values, in certain embodiments, the substitution of amino acids whose hydrophilicity values are within ±2 is included, in certain embodiments, those which are within ±1 are included, and in certain embodiments, those within ±0.5 are included. In certain instances, one may also identify epitopes from primary amino acid sequences on the basis of hydrophilicity. These regions are also referred to as “epitopic core regions.”
Exemplary amino acid substitutions are set forth in Table 1.







TABLE 1







Amino Acid Substitutions













More specific



Original
Exemplary
exemplary



Residues
Substitutions
Substitutions







Ala
Val, Leu, Ile
Val



Arg
Lys, Gln, Asn
Lys



Asn
Gln
Gln



Asp
Glu
Glu



Cys
Ser, Ala
Ser



Gln
Asn
Asn



Glu
Asp
Asp



Gly
Pro, Ala
Ala



His
Asn, Gln, Lys, Arg
Arg



Ile
Leu, Val, Met, Ala,
Leu




Phe, Norleucine



Leu
Norleucine, Ile,
Ile




Val, Met, Ala, Phe



Lys
Arg, 1,4 Diamino-butyric
Arg




Acid, Gln, Asn



Met
Leu, Phe, Ile
Leu



Phe
Leu, Val, Ile, Ala,
Leu




Tyr



Pro
Ala
Gly



Ser
Thr, Ala, Cys
Thr



Thr
Ser
Ser



Trp
Tyr, Phe
Tyr



Tyr
Trp, Phe, Thr, Ser
Phe



Val
Ile, Met, Leu, Phe,
Leu




Ala, Norleucine










In certain embodiments, conservative amino acid substitutions encompass non-naturally occurring amino acid residues, which are typically incorporated by chemical peptide synthesis rather than by synthesis in biological systems. Those non-naturally occurring amino acid residues include, but are not limited to, peptidomimetics and other reversed or inverted forms of amino acid moieties.
A skilled artisan will be able to determine suitable substitution variants of a reference polypeptide as set forth herein using well-known techniques. In certain embodiments, one skilled in the art may identify suitable areas of the molecule that may be changed without destroying activity by targeting regions not believed to be important for activity. In certain embodiments, one can identify residues and portions of the molecules that are conserved among similar polypeptides. In certain embodiments, even areas that may be important for biological activity, including, but not limited to, the CDRs of an antibody, or that may be important for structure may be subject to conservative amino acid substitutions without destroying the biological activity or without adversely affecting the polypeptide structure.
Additionally, in certain embodiments, one skilled in the art can review structure-function studies identifying residues in similar polypeptides that are important for activity and/or structure. In view of such a comparison, in certain embodiments, one can predict the importance of amino acid residues in a polypeptide that correspond to amino acid residues which are important for activity or structure in similar polypeptides. In certain embodiments, one skilled in the art may opt for chemically similar amino acid substitutions for such predicted important amino acid residues.
In certain embodiments, one skilled in the art can also analyze the three-dimensional structure and amino acid sequence in relation to that structure in similar polypeptides. In view of such information, one skilled in the art may predict the alignment of amino acid residues of an antibody with respect to its three dimensional structure. In certain embodiments, one skilled in the art may choose not to make radical changes to amino acid residues predicted to be on the surface of the protein, since such residues may be involved in important interactions with other molecules. Moreover, in certain embodiments, one skilled in the art may generate test variants containing a single amino acid substitution at each desired amino acid residue. In certain embodiments, the variants can then be screened using activity assays known to those skilled in the art. For example, in certain embodiments, the variants can be screened for their ability to bind to CD40L. In certain embodiments, such variants could be used to gather information about suitable variants. For example, in certain embodiments, if one discovered that a change to a particular amino acid residue resulted in destroyed, undesirably reduced, or unsuitable activity, variants with such a change may be avoided. In other words, based on information gathered from such routine experiments, one skilled in the art can readily determine the amino acids where further substitutions should be avoided, either alone or in combination with other mutations.
A number of scientific publications have been devoted to the prediction of secondary structure. See Moult J., Curr. Op. in Biotech., 7(4):422-427 (1996), Chou et al., Biochemistry, 13(2):222-245 (1974); Chou et al., Biochemistry, 113(2):211-222 (1974); Chou et al., Adv. Enzymol. Relat. Areas Mol. Biol., 47:45-148 (1978); Chou et al., Ann. Rev. Biochem., 47:251-276 and Chou et al., Biophys. J., 26:367-384 (1979). Moreover, computer programs are currently available to assist with predicting secondary structure. One method of predicting secondary structure is based upon homology modeling. For example, two polypeptides or proteins which have a sequence identity of greater than 30%, or similarity greater than 40% often have similar structural topologies. The recent growth of the protein structural database (PDB) has provided enhanced predictability of secondary structure, including the potential number of folds within a polypeptide's or protein's structure. See Holm et al., Nucl. Acid. Res., 27(1):244-247 (1999). It has been suggested that there are a limited number of foldsin a given polypeptide or protein and that once a critical number of structures have been resolved, structural prediction will become dramatically more accurate. See, e.g., Brenner et al., Curr. Op. Struct. Biol., 7(3):369-376 (1997).
Additional exemplary methods of predicting secondary structure include, but are not limited to, “threading” (Jones, D., Curr. Opin. Struct. Biol., 7(3):377-87 (1997); Sippl et al., Structure, 4(1):15-19 (1996)), “profile analysis” (Bowie et al., Science, 253:164-170 (1991); Gribskov et al., Meth. Enzym., 183:146-159 (1990); Gribskov et al., Proc. Nat. Acad. Sci., 84(13):4355-4358 (1987)), and “evolutionary linkage” (See Holm, supra (1999), and Brenner, supra (1997).).
In certain embodiments, the identity and similarity of related polypeptides can be readily calculated by known methods. Such methods include, but are not limited to, those described in Computational Molecular Biology, Lesk, A. M., ed., Oxford University Press, New York (1988); Biocomputing:Informatics and Genome Projects, Smith, D. W., ed., Academic Press, New York (1993); Computer Analysis of Sequence Data, Part 1, Griffin, A. M., and Griffin, H. G., eds., Humana Press, New Jersey (1994); Sequence Analysis in Molecular Biology, von Heinje, G., Academic Press (1987); Sequence Analysis Primer, Gribskov, M. and Devereux, J., eds., M. Stockton Press, New York (1991); and Carillo et al., SIAM J. Applied Math., 48:1073 (1988). In certain embodiments, polypeptides have amino acid sequences that are about 90 percent, or about 95 percent, or about 96 percent, or about 97 percent, or about 98 percent, or about 99 percent identical to amino acid sequences shown in FIGS. 1-74.
In certain embodiments, methods to determine identity are designed to give the largest match between the sequences tested. In certain embodiments, certain methods to determine identity are described in publicly available computer programs. Certain computer program methods to determine identity between two sequences include, but are not limited to, the GCG program package, including GAP (Devereux et al., Nucl. Acid. Res., 12:387 (1984); Genetics Computer Group, University of Wisconsin, Madison, Wis., BLASTP, BLASTN, and FASTA (Altschul et al., J. Mol. Biol., 215:403-410 (1990)). The BLASTX program is publicly available from the National Center for Biotechnology Information (NCBI) and other sources (BLAST Manual, Altschul et al. NCB/NLM/NIH Bethesda, Md. 20894; Altschul et al., supra (1990)). In certain embodiments, the Smith Waterman algorithm, which is known in the art, may also be used to determine identity.
Certain alignment schemes for aligning two amino acid sequences may result in the matching of only a short region of the two sequences, and this small aligned region may have very high sequence identity even though there is no significant relationship between the two full-length sequences. Accordingly, in certain embodiments, the selected alignment method (GAP program) will result in an alignment that spans at least 50 contiguous amino acids of the target polypeptide.
For example, using the computer algorithm GAP (Genetics Computer Group, University of Wisconsin, Madison, Wis.), two polypeptides for which the percent sequence identity is to be determined are aligned for optimal matching of their respective amino acids (the “matched span”, as determined by the algorithm). In certain embodiments, a gap opening penalty (which is calculated as 3× the average diagonal; the “average diagonal” is the average of the diagonal of the comparison matrix being used; the “diagonal” is the score or number assigned to each perfect amino acid match by the particular comparison matrix) and a gap extension penalty (which is usually 1/10 times the gap opening penalty), as well as a comparison matrix such as PAM 250 or BLOSUM 62 are used in conjunction with the algorithm. In certain embodiments, a standard comparison matrix is also used by the algorithm. See, e.g., Dayhoff et al., Atlas of Protein Sequence and Structure, 5(3)(1978) for the PAM 250 comparison matrix; Henikoff et al., Proc. Natl. Acad. Sci USA, 89:10915-10919 (1992) for the BLOSUM 62 comparison matrix.
In certain embodiments, the parameters for a polypeptide sequence comparison include the following:












