CHIMERIC ACTIVATORS: QUANTITATIVELY DESIGNED PROTEIN THERAPEUTICS AND USES THEREOF

Info

Publication number: 20170306030
Type: Application
Filed: Jun 19, 2017
Publication Date: Oct 26, 2017
Applicant: President and Fellows of Harvard College (Cambridge, MA)
Inventors: Pamela A. Silver (Cambridge, MA), Pablo Cironi (Madrid), David G. Miguez (Barcelona)
Application Number: 15/626,439

Abstract

Aspects of the invention provide methods for harnessing the potential of proteins that occur naturally (e.g., in humans) and that have serious but finite toxicity. Aspects of the invention relate to a quantitative systems-biological and structural approach to design a class of chimeric proteins that avoid the toxicity of protein drugs while retaining their desired activities. In particular, chimeric proteins containing a variant form of a natural protein fused to a targeting moiety may be administered to a subject to target a signal (e.g., induction of apoptosis) to particular cells without having a generalized toxic effect in the subject.

Description

Description

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation of co-pending U.S. application Ser. No. 12/594,747 filed Apr. 16, 2010, which is a 35 U.S.C. §371 National Phase Entry Application of International Application No. PCT/US08/04435 filed Apr. 5, 2008, which designates the U.S. and which claims the benefit under 35 U.S.C. §119(e) from U.S. provisional applications Ser. No. 60/910,390 filed Apr. 5, 2007, Ser. No. 61/005,775 filed Dec. 7, 2007 and Ser. No. 61/065,937 filed Feb. 15, 2008, the entire contents of which are herein incorporated by reference.

SEQUENCE LISTING

The instant application contains a Sequence Listing which has been submitted in ASCII format via EFS-Web and is hereby incorporated by reference in its entirety. Said ASCII copy, created on Jun. 19, 2017, is named Sequence-Listing-12594747.txt and is 56,625 bytes in size.

FIELD OF THE INVENTION

The invention relates to chimeric proteins, fusion proteins, and therapeutic proteins.

BACKGROUND OF THE INVENTION

Many therapeutic proteins such as interferon alpha (IFNα), TNF and IL-2 act locally in their natural state. Systemic administration of these proteins results in side effects that limit the dose levels that can be used therapeutically. For example, IFNα is useful in treating hepatitis and certain cancers, but causes side effects such as flu-like symptoms and suicidal thoughts. There are needs for targeting mechanisms to permit therapeutic proteins to be delivered locally and to minimize the side effects of systemic administration of therapeutic proteins.

Several laboratories have performed protein-based targeting of toxins to cancer cells. The laboratory of Ira Pastan has been working on cancer-targeted toxins for many years. In 1987, this group described a chimeric protein consisting of Pseudomonas exotoxin and TGFα. This toxin normally binds to the cell surface, is internalized into the endosome, and then somehow enters the cytoplasm where it inactivates Elongation Factor II. TGFα is an EGF-like ligand that binds to EGF receptor. Over the years, the Pastan group has fused variants of this exotoxin to diverse ligands and antibody V regions that bind to cell surface receptors. Some of these have been in Phase I/II-type clinical trials, but none have shown enough efficacy to be developed further. Thus, in addition to the needs for targeting mechanisms to permit therapeutic proteins to be delivered locally and to minimize the side effects of systemic administration of therapeutic proteins, there is also a need to maintain the efficacy of therapeutic proteins while meeting one or both of these two needs.

Another example of protein-based targeting of toxins to cancer cells is Mylotarg™ Mylotarg™ is a monoclonal antibody chemically conjugated to the toxin calicheamycin (Giles et al. (2003) Cancer 98: 2095). Calicheamycin causes double-stranded breaks in DNA and is highly toxic. However, when covalently bonded to an antibody, this chemical is not toxic because it has no access to DNA. When Mylotarg™ binds to the CD33 receptor protein on a tumor cell, the antibody-receptor complex is internalized and the antibody is degraded. The calicheamycin is then liberated to bind to the DNA of the tumor cell. Mylotarg™ received accelerated approval by the FDA for treatment of acute myelogenous leukemia (AML) in 2000.

Other examples are Zevalin™ and Bexxar™. Zevalin™ and Bexxar™ consist of radioisotopes chemically conjugated to monoclonal antibodies against the B cell marker CD20. These proteins are use to treat B cell lymphoma. The radioisotopes used, yttrium-90 and iodine-131 respectively, have short decay path-lengths, so that when the antibody binds to the surface of a tumor cell, there is local irradiation of the tumor. Zevalin™ was approved by the FDA in 2002. Bexxar™ was approved in 2003.

Thus far, targeting of toxic molecules to specific cells has been successful for the delivery of small molecules (such as radioisotope delivery by conjugates such as Zevalin™ and Bexxar™ and delivery of a chemical toxin in Mylotarg™), but not for the delivery of cell-killing proteins such as Pseudomonas exotoxin, RNAse, tumor necrosis factor, or interferons. A consistent problem has been that the toxic proteins act on bystander cells as they are being delivered to target tissue.

SUMMARY OF THE INVENTION

Aspects of the invention relate to methods and compositions for specifically targeting the activity of naturally-occurring proteins to certain cells or tissues where their activity can be therapeutically useful. In some aspects, the invention provides therapeutic applications for naturally-occurring proteins that otherwise have serious but finite toxicity. Methods and compositions of the invention can be used to target the cell-activating properties of a protein to a subset of target cells without activating non-target cells. Aspects of the invention relate to chimeric proteins that include a variant of a cell-activating element (also referred to herein as an Activity element) that has reduced cell-activating properties relative to its wild-type counterpart. The chimeric proteins also include a cell-targeting element (also referred to herein as a targeting element) that preferentially binds to target cells of interest. The cell-activating variant and the cell-targeting element are connected via a linker. According to aspects of the invention, the activating and targeting elements are selected so that the resulting chimeric protein only activates cells that are bound by the targeting element. The activating element variant is selected such that it can only activate a cell when present in a sufficiently high amount (e.g., concentration) on or near a cell-surface. The targeting element is selected such that it can target a sufficient amount of the activating element to the surface of a target cell in order to activate it. In some embodiments, the linker is selected so that it allows simultaneous binding of the activating and targeting elements to different receptors on the target cell. Accordingly, chimeric proteins of the invention can be used to avoid or reduce unwanted side effects caused by the activating element activating non-target cells.

Aspects of the invention are particularly useful for targeting the activity of toxic activating elements to target cells (e.g., to target cytotoxic elements to cancer cells) without killing surrounding non-target cells. Aspects of the invention can be useful to harness certain functions of natural proteins that otherwise may be toxic (or have serious toxic side effects) when administered therapeutically. For example, IFNα is normally secreted by virus-infected cells and promotes the death of cells in the immediate vicinity. TNF is secreted in response to the presence of bacterial molecules such as lipopolysaccharide and is thought to play an important role in wound-healing. Other similar molecules include, but are not limited to, IFNβ, IL-2, IFNγ, and IL-1. These therapeutic proteins are usually administered systemically and all have serious side effects, but nonetheless can be very useful. Erythropoietin can also have serious side effects when treating anemia associated with cancer, since erythropoietin can stimulate the growth and survival of certain cancer cells. However, by using less active variants of these proteins in combination with targeting elements of the invention, the general toxicity of protein drugs can be avoided while retaining desired activities (e.g., cell killing activities, enzymatic activities, signal transduction activities, etc., or any combination thereof).

In some embodiments, a recombinant protein of the invention includes a first element that binds to a first receptor on a target cell; a second element that binds to a second receptor on the target cell; and, optionally, a linker that connects the first and second elements, wherein the linker allows the first and second elements to bind simultaneously to the first and second receptors on the target cell, wherein the first element comprises a mutation that reduces its binding affinity for its receptors, and wherein the first element transmits a signal to the host cell when it is bound to the first receptor. In some embodiments, the first element is an enzyme, a substrate, a receptor, a ligand, or other peptide that can interact (e.g., bind to and/or catalyze a reaction and/or transduce a signal) to the receptor on the cell surface. It should be appreciated that the receptor may be any cell-surface protein that can receive a signal (e.g., resulting in a molecular and/or cellular change) upon interaction with the first element. In some embodiments, the first element is a variant of an activity element that binds to and/or interacts with more than one receptor (e.g., 2, 3, 4, 5 or more different receptors) in nature. In some embodiments, the variant activity element (e.g., a natural or engineered mutant element) has reduced affinity for one or more of its natural receptors (e.g., for about 10%-20%, about 20%-40%, about 50%, about 40%-60%, about 60%-80%, about 80%-100% or for all of the different natural receptors). In particular, a variant activity element may have reduced binding affinity for the receptor (e.g., a signal transduction receptor, enzyme, or other cell surface molecule that can mediate a signal or other desired biochemical or cellular change) or receptors that are being targeted for activation in the target cells. Accordingly, a variant activity element may have reduced signaling (e.g., more than about 10%, more than about 25%, more than about 50%, more than about 75%, more than about 80%, more than about 90%, or more than about 95% loss of signaling activity, or complete loss of detectable signaling activity) via the receptor(s) of interest in the absence of the targeting element when compared to the wild-type activity element.

In some embodiments, recombinant proteins of the invention may bind to their target cells as monomers. In some embodiments, the targeting element binds to its target molecule as a monomer (e.g., as a single copy of the targeting element such as a single copy of an antibody). In some embodiments, the activity element interacts with its receptor or target as a monomer. In some embodiments, both the targeting and activity elements interact with their receptors or targets as monomers. In some embodiments, the cell-surface receptors themselves are monomers. However, they may be multimers as the invention is not limited in this respect.

In some embodiments, the first and second elements are connected via a linker. A linker may be any suitable length as described herein (e.g., about 5-10, about 10-20, about 25, about 20-50, about 50, about 50-70 amino acids long, or longer or shorter). In some embodiments, the linker may be flexible.

Accordingly, aspects of the invention relate to chimeric activators including an activity element and a targeting element, optionally joined by a linker, wherein the targeting element binds to a first binding site on a target cell, and wherein the activity element binds to a second binding site on a target cell, and wherein the linker length has been optimized for maximizing binding efficiency of the activity element to the second binding site when the targeting element is bound to the first binding site. In some embodiments the first binding site is a ligand binding site, a receptor, or an epitope on a cell surface. In some embodiments the second binding site is a signal-transduction receptor on a cell surface. In some embodiments the targeting element is an antibody, an antibody fragment, an Fc region, a natural or synthetic ligand, or a protein interaction motif. In some embodiments the activity element is a cytokine, a cytotoxic protein, a regulatory protein, or an active fragment of any one thereof.

Described herein are chimeric activators wherein the linker length has been optimized. In some embodiments the linker length is at least equal to the minimum distance between the first and second binding sites on the cell surface. In some embodiments the linker length is at least twice the minimum distance between the first and second binding sites on the cell surface. In some embodiments the linker length is at most five-six times the minimum distance between the first and second binding sites on the cell surface. In some embodiments the activity element is mutated such that the binding affinity of the activity element for the second binding site is lower than the binding affinity of the targeting element for the first binding site.

Aspects of the invention relate to methods for manufacturing a chimeric activator including an activity element and a targeting element joined by a linker, wherein the targeting element binds to a first binding site on a target cell, and wherein the activity element binds to a second binding site on a target cell, and wherein the linker length has been optimized for maximizing binding efficiency of the activity element to the second binding site when the targeting element is bound to the first binding site. In some embodiments methods include: i) optimizing the linker length as a function of the concentration of the first and second binding sites, the size of the activity element and targeting element, the minimum distance between the binding sites of the targeting element and the activity element, and the affinities of the activity element and the targeting element for the first and second binding sites; and ii) preparing a chimeric activator having an optimal linker length.

In some embodiments, methods include: i) mutating the activity element such that the binding affinity of the activity element for the second binding site is lower than the binding affinity of the targeting element for the first binding site; i) optimizing the linker length as a function of the concentration of the first and second binding sites, the size of the activity element and targeting element, the minimum distance between the binding sites of the targeting element and the activity element, and the affinities of the activity element and the targeting element for the first and second binding sites; and iii) preparing a chimeric activator.

Aspects of the invention relate to methods for targeted cellular regulation, the method including: administering to a subject a therapeutically effective amount of a chimeric activator including an activity element and a targeting element joined by a linker, wherein the targeting element binds to a first binding site on a target cell, and wherein the activity element binds to a second binding site on a target cell, and wherein the linker length has been optimized for maximizing binding efficiency of the activity element to the second binding site when the targeting element is bound to the first binding site.

Further described herein are methods for treating cancer, the method including: administering to a subject having a cancer a therapeutically effective amount of a composition including a chimeric activator including an activity element and a targeting element joined by a linker, wherein the targeting element binds to a first binding site on a target cell, and wherein the activity element binds to a second binding site on a target cell, and wherein the linker length has been optimized for maximizing binding efficiency of the activity element to the second binding site when the targeting element is bound to the first binding site.

However, it should be appreciated that aspects of the invention may be used to selectively target any activity (e.g., any activity mediated by a cell surface receptor) to target cells that selectively express a cell surface marker that is different (or expressed at different, for example higher, levels) than on non-target cells. Accordingly, aspects of the invention may be used to target cytotoxic or cytostatic activity to any cells associated with a disease or disorder (e.g., cancer cells, immune system cells associated with allergic or chronic inflammatory disorders or reactions, infected cells, pathogen cells, cells that are degenerating, or any other target cells of interest). Aspects of the invention also may be used to selectively deliver other activating signals to target cells (e.g., other than cytotoxic or cytostatic). For example, other activating signals may include on or more proliferation, differentiation, stimulation, or other signals that may be useful in different applications. These and other aspects of the invention are described in more details herein.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 illustrates a non-limiting embodiment of a general structure of a Chimeric Activator (“mut” indicates that the activity element has a mutation);

FIG. 2 shows, without wishing to be bound by theory, a proposed mechanism of specific binding of “Chimeric Activators” to target cells;

FIG. 3 shows a molecular model of an IFNα-EGF Chimeric Activator;

FIG. 4 illustrates an example of activation of IFNα signaling by chimeric activators;

FIG. 5 illustrates an example of the targeting effect in a Daudi cell line constructed to express EGFR;

FIG. 6 illustrates an example of the dependence of Chimeric Activator function on the receptor for the targeting element;

FIG. 7 illustrates an example of a Chimeric Activator function blocked by antibodies against the receptor for the targeting element;

FIG. 8 shows an example of a TNF-EGF Chimeric Activator;

FIG. 9 illustrates the use of antibody V regions instead of EGF as a targeting element;

FIG. 10 illustrates non-limiting aspects of chimeric activation, 10A) illustrates a general structure of a chimeric activator, 10B) shows a molecular model of an IFNα2a-EGF chimeric activator (space-filling structure), 10C)-10D) illustrate a mechanism of specific binding of chimeric activators to target cells, in 10C) the chimeric activator binds poorly to non-target cells because the intrinsic binding affinity of the mutant activity element to its receptor is low, in contrast in 10D) the targeting element binds to receptors on a target cell at a high rate (after the targeting element complexes with its receptor, the activity element is in a high local concentration relative to its receptor, so that the activity element can then bind and stimulate signal transduction);

FIG. 11 illustrates an embodiment of EGFR activation upon treatment with IFNα2a-EGF chimeric activators;

FIG. 12 illustrates an example of STAT1 activation upon treatment with IFNα2a-EGF chimeric activators;

FIG. 13 illustrates an example of EGFR neutralization;

FIG. 14 illustrates an example of EGFR-dependent anti-proliferative activity of IFNα2a-EGF chimeric proteins;

FIG. 15 shows a schematic of an embodiment of the chimera-receptor binding and receptor endocytosis where all model parameters are represented (the average distance between two receptors is shown as b_i;j);

FIG. 16 shows a schematic of an embodiment of the binding mechanism between a receptor and a free ligand or a chimeric ligand;

FIG. 17 shows a plot of the C₁concentration in time, for different initial values of total R₁;

FIG. 18 shows plots of C₂over time for different IF mutants (lower darker colored dots correspond to IF, and upper lighter colored dots correspond to chimeric protein);

FIG. 19 shows a plot of C₂at 30 min versus linker length for different IFN mutants;

FIG. 20 shows a time plot of an embodiment of the collision rate; and

FIG. 21 shows a plot of an embodiment of collision rate versus linker size.

DETAILED DESCRIPTION OF THE INVENTION

Aspects of the invention relate to chimeric proteins that include a targeting element connected to an activity element. In some embodiments, the targeting element binds to molecules that are selectively present on target cells. In some embodiments, the activity element is a variant of a naturally occurring protein that activates cells by binding to one or more cell surface receptors. The variant is selected such that it has reduced or no cell activating properties in the absence of the targeting element. The targeting element is selected such that it selectively binds to target cells thereby increasing the local concentration of the variant activity element on the target cells to a level that results in activation of those cells. In some embodiments, cell activation results in cell death or a reduction or absence of cell proliferation. However, it should be appreciated that other forms of cell activation may be targeted to specific cells using methods and compositions described herein.

An activity element may be a receptor binding protein (or functional portion or domain thereof) that binds to one or more naturally-occurring receptors on a cell surface, thereby mediating signaling to the cell (e.g., via signal transduction). A variant activity element may include one or more naturally occurring and/or engineered mutations that result in reduced binding to one or more (e.g., all) natural receptors that are bound by the wild-type activity element. For example, the binding affinity of the variant activity element for one or more of its receptors may be at least 2 fold lower and preferably at least 5 fold lower or 8 fold lower (e.g., at least 10 fold lower, about 10-50 fold lower, about 50-100 fold lower, about 100-150 fold lower, about 150-200 fold lower, or more than 200 fold lower) than the binding affinity of the wild-type activity element for its natural receptor(s). As a result, in some embodiments the activity element by itself is significantly less active (e.g., substantially inactive) because it cannot bind to its receptor(s). Accordingly, chimeric proteins of the invention are useful to avoid unwanted side effects caused by the activity element binding to its natural receptor on non-target cells. However, the activity element is active on target cells because the targeting element provides the missing binding affinity required for activation.

A targeting element may be a receptor binding protein, an antibody, or any other natural or engineered protein that binds to a molecule that is preferentially present on target cells of interest relative to non-target cells. According to some embodiments of the invention, the affinity of the targeting element for its target molecule (e.g., receptor) may be similar to the binding affinity of the variant activity element for its receptor(s). However, the affinity of the targeting element for its target molecule is typically higher (e.g., at least 2 fold, at least 5 fold, about 5-10 fold, about 10-50 fold, about 50-100 fold, about 100-500 fold, about 500-1,000 fold, at least 1,000 fold, at least 10,000 fold, or at least 100,000 fold higher) than the binding affinity of the variant activity element for its receptor(s).

In some embodiments, the activity and targeting elements are connected via a linker. The linker may be a natural or artificial peptide that provides sufficient flexibility to allow both the targeting element and the activity element of a chimeric activator to bind simultaneously to their targets and/or receptors on a target cell. The linker length may be optimized for the sizes of the target molecules and/or receptors being bound by targeting and activity elements, the sizes of the targeting and activity elements themselves, and other factors described herein in more detail. However, in some embodiments, a linker may not be required (or only a short linker may be required) if one or both of the targeting and activity elements are flexible or are connected to each other by flexible domains.

Accordingly, aspects of the invention relate to Chimeric Activators—proteins that include a targeting element and an activity element that are capable of simultaneously binding to multiple (two or more) unrelated receptors on the same target cell. In some embodiments, a Chimeric Activator has an activity element, a linker, and a targeting element. See, for example, FIG. 1. It should be appreciated that the linker, if present, is located between the targeting and activity elements. However, aspects of the invention are not limited by the relative positions of the targeting and activity elements. For example, the targeting element may be N-terminal to the activity element (regardless of whether a linker separates the two elements). Alternatively, the activity element may be N-terminal to the targeting element (regardless of whether a linker separates the two elements). In addition, proteins of the invention may include one or more additional peptide elements (at the N-terminus, the C-terminus, or within the protein) for purification and/or detection (e.g., peptide tags), stability, function (e.g., secretion and or other function), etc., or any combination thereof. It should be appreciated that targeting and activity elements may bind to overlapping types of molecules (e.g., receptors, substrates, enzymes, or other molecules) that are present on a cell surface. However, in any particular configuration, the element that is being used as a targeting element has sufficient affinity to target a chimeric protein to a cell-surface molecule that is preferentially (e.g., uniquely or selectively or specifically) present or exposed on a target cell of interest. In contrast, an element that is being used as an activity element may have relatively low affinity for a cell surface molecule. However, the element that is being used as an activity element may interact equally with a molecule that is present on all cell types, but only activates the target cell types due to its linkage to the targeting element. However, it should be appreciated that in some embodiments, both the targeting and activity elements interact with different cell surface molecules that all are preferentially present or exposed on the target cells.

Aspects of the invention may be useful to increase the therapeutic index (e.g., by about 2 fold, about 5 fold, about 10 fold, about 50 fold, about 100 fold, about 200 fold, or more) of any protein therapeutic (e.g., based on a naturally occurring or engineered protein or fragment thereof) by reducing the general toxicity of the protein and maintaining or increasing the selective effect of the protein on target cells or tissue. It should be appreciated that aspects of the invention may be used to treat any disease where selective cell activation is beneficial as described herein. In some embodiments, the targeting element may be selected on the basis that it target certain diseased cells (e.g., due to the presence of disease-specific antigens on the target cells). However, in certain embodiments, specific cell types or tissue types may be targeted (e.g., via cell or tissue specific cell surface antigens). In some embodiments, pathogen-specific molecules may be targeted (e.g., on the cells of a pathogen or on host cells infected with a pathogen).

Accordingly, methods and compositions described herein have broad application to treating disorders, including infections, cancer, anemia, allergy, and many other disorders where it is beneficial to activate (e.g., kill, stimulate or otherwise activate) one or more particular cell types. In some embodiments, the invention is useful to treat cancer. Cancer is disease characterized by uncontrolled cell proliferation and other malignant cellular properties. As used herein, the term cancer includes, but is not limited to, the following types of cancer: breast cancer; biliary tract cancer; bladder cancer; brain cancer including glioblastomas and medulloblastomas; cervical cancer; choriocarcinoma; colon cancer; endometrial cancer; esophageal cancer; gastric cancer; hematological neoplasms including acute lymphocytic and myelogenous leukemia; T-cell acute lymphoblastic leukemia/lymphoma; hairy cell leukemia; chronic myelogenous leukemia, multiple myeloma; AIDS-associated leukemias and adult T-cell leukemia/lymphoma; intraepithelial neoplasms including Bowen's disease and Paget's disease; liver cancer; lung cancer; lymphomas including Hodgkin's disease and lymphocytic lymphomas; neuroblastomas; oral cancer including squamous cell carcinoma; ovarian cancer including those arising from epithelial cells, stromal cells, germ cells and mesenchymal cells; pancreatic cancer; prostate cancer; rectal cancer; sarcomas including leiomyosarcoma, rhabdomyosarcoma, liposarcoma, fibrosarcoma, and osteosarcoma; skin cancer including melanoma, Merkel cell carcinoma, Kaposi's sarcoma, basal cell carcinoma, and squamous cell cancer; testicular cancer including germinal tumors such as seminoma, non-seminoma (teratomas, choriocarcinomas), stromal tumors, and germ cell tumors; thyroid cancer including thyroid adenocarcinoma and medullar carcinoma; and renal cancer including adenocarcinoma and Wilms tumor. Other cancers will be known to one of ordinary skill in the art.

In some embodiments, a targeting element comprises a protein component that selectively directs the binding of the chimeric protein to the surface of a desired cell or cells. Accordingly, a targeting element binds specifically to a cell-surface moiety (e.g., an antigen, epitope, protein, glycoprotein, lipid, carbohydrate, or other molecule or portion thereof) that is either only present or exposed on the target cell or is present or exposed in higher amounts on the target cell relative to non-target cells (e.g., about 2 fold, about 5 fold, about 10 fold, about 50 fold, about 100 fold, about 200 fold, about 500 fold, about 1,000 fold, about 10,000 fold, or more on the target cell). The targeting element can be any protein that binds to a cell-surface molecule. Targeting elements typically target to a subset of cells, such as tumor cells. In some embodiments a targeting element is an antibody or a portion of an antibody. In certain embodiments a targeting element is a ligand (e.g., a naturally occurring ligand or portion thereof that retains binding properties, or a synthetic ligand that binds, for example, to a receptor on a target cell).

In specific embodiments, the targeting element binds to cancers cells (e.g., is a cancer targeting element). In some embodiments, the targeting element is an antibody, a growth factor, a hormone, a peptide, an aptamer, a cytokine, interferon, vitamin, or a mixture thereof, for example. The antibody may be further defined as a full-length antibody, chimeric antibody, Fab′, Fab, F(ab′)2, single domain antibody (DAB), Fv, single chain Fv (scFv), minibody, diabody, triabody, or a mixture thereof, for example. In particular embodiments, the antibody is an anti-HER-2/neu antibody, such as scFv23, for example. In additional specific embodiments, the antibody is an anti-gp240 antigen antibody, such as one that comprises scFvMEL, for example.

Significantly, as is well known in the art, only a small portion of an antibody molecule, the paratope, is involved in the binding of the antibody to its epitope (see, in general, Clark, W. R. (1986) The Experimental Foundations of Modern Immunology Wiley & Sons, Inc., New York; Roitt, I. (1991) Essential Immunology, 7th Ed., Blackwell Scientific Publications, Oxford). The pFc′ and Fc regions, for example, are effectors of the complement cascade but are not involved in antigen binding. An antibody from which the pFc′ region has been enzymatically cleaved, or which has been produced without the pFc′ region, designated an F(ab′)2 fragment, retains both of the antigen binding sites of an intact antibody. Similarly, an antibody from which the Fc region has been enzymatically cleaved, or which has been produced without the Fc region, designated an Fab fragment, retains one of the antigen binding sites of an intact antibody molecule. Proceeding further, Fab fragments consist of a covalently bound antibody light chain and a portion of the antibody heavy chain denoted Fd. The Fd fragments are the major determinant of antibody specificity (a single Fd fragment may be associated with up to ten different light chains without altering antibody specificity) and Fd fragments retain epitope-binding ability in isolation.

Within the antigen-binding portion of an antibody, as is well-known in the art, there are complementarity determining regions (CDRs), which directly interact with the epitope of the antigen, and framework regions (FRs), which maintain the tertiary structure of the paratope (see, in general, Clark, 1986; Roitt, 1991). In both the heavy chain Fd fragment and the light chain of IgG immunoglobulins, there are four framework regions (FR1 through FR4) separated respectively by three complementarity determining regions (CDR1 through CDR3). The CDRs, and in particular the CDR3 regions, and more particularly the heavy chain CDR3, are largely responsible for antibody specificity.

It is now well established in the art that the non-CDR regions of a mammalian antibody may be replaced with similar regions of conspecific or heterospecific antibodies while retaining the epitopic specificity of the original antibody. This is most clearly manifested in the development and use of “humanized” antibodies in which non-human CDRs are covalently joined to human FR and/or Fc/pFc′ regions to produce a functional antibody. See, e.g., U.S. Pat. Nos. 4,816,567, 5,225,539, 5,585,089, 5,693,762 and 5,859,205. Fully human monoclonal antibodies also can be prepared by immunizing mice transgenic for large portions of human immunoglobulin heavy and light chain loci. Following immunization of these mice (e.g., XenoMouse (Abgenix), HuMAb mice (Medarex/GenPharm)), monoclonal antibodies can be prepared according to standard hybridoma technology. These monoclonal antibodies will have human immunoglobulin amino acid sequences and therefore will not provoke human anti-mouse antibody (HAMA) responses when administered to humans.

Thus, as will be apparent to one of ordinary skill in the art, the present invention also provides for F(ab′)2, Fab, Fv and Fd fragments; chimeric antibodies in which the Fc and/or FR and/or CDR1 and/or CDR2 and/or light chain CDR3 regions have been replaced by homologous human or non-human sequences; chimeric F(ab′)2 fragment antibodies in which the FR and/or CDR1 and/or CDR2 and/or light chain CDR3 regions have been replaced by homologous human or non-human sequences; chimeric Fab fragment antibodies in which the FR and/or CDR1 and/or CDR2 and/or light chain CDR3 regions have been replaced by homologous human or non-human sequences; and chimeric Fd fragment antibodies in which the FR and/or CDR1 and/or CDR2 regions have been replaced by homologous human or non-human sequences. The present invention also includes so-called single chain antibodies. In some embodiments, the targeting element of a chimeric protein is an antibody moiety that has been expressed from a single linear nucleic acid as a single peptide and that can fold into a fully functional antibody. In some embodiments, the chimeric protein is expressed from a nucleic acid that encodes a portion of an antibody (e.g., a heavy chain, a light chain, or a portion thereof as described herein) fused to the activity element (via the optional linker). The remainder of the antibody required for specific binding can be provided in trans (e.g., expressed from a different coding sequence in the same cell or expressed in a different cells and mixed in vitro, etc., or any combination thereof). Accordingly, it should be appreciated that a chimeric protein of the invention may be a single linear polypeptide chain or it may include additional polypeptide chains of an antibody or other binding protein required for specific binding to a target molecule.