Algorithm: Needleman et al., J. Mol. Biol., 48: 443-453 (1970);


Comparison matrix: BLOSUM 62 from Henikoff et al., supra (1992);


Gap Penalty: 12


Gap Length Penalty: 4


Threshold of Similarity: 0









In certain embodiments, the GAP program may be useful with the above parameters. In certain embodiments, the aforementioned parameters are the default parameters for polypeptide comparisons (along with no penalty for end gaps) using the GAP algorithm.
According to certain embodiments, amino acid substitutions are those which:(1) reduce susceptibility to proteolysis, (2) reduce susceptibility to oxidation, (3) alter binding affinity for forming protein complexes, (4) alter binding affinities, and/or (4) confer or modify other physicochemical or functional properties on such polypeptides. According to certain embodiments, single or multiple amino acid substitutions (in certain embodiments, conservative amino acid substitutions) may be made in the naturally-occurring sequence (in certain embodiments, in the portion of the polypeptide outside the domain(s) forming intermolecular contacts).
Peptide analogs are commonly used in the pharmaceutical industry as non-peptide drugs with properties analogous to those of the template peptide. These types of non-peptide compound are termed “peptide mimetics” or “peptidomimetics”. Fauchere, J. Adv. Drug Res. 15:29 (1986); Veber and Freidinger TINS p. 392 (1985); and Evans et al. J. Med. Chem. 30:1229 (1987). Such compounds are often developed with the aid of computerized molecular modeling. Peptide mimetics that are structurally similar to therapeutically useful peptides may be used to produce a similar therapeutic or prophylactic effect. Generally, peptidomimetics are structurally similar to a paradigm polypeptide (i.e., a polypeptide that has a biochemical property or pharmacological activity), such as human antibody, but have one or more peptide linkages optionally replaced by a linkage selected from:—CH2NH—, —CH2S—, —CH2—CH2—, —CH═CH— (cis and trans), —COCH2—, —CH(OH)CH2—, and —CH2SO—, by methods well known in the art. Systematic substitution of one or more amino acids of a consensus sequence with a D-amino acid of the same type (e.g., D-lysine in place of L-lysine) may be used in certain embodiments to generate more stable peptides. In addition, constrained peptides comprising a consensus sequence or a substantially identical consensus sequence variation may be generated by methods known in the art (Rizo and Gierasch Ann. Rev. Biochem. 61:387 (1992)); for example, by adding internal cysteine residues capable of forming intramolecular disulfide bridges which cyclize the peptide.
The term “specific binding agent” refers to a natural or non-natural molecule that specifically binds to a target. Examples of specific binding agents include, but are not limited to, proteins, peptides, nucleic acids, carbohydrates, lipids, and small molecule compounds. In certain embodiments, a specific binding agent is an antibody. In certain embodiments, a specific binding agent is an antigen binding region.
The term “specific binding agent to an EGFr polypeptide” refers to a specific binding agent that specifically binds any portion of an EGFr polypeptide. In certain embodiments, a specific binding agent to an EGFr polypeptide is an antibody to an EGFr polypeptide. In certain embodiments, a specific binding agent to an EGFr polypeptide is an antigen binding region. In certain embodiments, a specific binding agent to an EGFr polypeptide is an antibody to EGFr. In certain embodiments, a specific binding agent to an EGFr polypeptide is panitumumab.
The term “specifically binds” refers to the ability of a specific binding agent to bind to a target with greater affinity than it binds to a non-target. In certain embodiments, specific binding refers to binding for a target with an affinity that is at least 10, 50, 100, 250, 500, or 1000 times greater than the affinity for a non-target. In certain embodiments, affinity is determined by an affinity ELISA assay. In certain embodiments, affinity is determined by a BIAcore® assay. In certain embodiments, affinity is determined by a kinetic method. In certain embodiments, affinity is determined by an equilibrium/solution method. In certain embodiments, affinity is determined using flow cytometry.
The affinity of an agent for a first polypeptide is “similar” to the affinity of the agent for a second polypeptide when there is less than a 2-fold difference in the affinities as determined by a selected method. The affinity of an agent for a first polypeptide is “greater” than the affinity of the agent for a second polypeptide when the affinity of the agent for the first polypeptide is at least 2-fold greater than the affinity for the agent for the second polypeptide as determined by a selected method.
“Native antibodies” and “native immunoglobulins”, in certain instances, are usually heterotetrameric glycoproteins of about 150,000 daltons, composed of two identical light (L) chains and two identical heavy (H) chains. Each light chain is linked to a heavy chain by one covalent disulfide bond, while the number of disulfide linkages varies between the heavy chains of different immunoglobulin isotypes. Each heavy and light chain also has regularly spaced intrachain disulfide bridges. Each heavy chain has at one end a variable domain (VH) followed by a number of constant domains. Each light chain has a variable domain at one end (VL) and a constant domain at its other end; the constant domain of the light chain is aligned with the first constant domain of the heavy chain, and the light chain variable domain is aligned with the variable domain of the heavy chain. Particular amino acid residues are believed to form an interface between the light- and heavy-chain variable domains (Chothia et al. J. Mol. Biol. 186:651 (1985; Novotny and Haber, Proc. Natl. Acad. Sci. U.S.A. 82:4592 (1985); Chothia et al., Nature 342:877-883 (1989)).
“Antibody” or “antibody peptide(s)” both refer to an intact antibody, or a fragment thereof. In certain embodiments, the fragment includes contiguous portions of an intact antibody. In certain embodiments, the fragment includes non-contiguous portions of an intact antibody. In certain embodiments, the antibody fragment may be a binding fragment that competes with the intact antibody for specific binding. The term “antibody” also encompasses polyclonal antibodies and monoclonal antibodies. In certain embodiments, binding fragments are produced by recombinant DNA techniques. In certain embodiments, binding fragments are produced by enzymatic or chemical cleavage of intact antibodies. Binding fragments include, but are not limited to, Fab, Fab′, F(ab′)2, Fv, scFv, maxibodies, and single-chain antibodies. Non-antigen binding fragments include, but are not limited to, Fc fragments. The term “antibody” also encompasses anti-idiotypic antibodies that specifically bind to the variable region of another antibody. In certain embodiments, an anti-idiotypic antibody specifically binds to the variable region of an anti-EGFr antibody. In certain embodiments, anti-idiotypic antibodies may be used to detect the presence of a particular anti-EGFr antibody in a sample or to block the activity of an anti-EGFr antibody.
The term “polyclonal antibody” refers to a heterogeneous mixture of antibodies that bind to different epitopes of the same antigen.
The term “monoclonal antibodies” refers to a collection of antibodies encoded by the same nucleic acid molecule. In certain embodiments, monoclonal antibodies are produced by a single hybridoma or other cell line, or by a transgenic mammal. Monoclonal antibodies typically recognize the same epitope. The term “monoclonal” is not limited to any particular method for making an antibody.
“Chimeric antibody” refers to an antibody that has an antibody variable region of a first species fused to another molecule, for example, an antibody constant region of another second species. See, e.g., U.S. Pat. No. 4,816,567 and Morrison et al., Proc Natl Acad Sci (USA), 81:6851-6855 (1985). In certain embodiments, the first species may be different from the second species. In certain embodiments, the first species may be the same as the second species. In certain embodiments, a chimeric antibody is a CDR-grafted antibody.
The term “CDR-grafted antibody” refers to an antibody in which the CDR from one antibody is inserted into the framework of another antibody. In certain embodiments, the antibody from which the CDR is derived and the antibody from which the framework is derived are of different species. In certain embodiments, the antibody from which the CDR is derived and the antibody from which the framework is derived are of different isotypes.
The term “multi-specific antibody” refers to an antibody wherein two or more variable regions bind to different epitopes. The epitopes may be on the same or different targets. In certain embodiments, a multi-specific antibody is a “bi-specific antibody,” which recognizes two different epitopes on the same or different antigens.
The term “catalytic antibody” refers to an antibody in which one or more catalytic moieties is attached. In certain embodiments, a catalytic antibody is a cytotoxic antibody, which comprise a cytotoxic moiety.
The term “humanized antibody” refers to an antibody in which all or part of an antibody framework region is derived from a human, but all or part of one or more CDR regions is derived from another species, for example, including, but not limited to, a mouse.
The term “fully human antibody” refers to an antibody in which both the CDR and the framework comprise substantially human sequences. In certain embodiments, fully human antibodies are produced in non-human mammals, including, but not limited to, mice, rats, and lagomorphs. In certain embodiments, fully human antibodies are produced in hybridoma cells. In certain embodiments, fully human antibodies are produced recombinantly.
The term “anti-idiotype antibody” refers to an antibody that specifically binds to another antibody.
The term “heavy chain” includes any polypeptide having sufficient variable region sequence to confer specificity for a target. A full-length heavy chain includes a variable region domain, VH, and three constant region domains, CH1, CH2, and CH3. The VH domain is at the amino-terminus of the polypeptide, and the CH3 domain is at the carboxy-terminus. The term “heavy chain”, as used herein, encompasses a full-length heavy chain and fragments thereof.
The term “light chain” includes any polypeptide having sufficient variable region sequence to confer specificity for a target. A full-length light chain includes a variable region domain, VL, and a constant region domain, CL. Like the heavy chain, the variable region domain of the light chain is at the amino-terminus of the polypeptide. The term “light chain”, as used herein, encompasses a full-length light chain and fragments thereof.
The term “Fab fragment” refers to an antibody comprising one light chain and the CH1 and variable regions of one heavy chain. The heavy chain of a Fab fragment cannot form a disulfide bond with another heavy chain. In certain embodiments, the heavy chain of a Fab fragment forms a disulfide bond with the light chain of a Fab fragment.
The term “Fab′ fragment” refers to an antibody comprising one light chain, the variable and CH1 regions of one heavy chain, and some of the constant region between the CH1 and CH2 domains of the heavy chain. In certain embodiments, an interchain disulfide bond can be formed between two heavy chains of an Fab′ fragment to form a F(ab′)2 molecule.
The term “F(ab′)2 molecule” refers to an antibody comprising two Fab′ fragments connected by an interchain disulfide bond formed between two heavy chains.
An “Fv molecule” comprises the variable regions from both the heavy and light chains, but lacks the constant regions. A single chain variable fragment (scFv) comprises variable regions from both a heavy and a light chain wherein the heavy and light chain variable regions are fused to form a single polypeptide chain which forms an antigen-binding region. In certain embodiments, a scFV comprises a single polypeptide chain. A single-chain antibody comprises a scFV. In certain embodiments, a single-chain antibody comprises one or more additional polypeptides fused to a scFv. Exemplary additional polypeptides include, but are not limited to, one or more constant regions. Exemplary single-chain antibodies are discussed, e.g., in WO 88/01649 and U.S. Pat. Nos. 4,946,778 and 5,260,203.
The term “maxibody” refers to a scFv fused (may be by a linker or direct attachment) to an Fc or an Fc fragment. In certain embodiments, a single chain antibody is a maxibody. In certain embodiments, a single chain antibody is a maxibody that binds to EGFr. Exemplary Ig-like domain-Fc fusions are disclosed in U.S. Pat. No. 6,117,655.
An “Fc fragment” comprises the CH2 and CH3 domains of the heavy chain and contains some of the constant region, between the CH1 and CH2 domains, such that an interchain disulfide bond can be formed between two heavy chains.
As used herein, a “flexible linker” refers to any linker that is not predicted by one skilled in the art, according to its chemical structure, to be fixed in three-dimensional space. In certain embodiments, a peptide linker comprising three or more amino acids is a flexible linker.
The terms “variable region” and “variable domain” are used interchangeably herein to refer to a portion of the light and/or heavy chains of an antibody. In various instances, variable domains include approximately the amino-terminal 120 to 130 amino acids in the heavy chain and about 100 to 110 amino-terminal amino acids in the light chain. In certain embodiments, variable regions of different antibodies differ extensively in amino acid sequence even among antibodies of the same species. The variable region of an antibody, in various instances, determines specificity of a particular antibody for its target.
The term “immunologically functional immunoglobulin fragment” refers to a polypeptide fragment comprising at least the variable domains of an immunoglobulin heavy chain and an immunoglobulin light chain. In certain embodiments, an immunologically functional immunoglobulin fragment is capable of binding to a ligand, preventing binding of the ligand to its receptor, and thereby interrupting a biological response resulting from ligand binding to the receptor. In certain embodiments, an immunologically functional immunoglobulin fragment is capable of binding to a receptor, preventing binding of the ligand to its receptor, and thereby interrupting a biological response resulting from ligand binding to the receptor. In certain embodiments, an immunologically functional immunoglobulin fragment is capable of binding a receptor and activating that receptor. In certain embodiments, an immunologically functional immunoglobulin fragment is capable of binding a receptor and inactivating that receptor.
The term “epitope” refers to a portion of a molecule capable, of being bound by a specific binding agent. Exemplary epitopes may comprise any polypeptide determinant capable of specific binding to an immunoglobulin and/or T-cell receptor. Exemplary epitope determinants include, but are not limited to, chemically active surface groupings of molecules, for example, but not limited to, amino acids, sugar side chains, phosphoryl groups, and sulfonyl groups. In certain embodiments, epitope determinants may have specific three dimensional structural characteristics, and/or specific charge characteristics. In certain embodiments, an epitope is a region of an antigen that is bound by an antibody. Epitopes may be contiguous or non-contiguous. In certain embodiments, epitopes may be mimetic in that they comprise a three dimensional structure that is similar to an epitope used to generate the antibody, yet comprise none or only some of the amino acid residues found in that epitope used to generate the antibody.
The term “panitumumab epitope” refers to an epitope on an EGFr polypeptide that is specifically bound by panitumumab. In certain embodiments, a panitumumab epitope comprises at least a portion of the L2 domain of EGFr. In certain embodiments, a panitumumab epitope comprises at least amino acids P349, D355, F412, I438, K443, K465, and I467 of an EGFr polypeptide.
The term “agent” is used herein to denote a protein, polypeptide, peptide, nucleic acid, polynucleotide, oligonucleotide, carbohydrate, lipid, or a small molecule compound.
As used herein, the term “label” refers to any molecule that can be detected. In a certain embodiment, an antibody may be labeled by incorporation of a radiolabeled amino acid. In a certain embodiment, biotin moieties that can be detected by marked avidin (e.g., streptavidin containing a fluorescent marker or enzymatic activity that can be detected by optical or colorimetric methods) may be attached to the antibody. In certain embodiments, a label may be incorporated into or attached to another reagent which in turn binds to the antibody of interest. For example, a label may be incorporated into or attached to an antibody that in turn specifically binds the antibody of interest. In certain embodiments, the label or marker can also be therapeutic. Various methods of labeling polypeptides and glycoproteins are known in the art and may be used. Certain general classes of labels include, but are not limited to, enzymatic, fluorescent, chemiluminescent, and radioactive labels. Examples of labels for polypeptides include, but are not limited to, the following:radioisotopes or radionucleotides (e.g., 3H, 14C, 15N, 35S, 90Y, 99Tc, 111In, 125I, 131I), fluorescent labels (e.g., fluorescein isothocyanate (FITC), rhodamine, lanthanide phosphors, phycoerythrin (PE)), enzymatic labels (e.g., horseradish peroxidase, β-galactosidase, luciferase, alkaline phosphatase, glucose oxidase, glucose-6-phosphate dehydrogenase, alcohol dehyrogenase, malate dehyrogenase, penicillinase, luciferase), chemiluminescent, biotinyl groups, predetermined polypeptide epitopes recognized by a secondary reporter (e.g., leucine zipper pair sequences, binding sites for secondary antibodies, metal binding domains, epitope tags). In certain embodiments, labels are attached by spacer arms of various lengths to reduce potential steric hindrance.
The term “pharmaceutical agent or drug” as used herein refers to a chemical compound or composition capable of inducing a desired therapeutic effect when properly administered to a patient. As used herein, a therapeutic effect may or may not include a prophylactic effect.
The term “antineoplastic agent” is used herein to refer to agents that have the functional property of inhibiting a development or progression of a neoplasm in a human, particularly a malignant (cancerous) lesion, such as a carcinoma, sarcoma, lymphoma, or leukemia. Inhibition of metastasis is frequently a property of antineoplastic agents. In certain embodiments, an antineoplastic agent is panitumumab.