In some embodiments, the targeting element comprises one or more growth factors, such as, for example, transforming growth factor, epidermal growth factor, insulin-like growth factor, fibroblast growth factor, heregulin, platelet-derived growth factor, vascular endothelial growth factor, or hypoxia inducible factor. In an additional specific embodiment, the cancer cell-targeting moiety comprises one or more hormones, such as human chorionic gonadotropin, gonadotropin releasing hormone, an androgen, an estrogen, thyroid-stimulating hormone, follicle-stimulating hormone, luteinizing hormone, prolactin, growth hormone, adrenocorticotropic hormone, antidiuretic hormone, oxytocin, thyrotropin-releasing hormone, growth hormone releasing hormone, corticotropin-releasing hormone, somatostatin, dopamine, melatonin, thyroxine, calcitonin, parathyroid hormone, glucocorticoids, mineralocorticoids, adrenaline, noradrenaline, progesterone, insulin, glucagon, amylin, erythropoitin, calcitriol, calciferol, atrial-natriuretic peptide, gastrin, secretin, cholecystokinin, neuropeptide Y, ghrelin, PYY3-36, insulin-like growth factor-1, leptin, thrombopoietin, angiotensinogen, IL-1, IL-2, IL-3, IL-4, IL-5, IL-6, IL-7, IL-8, IL-9, IL-10, IL-11, IL-12, IL-13, IL-14, IL-15, IL-16, IL-17, IL-18, IL-19, IL-20, IL-21, IL-22, IL-23, IL-24, IL-25, IL-26, IL-27, IL-28, IL-29, IL-30, IL-31, IL-32, IL-33, IL-34, IL-35, and/or, IL-36, for example, and/or a combination thereof.

In some embodiments, the targeting element comprises one or more cytokines, such as IL1, IL2, IL3, IL4, IL5, IL6, IL7, IL8, IL9, IL10, IL11, IL12, IL13, IL14, IL15, IL-16, IL-17, IL-18, granulocyte-colony stimulating factor, macrophage-colony stimulating factor, granulocyte-macrophage colony stimulating factor, leukemia inhibitory factor, erythropoietin, granulocyte macrophage colony stimulating factor, oncostatin M, leukemia inhibitory factor, IFN-γ, IFN-α, IFN-β, LT-β, CD40 ligand, Fas ligand, CD27 ligand, CD30 ligand, 4-1BBL, TGF-β, IL 1β, IL-1β, IL-1 RA, MIF, IGIF, and/or a combination thereof.

In some embodiments, a targeting element binds to one or more tissue-specific cell surface markers. In some embodiments, a targeting element is based on the natural ligand of tissue-specific cell surface marker (e.g., a targeting element is a recombinant version of a natural ligand or fragment thereof). In some embodiments, a targeting element is binding agent, such as a peptide, antibody, or aptamer, that binds to one or more tissue-specific cell surface markers. Appropriate cell surface markers are known by the skilled artisan. A non-limiting list of exemplary tissue-specific markers includes: B cell surface markers: (Activated B Cells) CD28, CD38, CD69, CD80, CD83, CD86, DPP4, FCER2, IL2RA, TNFRSF8, TNFSF7; (Mature B Cells) CD19, CD22, CD24, CD37, CD40, CD72, CD74, CD79A, CD79B, CR2, IL1R2, ITGA2, ITGA3, MS4A1, ST6GAL1; (Other B cell surface markers) CD1C, CHST10, HLA-A, HLA-DRA, NTSE. T cell surface markers: (Cytotoxic T Cells) CD8A, CD8B1; Helper T Cells: CD4; (Activated T Cells) ALCAM, CD2, CD38, CD40LG, CD69, CD83, CD96, CTLA4, DPP4, HLA-DRA, IL12RB1, IL2RA, ITGA1, TNFRSF4, TNFRSF8, TNFSF7; (Other T cell surface markers) CD160, CD28, CD37, CD3D, CD3G, CD3Z, CD5, CD6, CD7, FAS, KLRB1, KLRD1, NT5E, ST6GAL1; (Natural Killer (NK) cell surface markers) CD2, CD244, CD3Z, CD7, CD96, CHST10, FCGR3B, IL12RB1, KLRB1, KLRC1, KLRD1, LAG3, NCAM1; Monocyte/macrophage surface markers: (Activated Macrophages) CD69, ENG, FCER2, IL2RA; (Other Monocyte/macrophage cell surface markers) ADAMS, C5R1, CD14, CD163, CD33, CD40, CD63, CD68, CD74, CD86, CHIT1, CHST10, CSF1R, DPP4, FABP4, FCGR1A, HLA-DRA, ICAM2, IL1R2, ITGA1, ITGA2, S100A8, TNFRSF8, TNFSF7; Endothelial cell surface markers: ACE, CD14, CD34, CDH5, ENG, ICAM2, MCAM, NOS3, PECAM1, PROCR, SELE, SELP, TEK, THBD, VCAM1, VWF; Smooth muscle cell surface markers: ACTA2, MYH10, MYH11, MYH9, MYOCD; Dendritic cell surface markers: CD1A, CD209, CD40, CD83, CD86, CR2, FCER2, FSCN1; Mast cell surface markers: C5R1, CMA1, FCER1A, FCER2, TPSAB1; Fibroblast (stromal) cell surface markers: ALCAM, CD34, COL1A1, COL1A2, COL3A1, PH-4; Epithelial cell surface markers: CD1D, K6IRS2, KRT10, KRT13, KRT17, KRT18, KRT19, KRT4, KRT5, KRT8, MUC1, TACSTD1; and Adipocyte surface markers: ADIPOQ, FABP4, RETN, and/or a combination of two or more thereof.

According to aspects of the invention, an activity element comprises a protein component that has the desired signaling activity. This component normally binds to a receptor on the surface of the desired target cell. The activity element can be any protein that binds to a cell-surface receptor and stimulates signal transduction. In some embodiments, the activity element is a variant form (e.g., it is mutated) that has an intrinsic binding to its receptor that is weak as compared to the wild-type protein, to the point that binding of the chimeric protein to a cell is driven by the binding of the targeting element to its receptor. For example, the Chimeric Activator first binds to a cell through the targeting element, and after this initial binding step, the mutated activity element is in a high local concentration relative to its own receptor, so binding takes place in spite of the mutation. In contrast, the chimeric protein may not significantly bind to cells that have only the activity element receptor and not the targeting element receptor, because the inherent binding of the activity element is simply too weak. The presence of one or more weakening mutations can be essential to reduce side effects from activation of non-target cells.

It should be appreciated that the choice of a particular mutation can be tuned to the on-rates and dissociation constants of the naturally occurring targeting element and activity element, the relative numbers of receptors of each type on the target cell, and the binding enhancement factor resulting from pre-binding of the chimeric protein to the receptor for the targeting element. In practice, mutations with a range of different strengths may be tested empirically using techniques known to one of ordinary skill in the art. FIG. 2 illustrates a non-limiting example of these processes. In A), a target cell expresses the Receptors for both the targeting element (R_T) and Receptors for the Activating Element (R_A). The Chimeric Activator first binds to the target cell surface via the targeting element (T). The resulting complex then undergoes two-dimensional diffusion in the cell membrane, and when the Activating Element (A) is near its receptor, binding will be driven by the high local concentration, in spite of the mutation in the Activating Element that reduces binding. Signal transduction results (lightning). In B), the chimeric activator does not bind to non-target cells because the intrinsic binding of the mutant Activator Element to its receptor is simply too low.

Aspects of the invention relate to creating mutations in the activity element, such that the mutated form of the activity element binds to its receptor with a reduced affinity relative to a wild-type form of the activity element. Accordingly, chimeric activators differ from fusion proteins in which an element with signaling activity may bind to more than one receptor type, and a mutation is introduced into this element to modulate the receptor type that is used (e.g., certain TNF chimeras, see also for example US20060263368). In contrast, Chimeric Activators of the invention differ from such distinct fusion proteins in that the signaling by a Chimeric Activator is directed through the receptor for which affinity has been reduced by the mutation in the activity element. As used herein, a “mutation” refers to a change in the nucleotide sequence encoding the activity element, relative to a wild-type form of the gene. A change in the nucleotide sequence may or may not lead to a change in the amino acid sequence, the three-dimensional structure of the protein, and/or the activity of the protein, relative to the wild-type form of the protein. In some embodiments a mutation may be a naturally occurring variant of the gene. In some embodiments a mutation may be a single amino acid substitution, two or more amino acid substitutions, one or more deletions, one or more insertions, or any combination of two or more thereof, in the protein sequence of the activity element. It will be understood that the selection of a suitable mutation in an activity element for the creation of a chimeric molecule will depend on multiple factors and in some embodiments will need to be determined empirically for different proteins.

It should be appreciated that variant activity elements of the invention may have a reduced binding affinity for their receptor(s) without a loss (or without a significant loss) of signal function (e.g., they substantially or completely retain their ability to promote signal transduction when bound to their receptor(s) even though their affinity for the receptor(s) may be significantly reduced). It also should be appreciated that the reduced binding affinity of the variant activity element preferably does not result in a protein element that will not bind to its natural receptor(s), for example, due to steric hindrance or charge repulsion or other negative interaction between the variant activity element and its natural receptor(s), even when the targeting element binds to a target molecule on the same cell (thereby increasing the local concentration of the variant activity element in the vicinity of its natural receptor(s)).

In some embodiments, appropriate levels of reduced binding affinity can be obtained by introducing one or more mutations in charged or hydrophilic amino acids (or amino acids thought to be pointing outward) that have the effect of shortening the side chain of the amino acid(s). According to aspects of the invention, the charged or hydrophilic side chains are likely to be pointing outward and not into the middle of the protein. Reducing the size of the amino acid side chain(s) removes a contact, but does not create steric hindrance that would completely block binding or signaling. In some embodiments, mutants may be created in an activity element, and those that reduce but do not abolish binding may be selected (e.g., using one or more binding and/or activity assays known to one of skill in the art) and used to construct a Chimeric Activator.

According to aspects of the invention, variant activity elements of the invention can be identified or selected for any appropriate cell-surface receptor that is involved in a signaling activity that is useful for a particular application of interest.

For example, tumor necrosis factor receptors (TNFR) (e.g., CD120), or death receptors, are a family of cytokine receptors that bind to various tumor necrosis factors (TNF) (e.g., TNF-alpha). Exemplary tumor necrosis factor receptor family members include: CD120a (TNFRSF1A), CD120b (TNFRSF1B), Lymphotoxin beta receptor (LTBR, TNFRSF3), CD134 (TNFRSF4), CD40 (CD40, TNFRSF5), FAS (FAS, TNFRSF6), TNFRSF6B (TNFRSF6B), CD27 (CD27, TNFRSF7), CD30 (TNFRSF8), CD137 (TNFRSF9), TNFRSF10A (TNFRSF10A), TNFRSF10B, (TNFRSF10B), TNFRSF10C (TNFRSF10C), TNFRSF10D (TNFRSF10D), RANK (TNFRSF11A), Osteoprotegerin (TNFRSF11B), TNFRSF12A (TNFRSF12A), TNFRSF13B (TNFRSF13B), TNFRSF13C (TNFRSF13C), TNFRSF14 (TNFRSF14), Nerve growth factor receptor (NGFR, TNFRSF16), TNFRSF17 (TNFRSF17), TNFRSF18 (TNFRSF18), TNFRSF19 (TNFRSF19), TNFRSF21 (TNFRSF21), and TNFRSF25 (TNFRSF25). Several groups have demonstrated that human tumor cells can display between 100 and 5000 TNF receptor sites per cell (Rosenblum et al., 1991; Rosenblum et al., 1995). Thus, TNFRs represent an attractive target for inhibiting cancer cell growth and/or survival.

In some embodiments, the activity elements of the invention are ligands (agonists or antagonists) that bind to one or more tumor necrosis factor receptors known in the art or disclosed herein. In some embodiments, the activity elements of the invention are tumor necrosis factors or fragments thereof, such as TNF-alpha or TNF-beta (lymphotoxin). In some embodiments, the activity elements are selected from the TNF Ligand Family: LTA (TNF-α), TNF (TNF-α), TNFSF5 (CD40 Ligand), TNFSF6 (FasL), TNFSF7 (CD27 Ligand), TNFSF8 (CD30 Ligand), TNFSF9 (4-1BB Ligand), TNFSF10 (TRAIL), TNFSF14 (HVEM-L), TNFSF18, or fragments thereof. In some embodiments, the activity elements of the invention are tumor necrosis factors or fragments thereof, such as TNF-alpha or TNF-beta (lymphotoxin). In some embodiments, the activity elements of the invention are tumor necrosis factors with attenuated function. In some embodiments, the attenuated function is a reduced binding affinity for target receptors.

It should be appreciated that certain peptide elements may be used as targeting elements in some embodiments (e.g., a cytokine that can be used to target cells that express the cytokine receptor) and activity elements in different embodiments (e.g., the same cytokine could be used to activate cells that are targeted using a different targeting element in other embodiments). When a peptide is used as a targeting element, its natural affinity for the target molecule may be retained in the chimeric molecule. In some embodiments, the affinity of a natural peptide for a target molecule may be increased (e.g., by mutation) in order to improve its use as a targeting element. In certain embodiments, the binding affinity may be retained and/or increased but the function activity (e.g., signal transduction or enzymatic activity) may be decreased or removed (e.g., by mutation) if that particular function is not required or is undesirable. In contrast, if the same peptide is being used as an activity element in a different chimeric molecule, a variant form (e.g., a naturally occurring or engineered mutated form) may be used to reduce binding affinity of the activity element to non-target cells as described herein. Accordingly, one or more of the growth factors and/or cytokines described or listed herein as candidates for targeting elements also may be used as activity elements in other embodiments where they may be mutated to reduce their binding affinity for their receptor or substrate or target molecule.

One criterion that may be evaluated in selecting activity elements and targeting elements is the affinity of the activity element for its receptor, and the ratio of the affinity of the activity element for its receptor relative to the affinity of the targeting element for its receptor. In some embodiments mutated activity elements will be selected such that the activity element has a lower affinity for its receptor than the affinity of the targeting element for its receptor, thus allowing the targeting element to control which cells are bound by the chimeric molecule. In some embodiments the affinity ratio may be 1/2, 1/5, 1/10, 1/25, 1/50, 1/75, 1/100, 1/500, 1/1000, or an intermediate value, or a smaller value. Another set of criteria that may be evaluated in selecting activity elements and targeting elements include the on-rates, off-rates, and dissociation constants for the binding of the activity element to its receptor and the targeting element to its receptor. In some embodiments mutated activity elements will be selected wherein one or both of the following conditions are met: the on-rate of the activity element is lower than that of the targeting element, or if the off-rates are faster than the internalization rate, then the equilibrium constant (K_on/K_off) of the targeting element is higher than that of the activity element.

Another criterion that may be involved in selecting mutated activity elements is an evaluation of the activity level of the activity element alone, and the activity level of the activity element when it is linked to the targeting element. In some embodiments mutated activity elements may be selected that have reduced activity or are inactive alone, relative to a wildtype form of the protein, due to their reduced binding efficiency, but are active when linked to a targeting element, because the binding of a targeting element to its receptor at the cell surface increases the local concentration of the activity element in the vicinity of its receptor at the cell surface. It should be appreciated that appropriate activity levels for a given protein and a given mutation will need to be determined empirically. In some embodiments wherein an activity element is being targeted to a cancer cell in order to kill the cell, a mutated activity element will be selected such that the mutated activity element will not have sufficient activity to kill a cell when the activity element is alone, due to its reduced binding capacity for its receptor. When the activity element is linked to a targeting element, the increased local concentration of the activity element at the cell surface allows it to be active and bind to its receptor and kill the cell.