As used herein, “substantially pure” means an object species is the predominant species present (i.e., on a molar basis it is more abundant than any other individual species in the composition). In certain embodiments, a substantially purified fraction is a composition wherein the object species comprises at least about 50 percent (on a molar basis) of all macromolecular species present. In certain embodiments, a substantially pure composition will comprise more than about 80%, 85%, 90%, 95%, or 99% of all macromolecular species present in the composition. In certain embodiments, the object species is purified to essential homogeneity (contaminant species cannot be detected in the composition by conventional detection methods) wherein the composition consists essentially of a single macromolecular species.
The term patient includes human and animal subjects.
The term “disease state” refers to a physiological state of a cell or of a whole mammal in which an interruption, cessation, or disorder of cellular or body functions, systems, or organs has occurred.
The terms “treat” or “treatment” refer to both therapeutic treatment and prophylactic (or preventative) measures. In various embodiments, the object of treatment is to prevent or slow down (lessen) an undesired physiological change or disorder, such as the development or spread of cancer. Certain exemplary desired clinical results from treatment include, but are not limited to, alleviation of symptoms, diminishment of extent of disease, stabilized (i.e., not worsening) state of disease, delay or slowing of disease progression, amelioration or palliation of the disease state, remission (whether partial or total), and prevention of onset of disease. In certain embodiments, “treatment” can also mean prolonging survival as compared to expected survival if not receiving treatment. Those in need of treatment include those already with the condition or disorder as well as those prone to have the condition or disorder or those in which the condition or disorder is to be prevented.
The term “responsive” as used herein means that a patient or tumor shows a complete response or a partial response after administering an agent, according to RECIST (Response Evaluation Criteria in Solid Tumors). The term “nonresponsive” as used herein means that a patient or tumor shows stable disease or progressive disease after administering an agent, according to RECIST. RECIST is described, e.g., in Therasse et al., February 2000, “New Guidelines to Evaluate the Response to Treatment in Solid Tumors,” J. Natl. Cancer Inst. 92(3):205-216, which is incorporated by reference herein in its entirety. Exemplary agents include, but are not limited to, specific binding agents to an EGFr polypeptide, including but not limited to, antibodies to EGFr.
A “disorder” is any condition that would benefit from one or more treatments. This includes chronic and acute disorders or disease including those pathological conditions which predispose the mammal to the disorder in question. Non-limiting examples of disorders to be treated herein include benign and malignant tumors, leukemias, and lymphoid malignancies, in particular breast, rectal, ovarian, stomach, endometrial, salivary gland, kidney, colon, thyroid, pancreatic, prostate, and bladder cancer. In certain embodiments, a disorder to be treated is a malignant tumor, such as cervical carcinomas and cervical intraepithelial squamous and glandular neoplasia, renal cell carcinoma (RCC), esophageal tumors, and carcinoma-derived cell lines.
A “disease or condition related to an EGFr polypeptide” includes one or more of the following:a disease or condition caused by an EGFr polypeptide; a disease or condition contributed to by an EGFr polypeptide; and a disease or condition that is associated with the presence of an EGFr polypeptide. In certain embodiments, a disease or condition related to an EGFr polypeptide is a cancer. Exemplary cancers include, but are not limited to, non small cell lung carcinoma, breast, colon, gastric, brain, bladder, head and neck, ovarian, and prostate carcinomas.
In “combined therapy,” patients are treated with a first specific binding agent for a target antigen in combination with a second specific binding agent for the target antigen and/or a chemotherapeutic or antineoplastic agent and/or radiation therapy. In certain embodiments, combined therapy comprises at least a first specific binding agent and a second specific binding agent. In certain embodiments, the first and second specific binding agents are agents that specifically bind to an EGFr polypeptide. In certain embodiments, the first specific binding agent is panitumumab and the second specific binding agent is an agent that binds at least a portion of a panitumumab epitope on an EGFr polypeptide. In certain embodiments, the first specific binding agent is panitumumab and the second specific binding agent is an agent that does not bind to a panitumumab epitope on an EGFr polypeptide. Protocol designs will address effectiveness as assessed by reduction in tumor mass as well as the ability to reduce usual doses of standard chemotherapy. These dosage reductions will allow additional and/or prolonged therapy by reducing dose-related toxicity of the chemotherapeutic agent.
“Monotherapy” refers to the treatment of a disorder by administering immunotherapy to patients without an accompanying chemotherapeutic or antineoplastic agent. In certain embodiments, monotherapy comprises administering a specific binding agent for a target antigen. In certain embodiments, a specific binding agent used in monotherapy binds a panitumumab epitope on an EGFr polypeptide. In certain embodiments, a specific binding agent used in monotherapy does not bind a panitumumab epitope on an EGFr polypeptide.
Certain Embodiments
Panitumumab is a fully human antibody that specifically binds to an EGFr polypeptide. Panitumumab (also known as antibody E7.6.3 and ABX-EGF) is described, e.g., in PCT Publication No. WO 98/50433 and in U.S. Pat. No. 6,235,883. Panitumumab prevents the formation of human epidermoid carcinoma A431 xenografts in athymic mice, and alse eradicates already-established A431 tumor xenografts. See, e.g., Yang et al., Crit. Rev. Oncol. Hematol. 38(1):17-23, 2001; and Yang et al., Cancer Res. 59(6):1236-43, 1999. Panitumumab has been approved by the FDA to treat patients with metastatic colorectal cancer.
Certain Methods for Selecting a Specific Binding Agent that Binds to at Least a Portion of a Panitumumab Epitope on an EGFr Polypeptide
In certain embodiments, a method is provided for selecting a specific binding agent to an epidermal growth factor (EGFr) polypeptide. In certain embodiments, a specific binding agent is selected that binds to at least a portion of a panitumumab epitope on an EGFr polypeptide. A specific binding agent that binds to at least a portion of a panitumumab epitope on an EGFr, in certain embodiments, may possess one or more similar in vivo activities as panitumumab.
In certain embodiments, a specific binding agent that binds to at least a portion of a panitumumab epitope on an EGFr polypeptide is selected as follows:a) an EGFr polypeptide is contacted with a first aliquot of an agent; b) the affinity of the agent for the EGFr polypeptide is determined; c) a mutant EGFr polypeptide is contacted with a second aliquot of the agent, wherein the mutant EGFr polypeptide comprises at least one point mutation at at least one amino acid position selected from P349, D355, F412, I438, K443, K465, and I467; d) the affinity of the agent for the mutant EGFr polypeptide is determined; and e) the agent is selected if the affinity of the agent for the EGFr polypeptide is greater than the affinity of the agent for the mutant EGFr polypeptide. In certain embodiments, steps (a) and (c) are carried out simultaneously and/or steps (b) and (d) are carried out simultaneously. In various embodiments, step (a) is carried out before step (b) or step (b) is carried out before step (a). In certain embodiments, the amount and/or concentration of the agent used in step (a) is the same as the amount and/or concentration of the agent used in step (c). In certain embodiments, the same method is used to determine the affinity of the agent for the EGFr polypeptide and to determine the affinity of the agent for the mutant EGFr polypeptide. In various embodiments, the agent is selected if the affinity of the agent for the EGFr polypeptide is at least 2-fold, at least 3-fold, at least 5-fold, or at least 10-fold the affinity of the agent for the mutant EGFr polypeptide.
In certain embodiments, a specific binding agent that binds to at least a portion of a panitumumab epitope on an EGFr polypeptide is selected as follows:a) a first EGFr polypeptide is contacted with a first aliquot of an agent, wherein the first EGFr polypeptide comprises an L2 domain; b) the affinity of the agent for the first EGFr polypeptide is determined; c) a second EGFr polypeptide is contacted with a second aliquot of the agent, wherein the second EGFr polypeptide lacks an L2 domain; d) the affinity of the agent for the first EGFr polypeptide is determined; and e) the agent is selected if the affinity of the agent for the first EGFr polypeptide is greater than the affinity of the agent for the second EGFr polypeptide. In certain embodiments, steps (a) and (c) are carried out simultaneously and/or steps (b) and (d) are carried out simultaneously. In various embodiments, step (a) is carried out before step (b) or step (b) is carried out before step (a). In certain embodiments, the amount and/or concentration of the agent used in step (a) is the same as the amount and/or concentration of the agent used in step (c). In certain embodiments, the same method is used to determine the affinity of the agent for the first EGFr polypeptide and to determine the affinity of the agent for the second EGFr polypeptide. In various embodiments, the agent is selected if the affinity of the agent for the first EGFr polypeptide is at least 2-fold, at least 3-fold, at least 5-fold, or at least 10-fold the affinity of the agent for the second EGFr polypeptide.
Certain Methods for Selecting a Specific Binding Agent that does not Bind to a Panitumumab Epitope on an EGFr Polypeptide
In certain embodiments, treating a patient with at least two specific binding agents to EGFr, wherein the specific binding agents bind to different epitopes on an EGFr polypeptide, may be more effective than treating a patient with only one specific binding agent to EGFr. See, e.g., Friedman et al., PNAS, 102:1915-1920 (2005). Thus, in certain embodiments, it may be desirable to select a specific binding agent to an EGFr polypeptide that does not bind to a panitumumab epitope on an EGFr polypeptide. In certain instances, the selected specific binding agent may then be administered as a combination therapy with panitumumab. Such combination therapy may, in certain embodiments, be more effective than panitumumab alone.
In certain embodiments, a method of selecting a specific binding agent to an epidermal growth factor receptor (EGFr) polypeptide is provided. In certain embodiments, the method selects a specific binding agent that does not bind to a panitumumab epitope on an EGFr polypeptide.
In certain embodiments, a specific binding agent that does not bind to a panitumumab epitope on an EGFr polypeptide is selected as follows: a) an EGFr polypeptide is contacted with a first aliquot of an agent; b) the affinity of the agent for the EGFr polypeptide is determined; c) a mutant EGFr polypeptide is contacted with a second aliquot of the agent, wherein the mutant EGFr polypeptide comprises at least one point mutation at least one amino acid position selected from P349, D355; F412, I438, K443, K465, and I467; d) the affinity of the agent for the mutant EGFr polypeptide is determined; and e) the agent is selected if the affinity of the agent for the EGFr polypeptide is similar to the affinity of the agent for the mutant EGFr polypeptide. In certain embodiments, steps (a) and (c) are carried out simultaneously and/or steps (b) and (d) are carried out simultaneously. In various embodiments, step (a) is carried out before step (b) or step (b) is carried out before step (a). In certain embodiments, the amount and/or concentration of the agent used in step (a) is the same as the amount and/or concentration of the agent used in step (c). In certain embodiments, the same method is used to determine the affinity of the agent for the EGFr polypeptide and to determine the affinity of the agent for the mutant EGFr polypeptide. In certain embodiments, the agent is selected if the affinity of the agent for the EGFr polypeptide is less than 2-fold different from the affinity of the agent for the mutant EGFr polypeptide.
In certain embodiments, a specific binding agent that does not bind to a panitumumab epitope on an EGFr polypeptide is selected as follows: a) a first EGFr polypeptide is contacted with a first aliquot of an agent, wherein the first polypeptide comprises an L2 domain; b) the affinity of the agent for the first EGFr polypeptide is determined; c) a second EGFr polypeptide is contacted with a second aliquot of the agent, wherein the second EGFr polypeptide lacks an L2 domain; d) the affinity of the agent for the second EGFr polypeptide is determined; and e) the agent is selected if the affinity of the agent for the first EGFr polypeptide is similar to the affinity of the agent for the second EGFr polypeptide. In certain embodiments, steps (a) and (c) are carried out simultaneously and/or steps (b) and (d) are carried out simultaneously. In various embodiments, step (a) is carried out before step (b) or step (b) is carried out before step (a). In certain embodiments, the amount and/or concentration of the agent used in step (a) is the same as the amount and/or concentration of the agent used in step (c). In certain embodiments, the same method is used to determine the affinity of the agent for the first EGFr polypeptide and to determine the affinity of the agent for the second EGFr polypeptide. In certain embodiments, the agent is selected if the affinity of the agent for the first EGFr polypeptide is less than 2-fold different from the affinity of the agent for the second EGFr polypeptide.
Certain Exemplary Methods of Determining Affinity
In various methods discussed herein, the affinity of an agent for an EGFr polypeptide and/or the affinity of an agent for a mutant EGFr polypeptide is determined. Certain methods of determining the affinity of an agent for a polypeptide are known in the art. One skilled in the art can select an appropriate method based on the particular application. Certain exemplary methods of determining affinity of an agent for a polypeptide include, but are not limited to, ELISA and RIA methods, BIAcore assays, Western blotting, flow cytometry methods, and equilibrium/solution methods, affinity selection-mass spectrometry (AS-MS), microchip-affinity capillary electrophoresis (MC-ACE), kinetic exclusion fluorescence immunoassay, Mesoscale Discovery (MSD) assays and other assays based on electrochemiluminescence (ECL), and cell-based reported assays using, e.g., luciferase or GFP. Certain exemplary methods of determining affinity of an agent are described, e.g., in Goldberg et al., Curr Opin Immunol. 5(2):278-81 (1993), Van Regenmortel, Dev Biol (Basel) 112:141-51 (2003), Geuijen et al., J. Immunol. Methods 302 (1-2):68-77 (2005), Annis et al., Anal Chem. 79(12):4538-42 (2007), Stettler et al., Electrophoresis 28(11):1832-8 (2007), Xie et al., J. Immunol Methods 304 (1-2):1-14 (2005).
In certain embodiments, a method of determining affinity produces a relative affinity measurement, which is expressed as an affinity relative to the affinity of a positive control and/or the affinity of a negative control. In certain embodiments, a method of determining affinity produces a binding constant, such as, for example, a ka and/or a kd, and/or an equilibrium constant, such as, for example, a KD. In certain embodiments, affinity is determined using a competition assay in which the concentration of a first agent is held constant while the concentration of a second agent is varied.
In certain embodiments, a method comprises at least one step that is carried out in a high-throughput format.
Certain Exemplary Agents
Certain exemplary agents include, but are not limited to, proteins, polypeptides, peptides, nucleic acids, polynucleotides, oligonucleotides, carbohydrates, lipids, and small molecule compounds. In certain embodiments, the agent is a protein. In certain embodiments, the agent is an antibody. In various embodiments, the method is carried out in a high-throughput manner using, e.g., a collection of antibodies. Certain collections are known in the art and include, but are not limited to, display libraries (e.g. phage, DNA, ribosomal), recombinant methods of recovering genetic sequences of antibody from B-cell populations (including, but not limited to, Selected Lymphocyte Antibody Method (SLAMTM) and OmnicolonalTM antibody technology), collections of antibody sequences generated using random mutagenesis, and collections of antibodies produced by hybridomas. In various embodiments, one skilled in the art can select an appropriate antibody collection for use in the methods.
In certain embodiments, the agent is a polypeptide. In various embodiments, the method is carried out in a high-throughput manner using, e.g., a collection of polypeptides. Certain collections are known in the art and an appropriate library can be selected for use in the method by one skilled in the art.
In certain embodiments, the agent is a small molecule compound. In various embodiments, the method is carried out in a high-throughput manner using, e.g., a collection of small molecule compounds. Certain collections are known in the art and an appropriate library can be selected for use in the method by one skilled in the art.
Certain Exemplary EGFr Polypeptides and Mutant EGFr Polypeptides
In certain embodiments, an EGFr polypeptide used in the methods is an EGFr polypeptide that lacks a cytoplasmic domain. In certain embodiments, an EGFr polypeptide used in the methods is an EGFr polypeptide that lacks both a transmembrane domain and a cytoplasmic domain. In certain embodiments, an EGFr polypeptide used in the methods is an EGFr ECD polypeptide. In certain embodiments, an EGFr polypeptide used in the methods is an EGFr ECD polypeptide comprising at least one domain selected from a CR1 domain, an L1 domain, a CR2 domain, and an L2 domain. In certain embodiments, an EGFr ECD polypeptide used in the methods comprises an L1 domain, a CR1 domain, an L2 domain, and a CR2 domain. In certain embodiments, an L1 domain of an EGFr polypeptide has the amino acid sequence of SEQ ID NO: 4. In certain embodiments, a CR1 domain of an EGFr polypeptide has the amino acid sequence of SEQ ID NO: 5. In certain embodiments, an L2 domain of an EGFr polypeptide has the amino acid sequence of SEQ ID NO: 3. In certain embodiments, a CR2 domain of an EGFr polypeptide has the amino acid sequence of SEQ ID NO: 6. In certain embodiments, an EGFr polypeptide used in the methods is a an EGFr ECD polypeptide comprising an L2 domain. In certain embodiments, an EGFr polypeptide used in the methods is an EGFr ECD polypeptide lacking an L2 domain.
In various embodiments, an EGFr polypeptide used in the methods comprises an amino acid sequence selected from any of SEQ ID NOs:1 to 8 and 13 to 15.