In some embodiments, targeting and activity elements are attached by a linker. The linker can be any amino acid sequence that allows the simultaneous binding of the activity element and the targeting element to their receptors on a given cell surface. Typically the linker is a non-folding, protease-resistant polypeptide segment that permits the targeting element and the activity element to bind to their cell-surface receptors, typically on the same cell surface, at the same time. Linkers may be of varied length (e.g., about 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100 amino acids long or intermediate or longer lengths) and/or amino acid composition. Linkers may be flexible or rigid.

In some embodiments linker length will be optimized for maximizing binding efficiency of the activity element to the second binding site when the targeting element is bound to the first binding site. Optimal linker length for a given chimeric activator can be determined at least in part using models disclosed herein. In optimizing linker length, multiple factors will be considered including, but not limited to: the concentration of the first and second binding sites, the sizes of the activity element and targeting element, the minimum distance between the binding sites of the targeting element and the activity element, and the affinities of the activity element and the targeting element for the first and second binding sites. In some embodiments a linker length will be chosen that is at least equal to the minimum distance between the first and second binding sites on the cell surface. In other embodiments a linker length will be chosen that is at least twice the minimum distance between the first and second binding sites on the cell surface. In some embodiments a linker length will be chosen that is at most five-six times the minimum distance between the first and second binding sites on the cell surface. It will be understood that optimal linker length will vary depending on the specific proteins selected as activity elements and targeting elements. In some embodiments a protein which is blocked at the N- or C-terminus may be selected as an activity element or a targeting element. In these embodiments a linker may be added elsewhere on the protein.

In some embodiments, the linker length is chosen based in part on the known or surmised heights from the cell surface of the targeting element and activity element when each is bound to its receptor. For example, when EGF is bound to EGFR, its N- and C-termini are about 90 Angstroms from the cell surface, and when interferon alpha is bound to its receptor, its N- and C-termini are about 75 Angstroms from the cell surface, so that a linker of at least 15 Angstroms must be used.

The invention also provides methods for calculating an optimal linker length for a chimeric protein with two elements that simultaneously bind to a cell surface, based on the density of the receptors for each of the two elements on a cell surface and the difference in height from the cell surface of the termini of the two elements when bound to their receptors. The method optionally involves knowledge of the on-rates and off-rates of each element for its receptor. The method optionally involves calculating, as linker length is increased, the trade-off on the one hand between the increasing volume that can be occupied by one element when the other is bound to its receptor on a cell surface (which negatively impacts on a second binding event), and the increasing portion of cell surface area that may be sampled by one element when the other is bound to its receptor on that cell surface (which positively impacts on a second binding event). For many situations the density of a targeting element receptor is more than 10,000 per cell and the difference in height from the cell membrane of the bound elements is less than about 50 Angstroms, and in such situations a linker of about 25 to 70 amino acids is found to be optimal, with a linker length of about 30 to 40 amino acids often being more optimal. The linker should be flexible.

In many cases it is preferable to have both a targeting element and an activity element that engage their receptors through monomeric interactions. For example, in an interferon alpha-EGF Chimeric Activator, both the interferon alpha element and the EGF element are monomeric. This is in contrast to the activity elements TNF and TRAIL, which are trimeric, and to targeting elements consisting of antibodies, which are generally dimeric or have higher-order multivalent binding properties. One advantage of using targeting elements and activity elements that function as monomers is that it is easier to quantitatively predict their properties and thus to design specific molecules with desired features. It is also generally easier to predict the structure of the complex on the cell surface in which the targeting element and activity element are simultaneously bound. Examples of functionally monomeric activity elements include interferon alpha, interferon beta, IL-1, IL-2, IL-3, IL-4, IL-6, IL-11, IL-12, IL-13, IL-15, IL-18, erythropoietin, insulin, insulin-like growth factor, thrombopoietin, EGF, and CNTF. Examples of functionally monomeric targeting elements include single-chain Fv proteins and Fabs, as well as CD4, IL-1, IL-2, IL-3, IL-4, IL-6, IL-11, IL-12, IL-13, IL-15, IL-18, erythropoietin, insulin, insulin-like growth factor, thrombopoietin, EGF, and CNTF. Therefore, the invention provides Chimeric Activators that contain a monomerically functioning activity element and a monomerically functioning targeting element. More broadly, the invention provides proteins comprising two monomerically binding peptide moieties, optionally connected by a linker, such that both moieties can simultaneously bind to their receptors and/or target molecules on a single cell surface, in which at least one moiety signals through its receptor, and for which the signaling moiety contains a mutation relative to its naturally occurring form that reduces the binding to the receptor through which the signaling moiety signals. In some embodiments, a monomeric portion of a naturally multimeric targeting element and/or activity element may be used (e.g., by removing a multimerization domain). In these embodiments, the activity element also may include an additional mutation to reduce its affinity for its receptor as described herein.

In some embodiments, a chimeric protein of the invention may include a recombinant binding protein such as recombinant antibody instead of the activity element. The binding protein may be engineered to have very low affinity (relative to specific antibody binding affinity) for a target molecule that can transduce a signal (or result in another biological or cellular response) upon binding by the binding protein (e.g., low affinity antibody). Accordingly, aspects of the invention described in the context of a chimeric protein including a variant activity element also may be used in connection with an chimeric protein that includes a low affinity engineered binding protein instead. The same considerations for the targeting element and the optional linker apply.

As used herein, the term “binding” refers to a non-covalent or a covalent interaction, preferably non-covalent, that holds two molecules together. For example, two such molecules could be an enzyme and an inhibitor of that enzyme. Another example would be an enzyme and its substrate. A third example would be an antibody and an antigen. Non-covalent interactions include, but are not limited to, hydrogen bonding, ionic interactions among charged groups, van der Waals interactions, and hydrophobic interactions among non-polar groups. One or more of these interactions can mediate the binding of two molecules to each other. Binding may exhibit discriminatory properties such as specificity or selectivity. Binding affinities may range from mM to pM (e.g., micromolar or nanomolar binding affinities) depending on the concentration of the receptors and the activity of the activator elements.

The term “HIS-tag” refers to an affinity tag consisting of multiple consecutive histidine amino acids. Generally six (hexa-HIS) residues are used, or multiples thereof. His-tagged proteins have a high selective affinity for Ni⁺ and a variety of other immobilized metal ions. Consequently a protein containing a His-tag generally can be selectively bound to a metal ion charged medium while other cellular proteins bind weakly or are washed out with binding or wash buffers. His-tags are small and therefore, tend to be less disruptive to the properties of the proteins on which they are attached.

The term “myc tag” refers to an epitope tag derived from myc protein, generally comprising the sequence amino acid SEQ ID NO: 17: EQKLISEEDL. A number of different antibodies are known to recognize the myc epitope tag, for example 9B11 and 9E10.

The term “RNA equivalent” refers to an RNA sequence corresponding to a DNA or amino acid sequence. Such equivalents may correspond directly to the original sequence (in the case of a protein the “coding sequence”), or may include additional sequence, such as untranslated regions and introns. In the case of an RNA equivalent for DNA the correspondence may be complementary to the DNA strand or anti-sense, allowing for the fact that in RNA “U” replaces “T” in the genetic code. DNA/RNA sequences of the sequence listing may be considered to follow this guidance.

Nucleic acids of the invention include isolated or recombinant nucleic acids comprising coding sequences for Chimeric Activators or components thereof described herein. The nucleic acids may be on vectors. The nucleic acids may be in host cells. It should be appreciated that the nucleic acids also may include regulatory sequences for transcription (e.g., promoters, activators, terminators, etc.) and translation (e.g., ribosome binding sequences, IRES elements, terminators, etc.) of the chimeric proteins in addition to sequences required for vector replication and/or selection and/or packaging in host cells (e.g., prokaryotic or eukaryotic host cells, including, but not limited to bacterial, mammalian, yeast, insect, and/or other host cells). Accordingly, aspects of the invention relate to recombinant vectors which include one or more nucleic acids of the invention (e.g., SEQ ID NOs: 1, 3, 5, 7, 9, 11, 13, and 15), as well as host cells containing the vectors or which are otherwise engineered to contain or express nucleic acids or polypeptides of the invention, and methods of making such vectors and host cells and their use in production of polypeptides of the invention by recombinant or synthetic techniques. In some embodiments, Targeting and activity elements may be isolated (e.g. expressed and purified) independently and linked via a synthetic linker.

In some embodiments, the polynucleotides of the invention are joined to a vector (e.g., a cloning or expression vector). The vector may be, for example, a phage, plasmid, or viral vector. Viral vectors may be replication competent or replication defective. In the latter case, viral propagation generally will occur only in complementing host cells. The polynucleotides may be joined to a vector containing a selectable marker for propagation in a host. Introduction of the vector construct into the host cell can be effected by techniques known in the art which include, but are not limited to, calcium phosphate transfection, DEAE-dextran mediated transfection, cationic lipid-mediated transfection, electroporation, transduction, infection or other methods. Such methods are described in many standard laboratory manuals, such as Davis et al. (1986) Basic Methods In Molecular Biology.

The polypeptides of the invention or fragments thereof may be provided in substantially pure form, that is to say free, to a substantial extent, from other proteins. Thus, a polypeptide may be provided in a composition in which it is the predominant component present (i.e., it is present at a level of at least 50%; preferably at least 75%, at least 90%, or at least 95%; when determined on a weight/weight basis excluding solvents, carriers, or coupling agents).

Polypeptides of the invention can be recovered and purified from recombinant cell cultures or organisms by well-known methods including, ammonium sulphate or ethanol precipitation, acid extraction, anion or cation exchange chromatography, phosphocellulose chromatography, affinity chromatography, hydrophobic interaction chromatography, hydroxylapatite chromatography, molecular sieving chromatography, centrifugation methods, electrophoresis methods and lectin chromatography. In one embodiment, Chimeric Activator proteins are expressed in and secreted from the yeast Pichia pastoris. In one embodiment, a combination of these methods is used. In another embodiment, high performance liquid chromatography is used. In a further embodiment, an antibody which specifically binds to a polypeptide of the invention can be used to deplete a sample comprising a polypeptide of the invention of the polypeptide or to purify the polypeptide. Techniques well-known in the art, may be used for refolding to regenerate native or active conformations of the polypeptides of the invention when the polypeptides have been denatured during isolation and or purification, should such be desired.

Polypeptides of the invention (and their corresponding DNA and RNA coding sequences) may comprise sequences, for example, epitope or affinity tags, that may aid in isolation or purification of the protein. However, they need not do so. For example, proteins of the invention (e.g., SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14, or 16) may be purified through use of reagents that bind myc and/or HIS tags, but the invention also contemplates embodiments in which the proteins lack the myc and/or HIS tags, or which utilize different epitope or affinity tags.

Chimeric Activator nucleic acids and/or polypeptides may be screened, such as in high-throughput screening of a library of Chimeric Activators to select for a Chimeric Activator of the desired characteristics, or may be screened individually. For example, measurement of signal transduction in mammalian cells using Western blots that detect phosphorylation at specific sites may be used to screen for Chimeric Activators of a desired signal transduction activity.

Chimeric activators may be of various functions, e.g., having activity working against cancer, viral infection, and obesity. Diverse proteins can be used as activity elements and targeting elements. These proteins can be structurally varied, including monomers, trimers, and heterodimers of alpha helices and beta sheets. Some design considerations are illustrated in the Examples. Activity elements may be a non-toxic pro-drug that is activated in the target locale, for example, by cancer cells. It should be appreciated that many functions are compatible with the chimeric activators of the claimed invention. In some embodiments, the targeting element targets the activity element to a specific cell or cell type in order to kill a specific cell or cell type. In other embodiments the targeting element targets the activity element to a specific cell or cell type, for a purpose other than to kill the specific cell or cell type (e.g. to upregulate or downregulate one or more proteins or cellular properties such as cell growth, or proliferation).

Chimeric Activator nucleic acids and/or polypeptides may be used in gene therapy or in pharmaceutical compositions. Chimeric Activator nucleic acids and/or polypeptides may be used in treatment of a subject or patient, and may be used in combination with other therapies. Use of Chimeric Activator nucleic acids and/or polypeptides may be indicated by a diagnostic or theranostic, for example, a biopsy, for the appropriate presence of receptors for the Targeting and/or activity element.

Aspects of the invention relate to the use of chimeric activator proteins in the treatment of disorders. In some embodiments chimeric activator proteins are used to treat subjects who have cancer. As used herein, the term “subject” refers to a human or non-human mammal or animal. Non-human mammals include livestock animals, companion animals, laboratory animals, and non-human primates. Non-human subjects also specifically include, without limitation, chickens, horses, cows, pigs, goats, dogs, cats, guinea pigs, hamsters, mink, and rabbits. In some embodiments of the invention, a subject is a patient. As used herein, a “patient” refers to a subject who is under the care of a physician or other health care worker, including someone who has consulted with, received advice from or received a prescription or other recommendation from a physician or other health care worker. A patient is typically a subject having or at risk of having cancer. The term “treatment” or “treating” is intended to refer to prophylaxis, amelioration, prevention and/or cure of a condition (e.g., cancer). Treatment after a condition (e.g., cancer) that has started aims to reduce, ameliorate or altogether eliminate the condition, and/or its associated symptoms, or prevent it from becoming worse. Treatment of subjects before a condition (e.g., cancer) has started (i.e., prophylactic treatment) aims to reduce the risk of developing the condition and/or lessen its severity if the condition does develop. As used herein, the term “prevent” refers to the prophylactic treatment of a subject who is at risk of developing a condition (e.g., cancer) resulting in a decrease in the probability that the subject will develop the disorder, and to the inhibition of further development of an already established disorder.

As used herein, the term “cancer” refers to an uncontrolled growth of cells that may interfere with the normal functioning of the bodily organs and systems, and includes both primary and metastatic tumors. Primary tumors or cancers that migrate from their original location and seed vital organs can eventually lead to the death of the subject through the functional deterioration of the affected organs. A metastasis is a cancer cell or group of cancer cells, distinct from the primary tumor location, resulting from the dissemination of cancer cells from the primary tumor to other parts of the body. Metastases may eventually result in death of a subject.

As used herein, the term “cancer” includes, but is not limited to, the following types of cancer: breast cancer (including carcinoma in situ), biliary tract cancer; bladder cancer; brain cancer including glioblastomas and medulloblastomas; cervical cancer; choriocarcinoma; colon cancer; endometrial cancer; esophageal cancer; gastric cancer; hematological neoplasms including acute lymphocytic and myelogenous leukemia; T-cell acute lymphoblastic leukemia/lymphoma; hairy cell leukemia; chromic myelogenous leukemia, multiple myeloma; AIDS-associated leukemias and adult T-cell leukemia lymphoma; intraepithelial neoplasms including Bowen's disease and Paget's disease; liver cancer; lung cancer; lymphomas including Hodgkin's disease and lymphocytic lymphomas; mesothelioma, neuroblastomas; oral cancer including squamous cell carcinoma; ovarian cancer including those arising from epithelial cells, stromal cells, germ cells and mesenchymal cells; pancreatic cancer; prostate cancer; rectal cancer; sarcomas including leiomyosarcoma, rhabdomyosarcoma, liposarcoma, fibrosarcoma, and osteosarcoma; skin cancer including melanoma, Merkel cell carcinoma, Kaposi's sarcoma, basal cell carcinoma, and squamous cell cancer; testicular cancer including germinal tumors such as seminoma, non-seminoma (teratomas, choriocarcinomas), stromal tumors, and germ cell tumors; thyroid cancer including thyroid adenocarcinoma and medullar carcinoma; and renal cancer including adenocarcinoma and Wilms tumor. Non-limiting examples of precancerous conditions include dysplasia, premalignant lesions, adenomatous colon polyp, and carcinoma in-situ such as Ductal carcinoma in-situ (DCIS), etc. Other cancers that can be treated with methods of the invention will be known to those of ordinary skill in the art. In some embodiments of the invention, the cancer is melanoma. In certain embodiments the cancer is adenocarcinoma. In some embodiments the cancer is a solid tumor cancer.

Administration

Compositions of the invention may be administered in effective amounts. An effective amount is a dosage of the composition of the invention sufficient to provide a medically desirable result. An effective amount means that amount necessary to delay the onset of, inhibit the progression of or halt altogether the onset or progression of the particular condition (e.g., cancer) being treated. An effective amount may be an amount that reduces one or more signs or symptoms of the condition (e.g., cancer). When administered to a subject, effective amounts will depend, of course, on the particular condition being treated (e.g., the cancer), the severity of the condition, individual subject parameters including age, physical condition, size and weight, concurrent treatment, frequency of treatment, and the mode of administration. These factors are well known to those of ordinary skill in the art and can be addressed with no more than routine experimentation.

Actual dosage levels of active ingredients in the compositions of the invention can be varied to obtain an amount of the composition of the invention that is effective to achieve the desired therapeutic response for a particular subject, compositions, and mode of administration. The selected dosage level depends upon the activity of the particular composition, the route of administration, the severity of the condition being treated, the condition, and prior medical history of the subject being treated. However, it is within the skill of the art to start doses of the composition at levels lower than required to achieve the desired therapeutic effort and to gradually increase the dosage until the desired effect is achieved. In some embodiments, lower dosages would be required for combinations of multiple compositions than for single compositions.

It should be appreciated that an optimized dosage may be based, at least in part, on the residual non-specific toxicity of the activity element in a chimeric activator, the concentration of target molecules on the target cells, the binding affinity of the targeting element of the chimeric activator for the target molecules, and the length and flexibility of the linker. The amount of compound added should be sufficient to obtain a concentration of chimeric activator on the target cells that is sufficient to promote the desired response in the target cells. However, the amount should not be higher than necessary to avoid exposing non-target cells with levels of variant activity element that would be sufficient to activate the non-target cells. It should be appreciated that the optimal amount may be different for different chimeric activators (e.g., with different relative binding of targeting and activity elements, etc.).

The compositions of the invention, can be administered to a subject by any suitable route. For example, the compositions can be administered orally, including sublingually, rectally, parenterally, intracisternally, intravaginally, intraperitoneally, topically and transdermally (as by powders, ointments, or drops), bucally, or nasally. The term “parenteral” administration as used herein refers to modes of administration other than through the gastrointestinal tract, which include intravenous, intramuscular, intraperitoneal, intrasternal, intramammary, intraocular, retrobulbar, intrapulmonary, intrathecal, subcutaneous and intraarticular injection and infusion. Surgical implantation also is contemplated, including, for example, embedding a composition of the invention in the body such as, for example, in the brain, in the abdominal cavity, under the splenic capsule, or in the cornea.

Dosage forms for topical administration of a composition of this invention include powders, sprays, ointments, and inhalants as described herein. The composition is mixed under sterile conditions with a pharmaceutically acceptable carrier and any needed preservatives, buffers, or propellants that may be required.

Pharmaceutical compositions of the invention for parenteral injection comprise pharmaceutically acceptable sterile aqueous or nonaqueous solutions, dispersions, suspensions, or emulsions, as well as sterile powders for reconstitution into sterile injectable solutions or dispersions just prior to use. Examples of suitable aqueous and nonaqueous carriers, diluents, solvents, or vehicles include water, ethanol, polyols (such as glycerol, propylene glycol, polyethylene glycol, and the like), and suitable mixtures thereof, vegetable oils (such as olive oil), and injectable organic esters such as ethyl oleate. Proper fluidity can be maintained, for example, by the use of coating materials such as lecithin, by the maintenance of the required particle size in the case of dispersions, and by the use of surfactants.

These compositions also can contain adjuvants such as preservatives, wetting agents, emulsifying agents, and dispersing agents. Prevention of the action of microorganisms can be ensured by the inclusion of various antibacterial and antifungal agents, for example, paraben, chlorobutanol, phenol sorbic acid, and the like. It also may be desirable to include isotonic agents such as sugars, sodium chloride, and the like. Prolonged absorption of the injectable pharmaceutical form can be brought about by the inclusion of agents that delay absorption, such as aluminum monostearate or gelatin.

In some cases, in order to prolong the effect of the composition, it is desirable to slow the absorption of the composition from subcutaneous or intramuscular injection. This result can be accomplished by the use of a liquid suspension of crystalline or amorphous materials with poor water solubility. The rate of absorption of the composition then depends upon its rate of dissolution, which, in turn, may depend upon crystal size and crystalline form. Alternatively, delayed absorption of a parenterally administered composition from is accomplished by dissolving or suspending the composition in an oil vehicle.

Injectable depot forms are made by forming microencapsule matrices of the composition in biodegradable polymers such a polylactide-polyglycolide. Depending upon the ratio of composition to polymer, and the nature of the particular polymer employed, the rate of composition release can be controlled. Examples of other biodegradable polymers include poly(orthoesters) and poly(anhydrides). Depot injectable formulations also are prepared by entrapping the drug in liposomes or microemulsions that are compatible with body tissue.

The injectable formulations can be sterilized, for example, by filtration through a bacterial- or viral-retaining filter, or by incorporating sterilizing agents in the form of sterile solid compositions, which can be dissolved or dispersed in sterile water or other sterile injectable medium just prior to use.

The invention provides methods for oral administration of a pharmaceutical composition of the invention. Oral solid dosage forms are described generally in Remington's Pharmaceutical Sciences, 18th Ed., 1990 (Mack Publishing Co. Easton Pa. 18042) at Chapter 89. Solid dosage forms for oral administration include capsules, tablets, pills, powders, troches or lozenges, cachets, pellets, and granules. Also, liposomal or proteinoid encapsulation can be used to formulate the present compositions (as, for example, proteinoid microspheres reported in U.S. Pat. No. 4,925,673). As is known in the art, liposomes generally are derived from phospholipids or other lipid substances. Liposomes are formed by mono- or multi-lamellar hydrated liquid crystals that are dispersed in an aqueous medium. Any nontoxic, physiologically acceptable, and metabolizable lipid capable of forming liposomes can be used. The present compositions in liposome form can contain, in addition to a compound of the present invention, stabilizers, preservatives, excipients, and the like. The preferred lipids are the phospholipids and the phosphatidyl cholines (lecithins), both natural and synthetic. Methods to form liposomes are known in the art. See, for example, Prescott, Ed., Methods in Cell Biology, Volume XIV, Academic Press, New York, N.Y. (1976), p 33, et seq. Liposomal encapsulation may include liposomes that are derivatized with various polymers (e.g., U.S. Pat. No. 5,013,556). In general, the formulation includes a composition of the invention and inert ingredients which protect against degradation in the stomach and which permit release of the biologically active material in the intestine.

In such solid dosage forms, the composition is mixed with, or chemically modified to include, a least one inert, pharmaceutically acceptable excipient or carrier. The excipient or carrier preferably permits (a) inhibition of proteolysis, and (b) uptake into the blood stream from the stomach or intestine. In one embodiment, the excipient or carrier increases uptake of the composition of the invention, overall stability of the composition, and/or circulation time of the composition in the body. Excipients and carriers include, for example, sodium citrate, or dicalcium phosphate, and/or (a) fillers or extenders such as starches, lactose, sucrose, glucose, cellulose, modified dextrans, mannitol, and silicic acid, as well as inorganic salts such as calcium triphosphate, magnesium carbonate and sodium chloride, and commercially available diluents such as FAST-FLO®, EMIDEX®, STA-RX 1500®, EMCOMPRESS® and AVICEL®, (b) binders such as, for example, methylcellulose ethylcellulose, hydroxypropyhnethyl cellulose, carboxymethylcellulose, gums (e.g., alginates, acacia), gelatin, polyvinylpyrrolidone, and sucrose, (c) humectants, such as glycerol, (d) disintegrating agents, such as agar-agar, calcium carbonate, potato or tapioca starch, alginic acid, certain silicates, sodium carbonate, starch including the commercial disintegrant based on starch, EXPLOTAB®, sodium starch glycolate, AMBERLITE®, sodium carboxymethylcellulose, ultramylopectin, gelatin, orange peel, carboxymethyl cellulose, natural sponge, bentonite, insoluble cationic exchange resins, and powdered gums such as agar, karaya or tragacanth; (e) solution retarding agents such a paraffin, (f) absorption accelerators, such as quaternary ammonium compounds and fatty acids including oleic acid, linoleic acid, and linolenic acid (g) wetting agents, such as, for example, cetyl alcohol and glycerol monosterate, anionic detergent surfactants including sodium lauryl sulfate, dioctyl sodium sulfosuccinate, and dioctyl sodium sulfonate, cationic detergents, such as benzalkonium chloride or benzethonium chloride, nonionic detergents including lauromacrogol 400, polyoxyl 40 stearate, polyoxyethylene hydrogenated castor oil 10, 50 and 60, glycerol monostearate, polysorbate 40, 60, 65, and 80, sucrose fatty acid ester, methyl cellulose and carboxymethyl cellulose; (h) absorbents, such as kaolin and bentonite clay, (i) lubricants, such as talc, calcium sterate, magnesium stearate, solid polyethylene glycols, sodium lauryl sulfate, polytetrafluoroethylene (PTFE), liquid paraffin, vegetable oils, waxes, CARBOWAX® 4000, CARBOWAX® 6000, magnesium lauryl sulfate, and mixtures thereof; (j) glidants that improve the flow properties of the drug during formulation and aid rearrangement during compression that include starch, talc, pyrogenic silica, and hydrated silicoaluminate. In the case of capsules, tablets, and pills, the dosage form also can comprise buffering agents.

Solid compositions of a similar type also can be employed as fillers in soft and hard-filled gelatin capsules, using such excipients as lactose or milk sugar, as well as high molecular weight polyethylene glycols and the like.

The solid dosage forms of tablets, dragees, capsules, pills, and granules can be prepared with coatings and shells, such as enteric coatings and other coatings well known in the pharmaceutical formulating art. They optionally can contain opacifying agents and also can be of a composition that they release the active ingredients(s) only, or preferentially, in a part of the intestinal tract, optionally, in a delayed manner. Exemplary materials include polymers having pH sensitive solubility, such as the materials available as EUDRAGIT® Examples of embedding compositions that can be used include polymeric substances and waxes.

The composition of the invention also can be in microencapsulated form, if appropriate, with one or more of the above-mentioned excipients.

Liquid dosage forms for oral administration include pharmaceutically acceptable emulsions, solutions, suspensions, syrups, and elixirs. In addition to the composition of the invention, the liquid dosage forms can contain inert diluents commonly used in the art, such as, for example, water or other solvents, solubilizing agents and emulsifiers, such as ethyl alcohol, isopropyl alcohol ethyl carbonate ethyl acetate, benzyl alcohol, benzyl benzoate, propylene glycol, 1,3-butylene glycol, dimethyl formamide, oils (in particular, cottonseed, groundnut, corn, germ, olive, castor, and sesame oils), glycerol, tetrahydroflirfuryl alcohol, polyethylene glycols, fatty acid esters of sorbitan, and mixtures thereof.

Besides inert diluents, the oral compositions also can include adjuvants, such as wetting agents, emulsifying and suspending agents, sweetening, coloring, flavoring, and perfuming agents. Oral compositions can be formulated and further contain an edible product, such as a beverage.

Suspensions, in addition to the composition of the invention, can contain suspending agents such as, for example ethoxylated isostearyl alcohols, polyoxyethylene sorbitol and sorbitan esters, microcrystalline cellulose, aluminum metahydroxide, bentonite, agar-agar, tragacanth, and mixtures thereof.

Also contemplated herein is pulmonary delivery of the composition of the invention. The composition is delivered to the lungs of a mammal while inhaling, thereby promoting the traversal of the lung epithelial lining to the blood stream. See, Adjei et al., Pharmaceutical Research 7:565-569 (1990); Adjei et al., International Journal of Pharmaceutics 63:135-144 (1990) (leuprolide acetate); Braquet et al., Journal of Cardiovascular Pharmacology 13 (suppl.5): s. 143-146 (1989)(endothelin-1); Hubbard et al., Annals of Internal Medicine 3:206-212 (1989)(α1-antitrypsin); Smith et al., J. Clin. Invest. 84:1145-1146 (1989) (α1-proteinase); Oswein et al., “Aerosolization of Proteins,” Proceedings of Symposium on Respiratory Drug Delivery II, Keystone, Colo., March, 1990 (recombinant human growth hormone); Debs et al., The Journal of Immunology 140:3482-3488 (1988) (interferon-γ and tumor necrosis factor α) and Platz et al., U.S. Pat. No. 5,284,656 (granulocyte colony stimulating factor).

Contemplated for use in the practice of this invention are a wide range of mechanical devices designed for pulmonary delivery of therapeutic products, including, but not limited to, nebulizers, metered dose inhalers, and powder inhalers, all of which are familiar to those skilled in the art.

Some specific examples of commercially available devices suitable for the practice of the invention are the ULTRAVENT® nebulizer, manufactured by Mallinckrodt, Inc., St. Louis, Mo.; the ACORN II® nebulizer, manufactured by Marquest Medical Products, Englewood, Colo.; the VENTOL® metered dose inhaler, manufactured by Glaxo Inc., Research Triangle Park, N.C.; and the SPINHALER® powder inhaler, manufactured by Fisons Corp., Bedford, Mass.

All such devices require the use of formulations suitable for the dispensing of a composition of the invention. Typically, each formulation is specific to the type of device employed and can involve the use of an appropriate propellant material, in addition to diluents, adjuvants, and/or carriers useful in therapy.

The composition may be prepared in particulate form, preferably with an average particle size of less than 10 μm, and most preferably 0.5 to 5 μm, for most effective delivery to the distal lung.