In certain embodiments, an amino acid substitution (or “point mutation”) is made to an EGFr polypeptide to make a mutant EGFr polypeptide that is predicted to have a lower binding affinity for panitumumab than the EGFr polypeptide. In certain embodiments, the amino acid substitution is made at one or more amino acid positions selected from P349, D355, F412, I438, K443, K465, and I467 of an EGFr polypeptide. In certain embodiments, an amino acid substitution replaces a non-alanine amino acid with an alanine. In certain embodiments, a conservative amino acid substitution is made. In various embodiments, the affinity of panitumumab for a mutant EGFr polypeptide is reduced by at least 50%, at least 60%, at least 70%, at least 80%, at least 85%, at least 90%, or at least 95% relative to the affinity of panitumumab for an EGFr polypeptide.
In various embodiments, the affinity of a specific binding agent for a mutant EGFr polypeptide is reduced by at least 50%, at least 60%, at least 70%, at least 80%, at least 85%, at least 90%, or at least 95% relative to the affinity of the specific binding agent for an EGFr polypeptide. In various embodiments, the affinity of a specific binding agent for a mutant EGFr polypeptide is less than 50%, less than 40%, less than 30%, less than 25%, less than 20%, less than 15%, less than 10%, or less than 5% the affinity of the specific binding agent for an EGFr polypeptide. In certain embodiments, the affinity of a specific binding agent for a mutant EGFr polypeptide is reduced by less than 50% relative to the affinity of the specific binding agent for an EGFr polypeptide.
In certain embodiments, a mutant EGFr polypeptide used in the methods lacks a cytoplasmic domain. In certain embodiments, a mutant EGFr polypeptide used in the methods lacks both a transmembrane domain and a cytoplasmic domain. In certain embodiments, a mutant EGFr polypeptide used in the methods is a mutant EGFr ECD polypeptide. In certain embodiments, a mutant EGFr polypeptide used in the methods comprises an L2 domain. In certain embodiments, a mutant EGFr polypeptide used in the methods comprises at least one point mutation at least one amino acid position selected from P349, D355, F412, I438, K443, K465, and I467. In certain embodiments, a mutant EGFr polypeptide comprises at least one point mutation selected from P349A, D355T, F412A, and I438K.
In various embodiments, a mutant EGFr polypeptide used in the methods comprises an amino acid sequence selected from any of SEQ ID NOs:1 to 3, 8, and 13 to 15 having at least one point mutation at least one amino acid position selected from P349, D355, F412, I438, K443, K465, and I467. In various embodiments, a mutant EGFr polypeptide comprises an amino acid sequence selected from SEQ ID NOs:9 to 12 and 21 to 23.
EXAMPLES
Example 1
Testing Panitumumab Binding to EGFR Extracellular Domain and EGFR Extracellular Domain Truncations
The following human EGFr polypeptides were separately expressed as avidin fusion proteins (with chicken avidin fused to the amino-terminus of the EGFr protein fragment) in transiently-transfected 293T cells using mammalian expression vector pCEP4 (Invitrogen):EGFr ECD (SEQ ID NO: 2), EGFr L1 domain (SEQ ID NO: 4), EGFr CR1 domain (SEQ ID NO: 5), EGFr L2 domain (SEQ ID NO: 3), EGFr CR2 domain (SEQ ID NO: 6), EGFr L1+CR1 domains (SEQ ID No: 7), and EGFr L1+CR1+L2 domains (SEQ ID NO: 8).
The EGFr polypeptide-avidin fusions were captured on biotin-coated polystyrene beads. Each of the captured EGFr polypeptide-avidin fusions was then incubated with 1 μg/ml panitumumab for one hour at room temperature in 200 μl 0.5% BSA in PBS. The captured EGFr polypeptide-avidin fusions were then incubated with an allophycocyanin (APC)-conjugated anti-human IgG secondary antibody (Vector Laboratories, Burlingame, Calif.) to detect binding of panitumumab to the EGFr polypeptide-avidin fusions and a FITC conjugated anti-avidin antibody (Jackson Immunoresearch Labs) to detect the avidin portion of the EGFr polypeptide-avidin fusions, for 30 minutes at room temperature in 200 μl 0.5% BSA in PBS.
Binding of panitumumab to the EGFr polypeptide-avidin fusions was detected by detecting the APC-conjugated anti-human IgG secondary antibody by flow cytometry. The EGFr polypeptide-avidin fusions were detected by detecting the FITC conjugated anti-avidin antibody by flow cytometry. The results of that experiment are shown in FIGS. 2A and 2B. Those figures shows that panitumumab bound to the EGFr ECD, the EGFr L2 domain, and the EGFr L1+CR1+L2 domains. Those results suggest that panitumumab bound to the L2 domain of EGFr.
Example 2
Testing Panitumumab Binding to EGFR L2 Domain Point Mutants
To determine what amino acids within the EGFr L2 domain are important for panitumumab binding, the following human EGFr L2 domain point mutants (“mutant EGFr L2 polypeptides”) were separately expressed as avidin fusion proteins (with chicken avidin fused to the amino-terminus of the EGFr protein fragment) in transiently-transfected 293T cells using mammalian expression vector pCEP4 (Invitrogen):EGFr L2 P349A polypeptide (SEQ ID NO: 9), EGFr L2 R353A polypeptide (SEQ ID NO: 16), EGFr L2 D355T polypeptide (SEQ ID NO: 10), EGFr L2 F357A polypeptide (SEQ ID NO: 17), EGFr L2 Q384A polypeptide (SEQ ID NO: 18), EGFr L2 Q408M polypeptide (SEQ ID NO: 19), EGFr L2H409E polypeptide (SEQ ID NO: 20), EGFr L2 F412A polypeptide (SEQ ID NO: 11), EGFr L2 I438A polypeptide (SEQ ID NO: 12), EGFr L2 K443A polypeptide (SEQ ID NO: 21), EGFr L2 K465A polypeptide (SEQ ID NO: 22), EGFr L2 I467A polypeptide (SEQ ID NO: 23), EGFr L2 N473A polypeptide (SEQ ID NO: 24), EGFr L2 D355T/F357A polypeptide (SEQ ID NO: 25), and EGFr L2 Q408M/H409E polypeptide (SEQ ID NO: 26).
The mutant EGFr polypeptide-avidin fusions were captured on biotin-coated polystyrene beads. Each of the captured mutant EGFr polypeptide-avidin fusions was then incubated with 1 μg/ml panitumumab for one hour at room temperature in 200 μl 0.5% BSA in PBS. The captured mutant EGFr polypeptide-avidin fusions were then incubated with an allophycocyanin (APC)-conjugated anti-human IgG secondary antibody (Jackson Immunoresearch Labs) to detect binding of panitumumab to the mutant EGFr polypeptide-avidin fusions and a FITC conjugated anti-avidin antibody (Vector Laboratories, Burlingame, Calif.) to detect the avidin portion of the mutant EGFr polypeptide-avidin fusions, for 30 minutes at room temperature in 200 μl 0.5% BSA in PBS.
Binding of panitumumab to the mutant EGFr L2 polypeptide-avidin fusions was detected by detecting the APC-conjugated anti-human IgG secondary antibody by flow cytometry. The mutant EGFr L2 polypeptide-avidin fusions were detected by detecting the FITC conjugated anti-avidin antibody by flow cytometry. The results of that experiment are shown as a bar graph in FIG. 3, which shows the identity of the mutant EGFr L2 polypeptide-avidin fusions on the x-axis, and the % binding of the mutant EGFr L2 polypeptide-avidin fusions to panitumumab, expressed as a percentage of wild-type EGFr polypeptide-avidin fusion binding to panitumumab, on the y-axis. The y-axis in FIG. 3 is a logarithmic scale.
In that experiment, the mutant EGFr L2 P349A polypeptide-avidin fusion, the mutant EGFr L2 D355T polypeptide-avidin fusion, the mutant EGFr L2 F412A polypeptide-avidin fusion, and the mutant EGFr L2 I438A polypeptide-avidin fusion did not bind panitumumab as strongly as the wild-type EGFr L2 polypeptide-avidin fusion or the other point mutants tested. The EGFr L2 domain P349A point mutation and the EGFr L2 domain D355T point mutatation each reduced panitumumab binding by 98%. The EGFr L2 domain F412A point mutation reduced panitumumab binding by 92%. The EGFr L2 domain I438A point mutation reduced panitumumab binding by 99%. The EGFr L2 domain K443A point mutation reduced panitumumab binding by 63%. The EGFr L2 domain K465A point mutation reduced panitumumab binding by 84%. The EGFr L2 domain 1467A point mutation reduced panitumumab binding by 77%. Those results suggest that the panitumumab epitope on EGFr includes amino acids P349, D355, F412, I438, K443, K465, and I467.
Three commercial antibodies were also tested for binding to certain mutant EGFr polypeptides by a similar method as described above (data not shown). Two of the three antibodies had a significantly different binding profile from panitumumab. For example, Upstate Biotechnology's EGFr antibody clone LA22 did not bind to the mutant EGFr L2 F357A polypeptide and did bind to the mutant EGFr L2 K443A polypeptide. Lab Vision's EGFr antibody clone 528 did not bind to the mutant EGFr L2 N473A polypeptide. Lab Vision's EGFr antibody clone B1D8 had a similar profile to panitumumab.
Example 3
Panitumumab Inhibition of Ligand-Induced EGFR Activation
To determine whether panitumumab inhibits EGFr activation by certain ligands, A549 non-small cell lung carcinoma (NSCLC) cells were treated with 20 mg/ml panitumumab for 1 hour and then separately stimulated for 15 minutes with each of the following EGFr ligands:TGF-α (10 ng/ml), amphiregulin (500 ng/ml), epiregulin (200 ng/ml), HB-EGF (200 ng/ml), betacellulin (10 ng/ml), and EGF (10 ng/ml). Inhibition of ligand-induced phosphorylation of EGFr was determined using an antibody that specifically binds to EGFr having a phosphate on tyrosine 1068 (pY1068) (Cell Signaling Technology, Beverly, Mass.).
The results of that experiment are shown in FIG. 4. In that experiment, panitumumab (“pmab”) inhibited ligand-induced phosphorylation by all of the EGFr ligands tested by at least 87%.








TABLE 2







Table of Sequences












SEQ ID




Description
NO:
Sequence













human EGFr,
1
leekkv cqgtsnkltq lgtfedhfls lqrmfnncev



Genbank

vlgnleityv qrnydlsflk tiqevagyvl ialntverip


AAX41033,

lenlqiirgn myyensyala vlsnydankt glkelpmrnl


without 24

qeilhgavrf snnpalcnve siqwrdivss dflsnmsmdf


amino acid

qnhlgscqkc dpscpngscw gageencqkl tkiicaqqcs


leader

grcrgkspsd cchnqcaagc tgpresdclv crkfrdeatc


sequence

kdtcpplmly npttyqmdvn pegkysfgat cvkkcprnyv




vtdhgscvra cgadsyemee dgvrkckkce gpcrkvcngi




gigefkdsls inatnikhfk nctsisgdlh ilpvafrgds




fthtppldpq eldilktvke itgflliqaw penrtdlhaf




enleiirgrt kqhgqfslav vslnitslgl rslkeisdgd




viisgnknlc yantinwkkl fgtsgqktki isnrgensck




atgqvchalc spegcwgpep rdcvscrnvs rgrecvdkcn




llegeprefv enseciqchp eclpqamnit ctgrgpdnci




qcahyidgph cvktcpagvm genntlvwky adaghvchlc




hpnctygctg pglegcptng pkipsiatgm vgalllllvv




algiglfmrr rhivrkrtlr rllqerelve pltpsgeapn




qallrilket efkkikvlgs gafgtvykgl wipegekvki




pvaikelrea tspkankeil deayvmasvd nphvcrllgi




cltstvqlit qlmpfgclld yvrehkdnig sqyllnwcvq




iakgmnyled rrlvhrdlaa rnvlvktpqh vkitdfglak




llgaeekeyh aeggkvpikw malesilhri ythqsdvwsy




gvtvwelmtf gskpydgipa seissilekg erlpqppict




idvymimvkc wmidadsrpk freliiefsk mardpqrylv




iqgdermhlp sptdsnfyra lmdeedmddv vdadeylipq




qgffsspsts rtpllsslsa tsnnstvaci drnglqscpi




kedsflqrys sdptgalted siddtflpvp eyinqsvpkr




pagsvqnpvy hngplnpaps rdphyqdphs tavgnpeyln




tvqptcvnst fdspahwaqk gshqisldnp dyqqdffpke




akpngifkgs taenaeylrv apqssefiga l


 


human EGFr
2
leekkv cqgtsnkltq lgtfedhfls lqrmfnncev


extracellular

vlgnleityv qrnydlsflk tiqevagyvl ialntverip


domain, amino

lenlqiirgn myyensyala vlsnydankt glkelpmrnl


acids 1 to 621

qeilhgavrf snnpalcnve siqwrdivss dflsnmsmdf




qnhlgscqkc dpscpngscw gageencqkl tkiicaqqcs




grcrgkspsd cchnqcaagc tgpresdclv crkfrdeatc




kdtcpplmly npttyqmdvn pegkysfgat cvkkcprnyv




vtdhgscvra cgadsyemee dgvrkckkce gpcrkvcngi




gigefkdsls inatnikhfk nctsisgdlh ilpvafrgds




fthtppldpq eldilktvke itgflliqaw penrtdlhaf




enleiirgrt kqhgqfslav vslnitslgl rslkeisdgd




viisgnknlc yantinwkkl fgtsgqktki isnrgensck




atgqvchalc spegcwgpep rdcvscrnvs rgrecvdkcn




llegeprefv enseciqchp eclpqamnit ctgrgpdnci




qcahyidgph cvktcpagvm genntlvwky adaghvchlc




hpnctygctg pglegcptng pkips


 


human EGFr L2
3
kvcngi gigefkdsls inatnikhfk nctsisgdlh


domain

ilpvafrgds fthtppldpq eldilktvke itgflliqaw




penrtdlhaf enleiirgrt kqhgqfslav vslnitslgl




rslkeisdgd viisgnknlc yantinwkkl fgtsgqktki




isnrgensck atgqvchalc spegcwgpep rdcvs


 


human EGFr L1
4
leekkv cqgtsnkltq lgtfedhfls lqrmfnncev


domain

vlgnleityv qrnydlsflk tiqevagyvi ialntverip




lenlqiirgn myyensyala vlsnydankt glkelpmrnl




qeilhgavrf snnpalcnve siqwrdivss dflsnmsmdf




qnhlgscqkc dpscpngscw gageencqkl


 


human EGFr
5
tkiicaqqcs grcrgkspsd cchnqcaagc tgpresdclv


CR1 domain

crkfrdeatc kdtcpplmly npttyqmdvn pegkysfgat




cvkkcprnyv vtdhgscvra cgadsyemee dgvrkckkce




gpcr


 


human EGFr
6
crnvs rgrecvdkcn llegeprefv enseciqchp


CR2 domain

eclpqamnit ctgrgpdnci qcahyidgph cvktcpagvm




genntlvwky adaghvchlc hpnctygctg pglegcptng




pkips


 


human EGFr L1 +
7
leekkv cqgtsnkltq lgtfedhfls iqrmfnncev


CR1 domains

vlgnleityv qrnydlsflk tiqevagyvl ialntverip




lenlqiirgn myyensyala vlsnydankt glkelpmrnl




qeilhgavrf snnpalcnve siqwrdivss dflsnmsmdf




qnhlgscqkc dpscpngscw gageencqkl tkiicaqqcs




grcrgkspsd cchnqcaagc tgpresdclv crkfrdeatc




kdtcpplmly npttyqmdvn pegkysfgat cvkkcprnyv




vtdhgscvra cgadsyemee dgvrkckkce gpcr


 


human EGFr
8
leekkv cqgtsnkltq lgtfedhfls lqrmfnncev


L1 + CR1 + L2

vlgnleityv qrnydlsflk tiqevagyvl ialntverip


domains

lenlqiirgn myyensyala vlsnydankt glkelpmrnl




qeilhgavrf snnpalcnve siqwrdivss dflsnmsmdf




qnhlgscqkc dpscpngscw gageencqkl tkiicaqqcs




grcrgkspsd cchnqcaagc tgpresdclv crkfrdeatc




kdtcpplmly npttyqmdvn pegkysfgat cvkkcprnyv




vtdhgscvra cgadsyemee dgvrkckkce gpcrkvcngi




gigefkdsls inatnikhfk nctsisgdlh ilpvafrgds




fthtppldpq eldilktvke itgflliqaw penrtdlhaf




enleiirgrt kqhgqfslav vslnitslgl rslkeisdgd




viisgnknlc yantinwkkl fgtsgqktki isnrgensck




atgqvchalc spegcwgpep rdcvs


 


human EGFr L2
9
kvcngi gigefkdsls inatnikhfk nctsisgdlh


domain P349A

ilavafrgds fthtppldpq eldilktvke itgflliqaw


point mutant

penrtdlhaf enleiirgrt kqhgqfslav vslnitslgl




rslkeisdgd viisgnknlc yantinwkkl fgtsgqktki




isnrgensck atgqvchalc spegcwgpep rdcvs


 


human EGFr L2
10
kvcngi gigefkdsls inatnikhfk nctsisgdlh


domain D355T

ilpvafrgts fthtppldpq eidilktvke itgflliqaw


point mutant

penrtdlhaf enleiirgrt kqhgqfslav vslnitslgl




rslkeisdgd viisgnknlc yantinwkkl fgtsgqktki




isnrgensck atgqvchalc spegcwgpep rdcvs


 


human EGFr L2
11
kvcngi gigefkdsls inatnikhfk nctsisgdlh


domain F412A

ilpvafrgds fthtppldpq eldilktvke itgflliqaw


point mutant

penrtdlhaf enleiirgrt kqhgqaslav vslnitslgl




rslkeisdgd viisgnknlc yantinwkkl fgtsgqktki




isnrgensck atgqvchalc spegcwgpep rdcvs


 


human EGFr L2
12
kvcngi gigefkdsls inatnikhfk nctsisgdlh


domain 1438A

ilpvafrgds fthtppldpq eldilktvke itgflliqaw


point mutant

penrtdlhaf enleiirgrt kqhgqfslav vslnitslgl




rslkeisdgd vaisgnknlc yantinwkkl fgtsgqktki




isnrgensck atgqvchalc spegcwgpep rdcvs


 


human EGFr
13
tkiicaqqcs grcrgkspsd cchnqcaagc tgpresdclv


CR1 + L2

crkfrdeatc kdtcpplmly npttyqmdvn pegkysfgat




cvkkcprnyv vtdhgscvra cgadsyemee dgvrkckkce




gpcrkvcngi gigefkdsls inatnikhfk nctsisgdlh




ilpvafrgds fthtppldpq eldilktvke itgflliqaw




penrtdlhaf enleiirgrt kqhgqfslav vslnitslgl




rslkeisdgd viisgnknlc yantinwkkl fgtsgqktki




isnrgensck atgqvchalc spegcwgpep rdcvs


 