Carriers include carbohydrates such as trehalose, mannitol, xylitol, sucrose, lactose, and sorbitol. Other ingredients for use in formulations may include lipids, such as DPPC, DOPE, DSPC and DOPC, natural or synthetic surfactants, polyethylene glycol (even apart from its use in derivatizing the inhibitor itself), dextrans, such as cyclodextran, bile salts, and other related enhancers, cellulose and cellulose derivatives, and amino acids.

In addition, the use of liposomes, microcapsules or microspheres, inclusion complexes, or other types of carriers is contemplated.

Formulations suitable for use with a nebulizer, either jet or ultrasonic, typically comprise a composition of the invention dissolved in water at a concentration of about 0.1 to 25 mg of biologically active protein per mL of solution. The formulation also can include a buffer and a simple sugar (e.g., for protein stabilization and regulation of osmotic pressure). The nebulizer formulation also can contain a surfactant to reduce or prevent surface-induced aggregation of the inhibitor composition caused by atomization of the solution in forming the aerosol.

Formulations for use with a metered-dose inhaler device generally comprise a finely divided powder containing the composition of the invention suspended in a propellant with the aid of a surfactant. The propellant can be any conventional material employed for this purpose, such as a chlorofluorocarbon, a hydrochlorofluorocarbon, a hydrofluorocarbon, or a hydrocarbon, including trichlorofluoromethane, dichlorodifluoromethane, dichlorotetrafluoroethanol, and 1,1,1,2-tetrafluoroethane, or combinations thereof. Suitable surfactants include sorbitan trioleate and soya lecithin. Oleic acid also can be useful as a surfactant.

Formulations for dispensing from a powder inhaler device comprise a finely divided dry powder containing the composition of the invention and also can include a bulking agent, such as lactose, sorbitol, sucrose, mannitol, trehalose, or xylitol, in amounts that facilitate dispersal of the powder from the device, e.g., 50 to 90% by weight of the formulation.

Nasal delivery of the composition of the invention also is contemplated. Nasal delivery allows the passage of the composition to the blood stream directly after administering the therapeutic product to the nose, without the necessity for deposition of the product in the lung. Formulations for nasal delivery include those with dextran or cyclodextran. Delivery via transport across other mucous membranes also is contemplated.

Compositions for rectal or vaginal administration are preferably suppositories that can be prepared by mixing the composition of the invention with suitable nonirritating excipients or carriers, such as cocoa butter, polyethylene glycol, or suppository wax, which are solid at room temperature, but liquid at body temperature, and therefore melt in the rectum or vaginal cavity and release the active compound.

The following examples are intended to be illustrative of certain embodiments and are non-limiting. Any of the linkers, activity elements, targeting elements or other components described herein may be combined independently with each other according to the teachings herein.

EXAMPLES Example 1: An IFNα EGF Chimeric Activator

In some embodiments, a Chimeric Activator protein was constructed with the following protein components: a mutated version of interferon alpha (IFNα) as the Activating Element, a linker, and epidermal growth factor (EGF) as the targeting element. An embodiment of this chimeric protein is illustrated in FIG. 3. In FIG. 3, the IFNα activity element is shown in region (1), the (Gly₄Ser)₇linker is shown in region (2), and the EGF targeting element is shown in region (3). In FIG. 3, the Chimeric Activator is bound to both IFNαR2 (shown as region (4)) and an active EGFR dimer (shown as region (5)). The figure shows only the extracellular domains of the receptors. The membrane-spanning domains would be at the bottom of the figure.

These elements were chosen based on the following considerations. The published structure of EGF receptor with a ligand (Garrett et al. (2002) Cell 110: 763-773) and a model of the IFNα structure (Quadt-Akabayov et al. (2006) Protein Sci. 15: 2656-2668) indicated that, in these receptor-ligand complexes, the EGF is about 90 Angstroms from the cell surface, and the IFNα is about 75 Angstroms from the cell surface, so that a linker of at least 15 Angstroms could bridge the two elements. A standard glycine-serine linker of 35 ([Gly₄Ser₁]₇) amino acids (Huston and Oppermann, 1993) was chosen. The structures also were useful for choosing whether to use the N-terminus or C-terminus of EGF and IFNα, and to design a linker of the right length. In addition, Piehler et al. (2000) J Biol Chem. 275: 40425-40433 published a precise characterization of the on-rates, off-rates, and K_Ds of a series of IFNα alanine-scanning mutants, so that a series of IFNα mutants with step-wise losses in binding affinity could be chosen (see Table 1 below). The on-rates and binding constants of EGF and IFNα are similar. The on-rates of both proteins are faster than diffusion-limited, because they are driven by charge-complementarity between these ligands and their receptors. It also was known that both EGF and IFNα could be expressed in Pichia pastori to give active proteins. Finally, IFNα and its PEGylated derivatives are used as drugs in the treatment of hepatitis B, hepatitis C, and certain forms of cancer. Side effects of IFNα treatment include flu-like symptoms, depression, and myelosuppression, which limit the dose and limit the therapeutic index. An engineered form of IFNα with reduced side effects may have the potential to replace IFNα for many diseases, and open up new treatments. A review of the literature on IFNα and cancer suggests that this protein ‘almost works’ for treatment of breast cancer, but is only somewhat too toxic to use—in other words, an improvement in therapeutic index of as little as 2- to 5-fold could dramatically extend the use of an IFNα-based compound to other types of cancer beyond melanoma and a few others. In contrast, other cell-killing elements such as Pseudomonas exotoxin are extremely toxic and might need an improvement in therapeutic index of >100-fold to become useful.

Although the considerations described in the preceding paragraph are helpful, it should be appreciated that compositions of the invention can be performed in the absence of such information as described herein.

Table 1 shows the binding characteristics of EGF and IFNα, and compares them with an anti-EGFR antibody that has been used in targeting studies.

TABLE 1 On-rates, off-rates, and dissociation constants of EGF, wild-type and mutant IFNα, and an anti- EGFR antibody. Based on these numbers, the binding of an IFNα-EGF Chimeric Activator should be driven by EGF. Note that the anti-EGFR antibody MR1-1 has an on-rate that is much lower than EGF or IFNα. K_on K_off K_d Reference EGF 2.5 × 10⁶/M/sec Bellot et al. (1990) J Cell Biol. 110: 491-502 IFNa (wild-type) 3.7 × 10⁶/M/sec 1 × 10⁻²/sec 3 × 10⁻⁹M Piehler et al. (2000) J Biol Chem. 275: 40425-40433 IFNa (K133A) 0.7 × 10⁶/M/sec 1.8 × 10⁻²/sec 26 × 10⁻⁹M Piehler et al. (2000) J Biol Chem. 275: 40425-40433 IFNa (R144A) 0.36 × 10⁶/M/sec 4 × 10⁻²/sec 120 × 10⁻⁹M Piehler et al. (2000) J Biol Chem. 275: 40425-40433 IFNa (R149A) Too low to measure 538 × 10⁻⁹M Piehler et al. (2000) J Biol Chem. 275: 40425-40433 Anti-EGFRvIII (MR1-1) 0.8 × 10⁶ 1.2 × 10⁻³/sec 1.5 × 10⁻⁹ Kuan et al. (2000) Int J Cancer. 88: 962-969

Based on these quantitative and structural considerations, four chimeric activators were constructed:

1. IFNα (wild-type)-(Gly₄Ser)₇-EGF;

2. IFNα (Lys133Ala)-(Gly₄Ser)₇-EGF;

3. IFNα (Arg144Ala)-(Gly₄Ser)₇-EGF;

4. IFNα (Arg149Ala)-(Gly₄Ser)₇-EGF.

These proteins were expressed as well as EGF alone and the corresponding individual IFNα mutants in the yeast Pichia pastoris. All of the proteins were epitope-tagged. The proteins were expressed at high levels. All of the Chimeric Activators showed EGF activity, based on their ability to stimulate phosphorylation of EGF receptor (data not shown).

The chimeric activators and the corresponding IFNα mutant proteins were compared for their ability to activate the IFNα receptor in HeLa cells, which naturally express EGFR and IFNαR. To measure IFNα signaling, STAT1 phosphorylation was detected by Western blotting; STAT1 tyrosine 701 is directly phosphorylated upon activation of IFNα receptor. The results shown in FIG. 4 indicate that an IFNα-EGF chimeric protein (without a mutation) and IFNα alone induce IFN signaling with about equal efficiency. The IFNα mutant proteins K133A, R144A, and R149A, which respectively are reduced by 10×, 40×, and 200× for IFNαR binding, show corresponding low levels of IFNα signaling. However, the Chimeric Activators with IFNα mutations fused to EGF show much higher levels of IFNα signaling than the corresponding IFNα mutants alone. In FIG. 4, chimeric activators (diamonds attached to octagons) and the corresponding IFNα protein without EGF (octagons) were added to cultures of HeLa cells at 0.3 nM, 0.8 nM, and 1.5 nM for 5 minutes. Cells were lysed, samples run on an SDS gel, blotted to nitrocellulose, and probed with an anti-phosphoSTAT1 antibody, which reflects IFNα signaling. Mutant IFNα proteins showed reduced signaling in a manner correlated with their reduced binding to IFNα receptor, while the IFNα-EGF mutant chimeric proteins showed much higher levels of signaling through STAT1. All lanes were loaded with an essentially equal amount of total cell protein.

To verify that the enhancement of IFNα signaling depended on binding to EGF receptor, a Daudi cell line was constructed to express EGFR and compared to the parent cell line for signaling induced by the chimeric activators. Daudi cells are a human Burkitt's lymphoma cell line whose proliferation and survival are inhibited by IFNα, but does not express EGFR. The results in FIG. 5 illustrate the experiments with the EGFR-expressing Daudi cell line. Cells were transfected with a plasmid that constitutively expresses EGFR. Parental cells, cells transfected with an empty plasmid vector, and EGFR-transfected cells were treated with EGF, and then phosphorylation of EGFR was detected by Western blotting. By comparing the activity of chimeric activators on cells with and without EGFR, the targeting effect can be demonstrated

When the chimeric activators were tested on Daudi and Daudi-EGFR cells (see FIG. 6), the results clearly indicated that their function depended on the presence of the receptor for the targeting element, in this case EGF receptor. Daudi cells engineered to express EGFR (FIG. 5) and parental Daudi cells were treated with Chimeric Activators and mutant IFNα proteins, and STAT1 phosphorylation was measured by Western blot. The IFNα(R149A)-EGF protein specifically induced signal transduction in cells expressing EGFR. The EGFR-expressing cells correspond to therapeutic target cells, while the cells lacking EGFR correspond to ‘side-effect’ cells. On cells with only IFNα receptor, activation with the mutant IFNα Chimeric Activator protein was poor or undetectable. Specifically, the IFNα(R149A)-EGF protein stimulated STAT1 phosphorylation only in Daudi-EGFR cells, while the IFNα-EGF protein and IFNα alone were active in both cell lines and the IFNα mutant did not work in either cell line. Chimeric activators with the intermediate-strength mutations K133A and R144A showed intermediate reductions in signaling in Daudi cells, consistent with their predicted quantitative properties (data not shown).

Accordingly, this experiment was useful to compare cells with and without EGFR, the Daudi-EGFR cells correspond to tumor cells expressing EGFR or another target receptor, and the parental Daudi cells are analogous to “side-effect cells”—other cells in the body with little or no target receptor. It was estimated that the addition of the EGF targeting element enhances the specificity of IFNα signaling by at least 20-fold in this system.

As a final control, it was tested whether the signaling by IFNα(mutant)-EGFR chimeric activators could be inhibited by an antibody against the receptor for the targeting element. The data illustrated below indicates that this is the case. Pre-binding of an anti-EGFR antibody (monoclonal 528 (Calbiochem, La Jolla, Calif.)) blocks the signaling of the IFNα(R149A)-EGF chimeric activator in HeLa cells. This is illustrated in FIG. 7. HeLa cells were treated with either IFNα, IFNα(R149A)-EGF, or IFNα(R149A), and STAT1 signaling was measured by Western blot. The IFNα(R149A)-EGF protein was not able to induce interferon-mediated signal transduction when EGFR was blocked with a neutralizing anti-EGFR antibody

Example 2: Chimeric Activator in an Animal Tumor Model

Chimeric Activators of Example 1 can be tested/screened for activity in animal tumor models. Pharmaceutical Product Development, Inc. (New York, N.Y.) can be used as a contract testing service to perform these tests. This type of experiment is standard in the development of anti-cancer drugs, and involves injection of human tumor cells into mice that have immune-suppressing mutations so that the tumor cells will not be rejected. In one form of the experiment, tumor cells are injected subcutaneously and then grow into a lump that can be measured with calipers. Once a tumor has reached a measurable size, treatment is started and the extent of tumor growth inhibition or shrinkage can be charted with time.

Using IFNα(R149A)-EGF as the test molecule, experiments can be performed in parallel sets of animals used paired tumor cell lines, one of which expresses the receptor for the targeting element, and one of which does not. The Daudi and Daudi-EGFR cells described above in Example 1 may be used. The host animal can be Nude mice, which are immunodeficient and therefore do not reject the tumor cells as foreign; use of Nude mice also means that the mice will not generate antibodies against the injected proteins.

PPD, Inc. offers testing for the Daudi models. They can also pre-test the engineered cell lines to verify that Daudi-EGFR cells can be used to generate tumors. PPD, Inc. can also perform mycoplasma testing on the tumor cell lines before they are used.

The treatment groups can be:

- a. A chemotherapeutic agent as a positive control, such as cyclophosphamide for Daudi cells.
- b. As a negative control, the appropriate IFNα mutant without the targeting element. About 10 micrograms of protein per dose will be given.
- c. A low-dose treatment group with a Chimeric Activator with the molar equivalent of 2 micrograms of IFNα.
- d. A high-dose treatment group with a Chimeric Activator with the molar equivalent of 10 micrograms of IFNα.

In some experiments, 8 to 10 mice may be used per group, for a total of about 80 mice for four dose groups in mice with the two different cell lines.

The amount of protein needed for these experiments may be less than 2 mgs for the entire experiment. The productivity of these Pichia pastoris lines is such that the culture supernatant contains about 1 mg/ml of the desired chimeric protein, and only small amounts of other proteins. The proteins, which contain a histidine tag, will be purified using a nickel column by standard techniques.

The protein can be administered by injection directly into subcutaneous tumors three times a week for three weeks. Tumor growth/shrinkage can be measured over a period of about a month. It can be tested whether appropriate signal transduction is activated in the tumor cells in vivo. Tumor biopsies can be frozen in liquid nitrogen, stored, and transferred back for Western blot analysis. The methods of Starostik et al. ((1998) Cancer Res. 58: 4552-4557) and Menon et al. ((2003) Am J Physiol Heart Circ Physiol. 284: H317-329) can be used to analyze the tissue for STAT1 phosphorylation.

Example 3: Tumor Necrosis Factor α (TNFα) as an Activity Element

To demonstrate the breadth of the Chimeric Activator concept, each element (activity element, a linker, and a targeting element) of the constructs of Example 1 can be replaced with an alternative component that is structurally different and/or has a different biological function. This is illustrated in this example and those that follow. These experiments may provide a molecule for testing in animals.

To demonstrate that IFNα can be replaced by other activators of signal transduction, a series of proteins with wild-type and mutant versions of Tumor Necrosis Factor (TNFα) can be constructed. Specifically, the following series of mutations defined by Zhang et al. ((1992) J Biol Chem. 267: 24069-24075) can be used:

Mutation Relative activity Wild-type 100% N39Y 30% S147Y 7% Y87H 0.6%

TNF is a trimer with a completely different structure from IFNα. The structure of the TNF/TNF receptor complex has been solved. The N-terminus and C-terminus are not part of the interface with the receptor, so they are free for linker attachment. Specifically, a chimeric protein with the TNF at the N-terminus followed by the linker and the EGF can be made. As for the IFNα-EGF chimeric proteins described in Example 1 above, a series of proteins with various mutations, as well as control wild-type and mutant TNF proteins lacking EGF, can be made. The proteins can have a histidine tag to aid in purification.

Molecular models of the TNF-linker-EGF Chimeric Activator by itself and in a complex with TNF receptor (see FIG. 8) illustrate how the TNF portion can still bind to its receptor when attached to the linker at EGF. Note that TNF has a trimeric structure, such that the chimeric protein is also a trimer in embodiments that include the trimerization domains.

TNF receptors are expressed on HeLa cells (Baglioni et al. (1985) J Biol Chem. 260: 13395-13397). TNF signaling will be measured using the same type of phosphorylation/Western blot analysis as described above for IFNα. TNF signaling by a molecule such as TNF(S147Y)-EGF may depend on the EGF-EGF receptor interaction, which can be tested by showing that TNF signaling can be inhibited by an anti-EGF antibody, and that signaling by the corresponding TNF(S147Y) mutant protein without EGF is much weaker or undetectable.

Example 4: Antibody V Regions as a Targeting Element

EGFRde(2-7) is a mutant form of the EGF receptor with a deletion in the extracellular domain that creates a novel junction. (Exons 2 through 7 are deleted, creating a novel protein joint from exon 1 and exon 8.) This mutant form of the receptor is oncogenic and is naturally found on many tumor types, glioblastoma in particular. Since EGFRde(2-7) comes about by a mutation in cancer cells, it is not present at all in normal cells and thus it is an absolutely cancer-specific surface protein. The Pastan and Bigner groups have generated and characterized an antibody that recognizes the novel peptide junction. The antibody, termed MR1-1, has been affinity-optimized and has an on-rate that is only about 4-fold lower than the on-rate of EGF (Kuan et al. (2000) Int J Cancer. 88: 962-969; see Table 1 above).

Experiments with an IFNα-MR1-1 Chimeric Activator can be performed. These may be analogous to the experiments performed above with the IFNα-EGF proteins, replacing the EGF targeting element with MR1-1 antibody V regions that recognize a tumor-specific EGFR variant, EGFRde(2-7). There are two publicly available cancer cell lines, U87MG and U87MG-EGFRde(2-7), where the second cell line was derived from the first by transfection with an expression construction for the EGFRde(2-7) mutant protein. The antibody MR1-1 only binds to the U87MG-EGFRde(2-7) line, allowing Chimeric Activators to be tested on both lines and determine whether a signaling event depends on the MR1-1 targeting element (see FIG. 9). In FIG. 9, EGFRvIII is a deleted form of EGF receptor that is only expressed on tumor cells. The deletion junction creates a novel amino acid sequence (*). MR1-1 is an antibody that recognizes this deletion junction, and does not recognize normal EGF receptor. A Chimeric Activator based on MR1-1 should be completely tumor-specific.

These paired cell lines have been extensively used and can be used in mouse tumor models. The U87MG nude mouse model is sensitive to IFNα (Iqbal Ahmed et al. (2001) Cancer Gene Ther. 8: 788-795). U87MG is derived from a human glioblastoma cell line.

Glioblastoma is one of the most difficult types of human cancer to treat, and many patients die within a year of diagnosis. Most glioblastoma tumor cells have the EGFRde(2-7) deletion, so an IFNα-MR1-1 Chimeric Activator should work in this type of patient. Because glioblastoma patients rarely respond to treatment and progress so quickly, it may be possible to detect responses to an IFNα-MR1-1 Chimeric Activator during the Phase I stage of clinical trials.

IFNα-MR1-1 Chimeric Activators can be constructed with wild-type IFNα and the same three mutants used above (K133A, R144A, and R149A). Specifically, the MR1-1 antibody V regions can be formatted as a “single-chain Fv” (scFv) to make molecules with IFNα at the N-terminus, a 35 amino acid glycine/serine linker, the heavy chain V region of MR1-1, a 15 amino acid glycine/serine linker, the light chain V region of MR1-1, and a histidine tag for purification. These chimeric proteins will be expressed in Pichia pastoris and purified as for the IFNα-EGF Chimeric Activators. Pichia is known to be a good system for expression of antibody V regions formatted as single-chain Fv molecules.

IFNα signaling can be measured using the STAT1 phosphorylation/Western blot assay described above. In order to test the impact of different linker lengths on the results, signaling can be measured using different linker lengths (e.g., the 35 amino acid glycine/serine linker can be doubled or tripled to create linkers of 70 and 105 amino acids between the IFNα and MR1-1 parts of the protein). It may also be necessary to introduce other amino acids besides glycine and serine, simply because the DNA sequences encoding the repeating peptide units may undergo genetic recombination because of the corresponding repeats in the DNA.

Example 5: A TNF-Leptin Chimeric Activator for Treatment of Obesity

Leptin is a hormone that is produced by adipocytes (fat cells) and also binds to receptors on adipocytes. At one time, leptin was thought to be a potential treatment for obesity, but further research indicated that in the vast majority of obese people, leptin is produced at high levels. In this example, leptin serves as a targeting element and its biological activity is not important to the function of the TNF-leptin Chimeric Activator.

One of the effects of TNF is to stimulate burning of lipids in adipocytes to help create fever. By targeting a mutated, less active TNF to adipocytes, fat burning and weight loss may result, as it does during illness, but without the other side effects of illness. Increased body temperature may still result from treatment with TNF-leptin, as this is a direct result of lipid oxidation in adipocytes. Leptin receptors are present on only a few other cell types in the body, such as cells in the hypothalamus that are thought to influence feeding and hunger. The action of TNF-leptin on these cells may be to inhibit feeding.

A series of TNF-leptin Chimeric Activators can be constructed using the same TNF mutations described above to bind to adipocytes (fat cells) and stimulate fat-burning for obesity treatment. Leptin would be the targeting element and a mutant form of TNF would be the activity element. The Chimeric Activators will have leptin at the C-terminus, since leptin has a disulfide bond that involves a cysteine at its very C-terminus, and a construct with the other orientation might have defective disulfide bond formation. The configuration of the leptin/leptin receptor complex is thought to be similar to the IFNα/IFNα receptor complex, and is favorable for the construction of a Chimeric Activator, as the C-terminus of TNF and the N-terminus of leptin are expected to be about the same distance away from the cell membrane.

To assay the activity of the TNF-leptin molecules, a stably transfected cell line that already expresses TNF receptor with an expression plasmid expressing a leptin receptor can be used. The activity of the TNF-leptin chimeric activators in the pair of cell lines with and without leptin receptor can be compared to demonstrate a specific requirement for the leptin receptor.

The biological activity of the TNF-leptin molecule can be tested in overweight mice. These would be normal mice that are fed a high-fat diet, which are a good representation of human obesity.

Example 6: An IFNα-CD4 Chimeric Activator for Treatment of HIV

CD4 is a surface protein on T cells that is the receptor for the HIV envelope protein, gp120. During later stages of HIV infection, the envelope protein appears on the cell surface and could be targeted by a Chimeric Activator with CD4 as a targeting element. The structures of the gp120/CD4 complex has been solved (Zhou et al. Nature 445: 732-737), and it indicates that the N-terminus of CD4 could be used as a junction for a protein fusion. The same IFNα mutations described above can be used. In some embodiments, only the N-terminal domain of CD4 is used, as depicted in the crystal structure, and IFNα-CD4 Chimeric Activators are constructed with a CD4 targeting element, targeting to the HIV envelope protein on HIV-infected cells.

To assay the activity of the IFNα-CD4 Chimeric Activator, a stably transfected Daudi cell line that already expresses IFNα receptor with an expression plasmid expressing gp120 can be used. The activity of the Chimeric Activators can be compared in the pair of cell lines with and without gp120, to demonstrate a specific requirement for the gp120.

The standard animal test system for HIV drugs is the SCID-hu mouse. In this system, an immunodeficient SCID mouse is populated with human immune cells, then infected with HIV.

Example 7

Evolution modulates the quantitative characteristics of protein interactions, and often uses combinations of weak interactions to achieve a particular specificity. How quantitative optimization might be used in the design of multidomain proteins was evaluated using a chimera containing epidermal growth factor (EGF) as a cell targeting element and interferon-alpha2a (IFNα2a) to initiate signal transduction. EGF and IFNα2a were connected via a linker that allows both ligands to bind to their receptors on a cell surface, then incorporated a series of mutations into the IFNα2a portion that progressively decrease both the on-rate and dissociation constant of the IFNα2a/IFNα receptor 2 (IFNAR2) interaction. Using this strategy, chimeric proteins were designed in which the activation of the IFNα receptor (IFNAR) in HeLa, A431 and engineered Daudi cells depends on the preysence of EGF receptor (EGFR) on the same cell. The mutant chimeric proteins also inhibit proliferation of IFNα-sensitive cells in an EGFR-dependent manner. These results provide insights into the quantitative requirements for specific binding to multi-subunit receptors, and illustrate the value of a quantitative approach in the design of synthetic-biological constructs.

Biological recognition events are often mediated by modular protein and nucleic acid segments that can be arbitrarily linked to give functional combinations. In the course of evolution, multidomain proteins have been repeatedly generated and constitute a large fraction of the proteins encoded by metazoan genomes. In the evolutionary improvement of such chimeras after a genetic rearrangement, an important but under-studied process is the quantitative optimization of the individual modules.

For many years, researchers have also constructed chimeric proteins with properties that derive from the parental modules. For example, one therapeutic approach has sought to use cell surface proteins as addresses to direct the delivery of specific molecules, such as toxins to tumor cells. In 1988, Pastan's group described a chimeric protein consisting of Pseudomonas exotoxin and IL-2, in which the IL-2 moiety directed the toxin to cells bearing IL-2 receptor (Lorberboum-Galski, H., FitzGerald, D., Chaudhary, V., Adhya, S., Pastan, I., (1998) Proc Natl Acad Sci USA 85(6), 1922-1926); they later described a Pseudomonas exotoxin-TGFα chimeric protein that binds to EGFR (Siegall, C. B., Xu, Y-H., Chaudhary, V. K., Adhya, S., Fitzgerald, D., Pastan, I., (1989) FASEB J 3(14), 2647-2652; Heimbrook, D. C., Stirdivant, S. M., Ahern, J. D., Balishin, N. L., Edwards, G. M., Defeo-Jones, D., FitzGerald, D. J., Pastan, I, Oliff. A., (1990) Proc Natl Acad Sci USA 87(12), 4697-4701; and Pai, L. H., Gallo, M. G., FitzGerald, D. J., Pastan, I., (1991) Cancer Res 51(11), 2808-2812), a hallmark of many tumors (Liu, T. F., Tatter, S. B., Willingham, M. C., Yang, M., Hu, J. J., Frankel, A. E., (2003) Mol Cancer Ther 2(8), 783-787). Similar strategies have been adapted by many groups (Kreitman, R. J., Pastan, I., (1999) Handbook of Experimental Pharmacology: Novel Therapeutics from Modern Biotechnology—Berlin, N.Y.: Springer-Verlag, p. 89-110; and Todhunter, D. A., Hall, W. A., Rustamzadeh, E., Shu, Y., Doumbia, S. O., Vallera, D. A., (2004) Protein Eng Des Sel 17(2), 157-164). A universal problem with this kind of approach is that when any targeted agent is administered to a patient, unwanted effects will occur as the drug travels through the body before reaching its target.

A strategy based on quantitative modulation of the signaling part of a targeted molecule was evaluated. Aspects of the invention build on the ideas of Adam and Delbruck (Adam, G., Delbruck, M., (1968) Reduction of dimensionality in biological diffusion processes—in: Rich A, Davidson N, editors, Structural chemistry and molecular biology, San Francisco: W. H. Freeman and Co. p. 198-215), who proposed that in biological systems, reaction rates are often enhanced by reduction of the dimension of a space in which diffusion occurs. According to aspects of the invention, but without wishing to be bound by theory, an initial rapid binding reaction to one cell surface protein could drive a second weak interaction on the same cell surface, because a cell surface is effectively two-dimensional. Accordingly, if the binding affinities of both the targeting agent and the activating ligand are tuned appropriately, a mutant chimeric protein can be developed that would show negligible activation on cells expressing just one of the relevant receptors. This strategy was tested using EGF as the targeting agent and IFNα2a as the toxin.

By combining quantitative information about protein binding kinetics and affinities with structural information about protein ligands and their cell-surface receptors, a new class of artificial proteins was developed that simultaneously bind to distinct cell surface receptors to create ligands with new cell-type specificities. In some embodiments, these proteins, termed “chimeric activators” have the following general structure: an activity element containing at least one mutation, a linker and a targeting element (FIG. 10A). The example of a general chimeric activator structure shown in FIG. 10A illustrates a ‘targeting element’ connected by a peptide linker to an ‘activity element’ with a mutation that reduces binding to the receptor for the activity element. According to aspects of the invention, this design takes advantage of multivalent interactions between ligands and cell-surfaces to ensure precise delivery of biological activities.

Experimental Procedures

Cell Lines and Culture Conditions:

Daudi, 293-T and HeLa cells were obtained from American type culture collection (Manassas, Va.). A431 cells were a gift from Thomas M. Roberts. A431, 293-T and HeLa cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS), 100 U ml⁻¹penicillin and 100 μg ml⁻¹streptomycin. Daudi cells were maintained in RPMI-1640 modified medium supplemented with 10% FBS, 100 U ml⁻¹penicillin and 100 μg ml⁻¹streptomycin. Stable Daudi-pLPCX-EGFR (Daudi-EGFR) and Daudi-pLPCX cell lines were generated by retroviral infection of Daudi cells following the protocol of Pear et al. (available at the website of the Nolan Laboratory, Stanford University). Infected Daudi cells were first selected with puromycin (1.5 μg/mL) and then cells were isolated with Dynabeads Pan mouse IgG from Invitrogen (Maryland, USA) pre-coated with anti-EGFR mAb following the manufacturer instructions. The constructs pLPCX and pLPCX-EGFR were kindly provided by Joan S. Brugge, Harvard Medical School (Reginato, M. J., Mills, K. R., Paulus, J. K., Lynch, D. K., Sgroi, D. C., Debnath, J., Muthuswamy, S. K., Brugge, J. S., (2003) Nature Cell Biol 5(8), 733-740).