human EGFr
14
kvcngi gigefkdsls inatnikhfk nctsisgdlh


L2 + CR2

ilpvafrgds fthtppldpq eldilktvke itgflliqaw




penrtdlhaf enleiirgrt kqhgqfslav vslnitslgl




rslkeisdgd viisgnknlc yantinwkkl fgtsgqktki




isnrgensck atgqvchalc spegcwgpep rdcvscrnvs




rgrecvdkcn llegeprefv enseciqchp eclpqamnit




ctgrgpdhci qcahyidgph cvktcpagvm genntlvwky




adaghvchlc hpnctygctg pglegcptng pkips


 


human EGFr
15
tkiicaqqcs grcrgkspsd cchnqcaagc tgpresdclv


CR1 + L2 + CR2

crkfrdeatc kdtcpplmly npttyqmdvn pegkysfgat




cvkkcprnyv vtdhgscvra cgadsyemee dgvrkckkce




gpcrkvcngi gigefkdsls inatnikhfk nctsisgdlh




ilpvafrgds fthtppldpq eldilktvke itgflliqaw




penrtdlhaf enleiirgrt kqhgqfslav vslnitslgl




rslkeisdgd viisgnknlc yantinwkkl fgtsgqktki




isnrgensck atgqvchalc spegcwgpep rdcvscrnvs




rgrecvdkcn llegeprefv enseciqchp eclpqamnit




ctgrgpdnci qcahyidgph cvktcpagvm genntlvwky




adaghvchlc hpnctygctg pglegcptng pkips


 


human EGFr L2
16
kvcngi gigefkdsls inatnikhfk nctsisgdlh


domain R353A

ilpvafagds fthtppldpq eldilktvke itgflliqaw


point mutant

penrtdlhaf enleiirgrt kqhgqfslav vslnitslgl




rslkeisdgd viisgnknlc yantinwkkl fgtsgqktki




isnrgensck atgqvchalc spegcwgpep rdcvs


 


human EGFr L2
17
kvcngi gigefkdsls inatnikhfk nctsisgdlh


domain F357A

ilpvafrgds athtppldpq eldilktvke itgflliqaw


point mutant

penrtdlhaf enleiirgrt kqhgqfslav vslnitslgl




rslkeisdgd viisgnknlc yantinwkkl fgtsgqktki




isnrgensck atgqvchalc spegcwgpep rdcvs


 


human EGFr L2
18
kvcngi gigefkdsls inatnikhfk nctsisgdlh


domain Q384A

ilpvafrgds fthtppldpq eldilktvke itgflliaaw


point mutant

penrtdlhaf enleiirgrt kqhgqfslav vslnitslgl




rslkeisdgd viisgnknlc yantinwkkl fgtsgqktki




isnrgensck atgqvchalc spegcwgpep rdcvs


 


human EGFr L2
19
kvcngi gigefkdsls inatnikhfk nctsisgdlh


domain Q408M

ilpvafrgds fthtppldpq eldilktvke itgflliqaw


point mutant

penrtdlhaf enleiirgrt kmhgqfslav vslnitslgl




rslkeisdgd viisgnknlc yantinwkkl fgtsgqktki




isnrgensck atgqvchalc spegcwgpep rdcvs


 


human EGFr L2
20
kvcngi gigefkdsls inatnikhfk nctsisgdlh


domain H409E

ilpvafrgds fthtppldpq eldilktvke itgflliqaw


point mutant

penrtdlhaf enleiirgrt kqegqfslav vslnitslgl




rslkeisdgd viisgnknlc yantinwkkl fgtsgqktki




isnrgensck atgqvchalc spegcwgpep rdcvs


 


human EGFr L2
21
kvcngi gigefkdsls inatnikhfk nctsisgdlh


domain K443A

ilpvafrgds fthtppldpq eldilktvke itgflliqaw


point mutant

penrtdlhaf enleiirgrt kqhgqfslav vslnitslgl




rslkeisdgd viisgnanlc yantinwkkl fgtsgqktki




isnrgensck atgqvchalc spegcwgpep rdcvs


 


human EGFr L2
22
kvcngi gigefkdsls inatnikhfk nctsisgdlh


domain K465A

ilpvafrgds fthtppldpq eldilktvke itgflliqaw


point mutant

penrtdlhaf enleiirgrt kqhgqfslav vslnitslgl




rslkeisdgd viisgnknlc yantinwkkl fgtsgqktai




isnrgensck atgqvchalc spegcwgpep rdcvs


 


human EGFr L2
23
kvcngi gigefkdsls inatnikhfk nctsisgdlh


domain 1467A

ilpvafrgds fthtppldpq eldilktvke itgflliqaw


point mutant

penrtdlhaf enleiirgrt kqhgqfslav vslnitslgl




rslkeisdgd viisgnknlc yantinwkkl fgtsgqktki




asnrgensck atgqvchalc spegcwgpep rdcvs


 


human EGFr L2
24
kvcngi gigefkdsls inatnikhfk nctsisgdlh


domain N473A

ilpvafrgds fthtppldpq eldilktvke itgflliqaw


point mutant

penrtdihaf enleiirgrt kqhgqfslav vslnitslgl




rslkeisdgd viisgnknlc yantinwkkl fgtsgqktki




isnrgeasck atgqvchalc spegcwgpep rdcvs


 


human EGFr L2
25
kvcngi gigefkdsls inatnikhfk nctsisgdlh


domain

ilpvafrgts athtppldpq eldilktvke itgflliqaw


D355T/F357A

penrtdlhaf enleiirgrt kqhgqfslav vslnitslgl


point mutant

rslkeisdgd viisgnknlc yantinwkkl fgtsgqktki




isnrgensck atgqvchalc spegcwgpep rdcvs


 


human EGFr L2
26
kvcngi gigefkdsls inatnikhfk nctsisgdlh


domain

ilpvafrgds fthtppldpq eldilktvke itgflliqaw


Q408M/H409E

penrtdlhaf enleiirgrt kmegqfslav vslnitslgl


point mutant

rslkeisdgd viisgnknlc yantinwkkl fgtsgqktki




isnrgensck atgqvchalc spegcwgpep rdcvs

## Claims

1. A method of selecting a specific binding agent to an epidermal growth factor receptor (EGFr) polypeptide, wherein the specific binding agent binds to at least a portion of a panitumumab epitope on an EGFr polypeptide, comprising:
a) contacting an EGFr polypeptide with an agent, wherein the EGFr polypeptide comprises the L2 domain of EGFr set forth in SEQ ID NO:3;
b) determining the affinity of the agent for the EGFr polypeptide;
c) contacting a mutant EGFr polypeptide with the agent, wherein the mutant EGFr polypeptide comprises at least one point mutation in at least one amino acid position selected from P349A, D355T, F412A, I438A, K443A, K465A, and I467A;
d) determining the affinity of the agent for the mutant EGFr polypeptide; and
e) selecting the agent if the affinity for the EGFr polypeptide is at least 2-fold greater than the affinity for the mutant EGFr polypeptide.

2. The method of claim 1, wherein the mutant EGFr polypeptide is the same as the EGFr polypeptide except for the at least one mutation.

3. The method of claim 1, wherein the agent is selected from a protein, peptide, nucleic acid, carbohydrate, lipid, and small molecule compound.

4. The method of claim 3, wherein the agent is an antibody.

5. The method of claim 3, wherein the agent is a small molecule compound.

6. The method of claim 1, wherein the affinity for the EGFr polypeptide is at least 5-fold greater than the affinity for the mutant EGFr polypeptide.

7. The method of claim 1, wherein the affinity for the EGFr polypeptide is at least 10-fold greater than the affinity for the mutant EGFr polypeptide.

8. A method of selecting a specific binding agent to an epidermal growth factor receptor (EGFr) polypeptide, wherein the specific binding agent does not bind to a panitumumab epitope on an EGFr polypeptide (EGFr), comprising:
a) contacting an EGFr polypeptide with an agent, wherein the EGFr polypeptide comprises the L2 domain of EGFr set forth in SEQ ID NO:3;
b) determining the affinity of the agent for the EGFr polypeptide;
c) contacting a mutant EGFr polypeptide with the agent, wherein the mutant EGFr polypeptide comprises at least one point mutation in at least one amino acid position selected from P349A, D355T, F412A, I438A, K443A, K465A, and I467A;
d) determining the affinity of the agent for the mutant EGFr polypeptide; and
e) selecting the agent if the affinity for the EGFr polypeptide is similar to the affinity for the mutant EGFr polypeptide.

9. The method of claim 8, wherein the mutant EGFr polypeptide is the same as the EGFr polypeptide except for the at least one mutation.

10. The method of claim 8, wherein the agent is selected from a protein, peptide, nucleic acid, carbohydrate, lipid, and small molecule compound.

11. The method of claim 10, wherein the agent is an antibody.

12. The method of claim 10, wherein the agent is a small molecule compound.

13. The method of claim 8, wherein there is less than a 2-fold difference between the affinity for the EGFr polypeptide and the affinity for the mutant EGFr polypeptide.