Antibodies:

Anti-phospho-STAT1 (Tyr⁷⁰¹) rabbit pAb and anti-EGFR rabbit pAb were purchased from Cell Signaling Technology (Beverly, Mass.); PhosohoDetect™ anti-phospho-EGFR (Tyr¹⁰⁶⁸) rabbit pAb, anti-EGFR mouse mAb (EGFR.1), anti-EGFR mouse mAb (528) and anti-EGF rabbit pAb were purchased from Calbiochem (San Diego, Calif.); anti-actin mouse mAb was purchased from Chemicon International (Temecula, Calif.); anti-human IFNα/β R1-phycoerythrin mouse mAb was purchased from R&D systems (Minneapolis, Minn.); anti-EGFR R-Phycoerythrin-conjugated mouse mAb was purchased from BD Biosciences (San Jose, Calif.).

Gene Synthesis, Protein Expression and Purification:

The coding sequence for the ‘wild-type’ chimeric activator, INFα-2a-(Gly₄-Ser)₇-EGF, consisting of the 165 amino acids of mature INFα-2a (GI:2781226), the 35 amino acid linker and the 53 amino acids of mature EGF (GI:24987355), was synthesized by Top Gene Technologies (Quebec, Canada). This sequence was codon optimized for expression in P. pastoris. The sequence was sub-cloned (with XhoI and XbaI restriction sites) into the pPICZα A vector (Invitrogen), which includes the alcohol oxidase promoter and the α-factor leader sequence, a c-myc epitope tag and a His₆tag for purification. The final sequence of the constructs was confirmed by DNA sequencing. Approximately 20 μg of the DNA construct were linearized with Pme I prior to transformation of P. pastoris X33 (Mut⁺) and KM71H (Mut^S) cells. The electroporation method of the EasySelect™ Pichia expression kit (version H; Invitrogen) was used for transformation, and the transformants were plated on MD and MM agar plates to screen for methanol utilization (Mut) phenotype. Several Mut⁺and Mut^Sclones were put on plates with high zeocin concentrations (0.5 to 1 mg/ml) to select for clones with multiple integration events. A Mut^Sclone was selected for the protein expression. Transformants were grown and induced with methanol according to the instructions from Invitrogen. The INFα-2a-(Gly₄-Ser)₇-EGF chimeric activator was secreted into the medium and was purified with the ProBond™ purification system (for purification of polyhistidine-containing recombinant proteins, version K, Invitrogen). Purity was checked by Coomassie blue stain and by immunblotting against EGF. The final yield was approximately 1 mg per ml of cell culture.

Variants of INFα-2a-(Gly₄-Ser)₇-EGF were constructed containing the IFNα2a mutations K133A, R144A, and R149A by standard recombinant DNA techniques using the Quick-Change™ site-directed mutagenesis kit from Stratagene (CA, USA). To produce control proteins, a set of Pichia expression vectors encoding IFNα2a wild-type and mutant proteins lacking the linker and EGF but containing the C-myc and His₆tags were also constructed by analogous techniques. The correctness of the constructs was confirmed by DNA sequencing. The transformation, expression and purification of the different constructs were performed as described above.

Cell Stimulation, Protein Extraction, Immunoblotting and Immunoprecipitation:

A431 and HeLa cells were seeded in 60 mm plates, Daudi and Daudi-EGFR were seeded in 50 mL bottles. Once they reached confluence the growth medium was replaced with fresh DMEM without FBS or antibiotics for 3 h (to reduce background signal from the serum).

EGFR Stimulation:

Cells were stimulated with human recombinant EGF from E. coli (Cell Signaling Technology), the chimeric activators, and Interferon-α □ A (Calbiochem) or vehicle (as negative controls) for 5 min at 37° C. and 5% CO₂. Stimulations were terminated by washing the cells once with ice-cold phosphate-buffered saline, and cells were lysed in NP40 lysis buffer (20 mM Tris-HCl at pH 7.5, 150 mM NaCl, 1% NP-40, 25 mM NaF, 10 mM β-glycerophosphate, 250 μM Na₃VO₄supplemented with protease inhibitor cocktail tablets (Roche)). Cells were solubilized for 15 min at 4° C. in lysis buffer follow by centrifugation at 15,000 g for 15 min at 4° C., the detergent extracts (supernatant) were then subjected to immunoprecipitation. Lysates were incubated with 1 μg of anti-EGFR (EGFR.1) mouse monoclonal antibody overnight at 4° C. EGFR was immunoprecipitated with a mixture of Protein A and G-Sepharose beads (Amersham Bioscience) for 1 h. at 4° C. Beads were washed with NP-40 lysis buffer and boiled in SDS sample buffer. Proteins were resolved on 8% SDS-polyacrylamide, transferred to nitrocellulose, and detected by immunoblotting using the anti-phosphoEGFR(Tyr1068) antiserum.

STAT1 Stimulation:

As described above cells were stimulated with the chimeric activators, the IFNα-only counterparts, Interferon-α A, or EGF or vehicle (as negative controls) for 30 min at 37° C. and 5% CO₂. Stimulations were terminated by washing the cells once with ice-cold phosphate-buffered saline, and lysed in RIPA buffer (150 mM NaCl, 1% Deoxycholate, 10 mM Tris-HCL at pH 7.2, 0.1% SDS, 1.0% Triton X-100, 5 mM EDTA, 25 mM NaF, 10 mM β-glycerophosphate, 250 μM Na₃VO₄supplemented with protease inhibitor cocktail tablets (Roche)). Proteins were resolved on 10% SDS-polyacrylamide, transferred to nitrocellulose, and detected by immunoblotting with anti-phospho STAT1(pTyr701) antiserum.

Neutralization of EGF Receptor and STAT1 Stimulation:

HeLa cells were seeded as previously described. Once they reach confluence the medium was changed for fresh DMEM and cells were incubated with anti-EGFR mouse mAb 528. After 2 h treatment cells were tested for STAT1 stimulation as described above.

Anti Proliferative Assay:

The anti-proliferative activity of IFNα-2a-linker-EGF chimeras, corresponding IFNα2a proteins, and commercial IFNα A on Daudi and Daudi-EGFR cell lines was assayed as follows. Proteins that had been previously filtered thorough a 0.2 μm PDVF filter unit (Millipore, Ireland) and then quantitated were serially diluted. Twenty serial dilutions were prepared in flat-bottomed 96-well plates for each tested protein. Daudi and Daudi-EGFR cells grown in RPMI-1680 medium were added (3×10⁴cells in 100 μL) to each well and were grown for an additional 60 h. in the presence of the different proteins. The number of living cells was then determined using a cell staining kit (Cell proliferation reagent WST-1, Roche) based on the colorimetric detection of the cleavage of the tetrazolium salt WST-1 into formazan. The WST-1 reaction solution was added according to the manufacturer's recommendation for a period of 4 h, after which the absorbance at 450 nm and 650 nm (reference wavelength) was recorded in an ELISA reader (Victor V, PerkinElmer).

Quantitative Rationale for Design of Chimeric Activators:

The design of chimeric activators with a desired cell specificity requires an understanding of the on-rates, off-rates, and equilibrium constants of each of the receptor-binding elements. An important aspect of ligand-receptor interactions is that k_onis primarily limited by diffusion. The off-rate for ligand-receptor interactions is often slower than the process of receptor-mediated endocytosis, and in such cases k_offis not relevant to signaling. As a result, the binding of a chimeric protein composed of a targeting element and an activity element might not be significantly influenced by the supposed targeting element. For example, EGF and IFNα2a both have similar on-rates (Table 2) (French, A. R., Tadaki, D. K., Niyogi, S. K., Lauffenburger, D. A., (1995) J Biol Chem 270(9), 4334-4340; and Piehler, J., Roisman, L. C., Schreiber, G., (2000) J Biol Chem 275(51), 40425-40433), so that fusion of EGF to IFNα2a may have very little effect on the binding of the latter to its receptor.

TABLE 2 On-rates, off-rates, and dissociation constants of EGF, and wild-type and mutant IFNα2. K_on K_off K_d (1/M · seg) (1/sec) (M) Chimeric Activators (CA) EGF 1 × 10⁶ 2.6 × 10⁻³ 2.6 × 10⁻⁹ IFNα-2a (wild-type) 3.7 × 10⁶ 1 × 10⁻² 3 × 10⁻⁹ IFNα-2a (wild-type) - (Gly₄Ser)₇- EGF (CA-wt) IFNα-2a (K133A) 0.7 × 10⁶ 1.8 × 10⁻² 26 × 10⁻⁹ IFNα-2a (K133A) - (Gly₄Ser)₇- EGF (CA-K133A) IFNα-2a (R144A) 0.36 × 10⁶ 4 × 10⁻² 120 × 10⁻⁹ IFNα-2a (R144A) - (Gly₄Ser)₇- EGF (CA-R144A) IFNα-2a (R149A) Too low to 538 × 10⁻⁹ IFNα-2a (R149A) - (Gly₄Ser)₇- measure EGF (CA-R149A)

In some embodiments, but without wishing to be bound by theory, for a chimeric activator to have a cell specificity driven by the targeting element, one or both of the following conditions should be met: the on-rate of the activity element should be lower than that of the targeting element, or if the off rates are faster than the internalization rate, then the equilibrium constant (K_on/K_off) of the targeting element should be higher than that of the activity element. Once such a chimeric activator binds to a cell surface via the receptor for the targeting element, binding of the activity element to its receptor should in principle be driven by its high local concentration relative to its receptor (FIGS. 10C and D).

A rationally designed set of chimeric activators were constructed, consisting of wild-type and mutant forms of IFNα2a as the activating element, and EGF as the targeting element (FIG. 10A). A choice of these elements may be based on the following considerations: 1) the three-dimensional structures of the EGF/EGFR and the IFNα2a/IFNAR2 complexes have been solved or modeled (Ogiso, H., Ishitani, R., Nureki, O., Fukai, S., Yamanaka, M., Kim, J. H., Saito, K., Sakamoto, A., Inoue, M., Shirouzu, M., Yokoyama, S., (2002) Cell 110(6), 775-787; Garrett, T. P., McKern, N. M., Lou, M., Elleman, T. C., Adams, T. E., Lovrecz, G. O., Zhu, H. J., Walker, F., Frenkel, M. J., Hoyne, P. A., Jorissen, R. N., Nice, E. C., Burgess, A. W., Ward, C. W., (2002) Cell 110(6), 763-773; and Roisman, L. C., Piehler, J., Trosset, J-Y., Scheraga, H. A., Schreiber, G., (2001) Proc Natl Acad Sci USA 98(23), 13231-13236), allowing appropriate positions to be chosen for linking and to design a linker of the right length; 2) a precise characterization of the on-rates, off-rates, and K_Ds of a series of IFNα alanine-scanning mutants was previously reported (Piehler, J., Roisman, L. C., Schreiber, G., (2000) J Biol Chem 275(51), 40425-40433), so that a series of IFNα2a mutants could be chosen with step-wise reductions in on-rates and affinity (Table 2); and 3) the on-rates and binding constants of wild-type EGF and IFNα are similar, so that the effect of mutations should be significant. The on-rates of both proteins are thought to be faster than diffusion-limited, because they are driven by charge-complementarity between these ligands and their receptors (Piehler, J., Roisman, L. C., Schreiber, G., (2000) J Biol Chem 275(51), 40425-40433; and Piehler, J., Schreiber, G., (1999) J Mol Biol 289(1), 57-67). Another consideration was that the molecules described here could serve as a proof-of-concept for a protein drug, and that targeting might improve the therapeutic index of a toxic molecule only by a limited amount. Thus, the fact that IFNα already has a preferential activity against abnormal cells such as cancer cells and virus-infected cells made it an attractive candidate (Platanias, L. C., (2005) Nat Rev Immunol 5(5), 375-386).

For the chimeric activator concept to work, the targeting element and activation element must be able to bind simultaneously to their respective receptors. The published structure of EGFR with a ligand and a model of the IFNα2a structure indicate that in these receptor-ligand complexes, the EGF is about 90 Å from the cell surface, and the IFNα2a is about 50 Å from the cell surface, so that a linker of at least 40 Å is needed to bridge the two elements. A standard glycine-serine linker of 35 amino acids ([Gly₄Ser]₇was selected with a length of roughly 120 Å; FIG. 10B (Huston, J. S., Tai, M. S., McCartney, J., Keck, P., Oppermann, H., (1993) Cell Biophys 22(1-3), 189-224). Four chimeric activators were constructed (Table 2). These consist of wild-type or mutant IFNα2a at the N-terminus, followed by the 35-amino acid linker, EGF, a myc epitope tag, and a (His)₆purification tag at the C-terminus. The IFNα2a mutations used were K133A, R144A, and R149A, which allow the protein to fold correctly but cause stepwise reductions in the on-rate and equilibrium binding of IFNα2a for its receptor (Table 2) (Piehler, J., Roisman, L. C., Schreiber, G., (2000) J Biol Chem 275(51), 40425-40433). The chimeric activators carrying wild-type INFα2a and these mutant forms were termed CA-wt, CA-K133A, CA-R144A and CA-R149A, respectively. FIG. 10B shows a molecular model of an IFNα2a-EGF chimeric activator (space-filling structure), showing how the IFNα2a and EGF components can simultaneously interact with their receptors (ribbons). Models for EGF/EGFR complex (Ogiso, H., Ishitani, R., Nureki, O., Fukai, S., Yamanaka, M., Kim, J. H., Saito, K., Sakamoto, A., Inoue, M., Shirouzu, M., Yokoyama, S., (2002) Cell 110(6), 775-787; and Garrett, T. P., McKern, N. M., Lou, M., Elleman, T. C., Adams, T. E., Lovrecz, G. O., Zhu, H. J., Walker, F., Frenkel, M. J., Hoyne, P. A., Jorissen, R. N., Nice, E. C., Burgess, A. W., Ward, C. W., (2002) Cell 110(6), 763-773), and the IFNα2a/IFNAR2 complex (Roisman, L. C., Piehler, J., Trosset, J-Y., Scheraga, H. A., Schreiber, G., (2001) Proc Natl Acad Sci USA 98(23), 13231-13236; Quadt-Akabayov, S. R., Chill, J. H., Levy, R., Kessler, N., Anglister, J., (2006) Protein Sci 15(11), 2656-2668), are shown with the C-termini of the receptor extracellular domains at the bottom. In each case, these C-termini are followed by the membrane-spanning segment of the receptor.

These chimeric activators and the corresponding individual IFNα2a and IFNα2a mutants were expressed in the yeast Pichia pastoris according to published methods, and purified them from culture supernatant (Clare, J. J., Romanos, M. A., Rayment, F. B., Rowedder, J. E., Smith, M. A., Payne, M. M., Sreekrishna, K., Henwood, C. A. (1991) Gene 105(2), 205-212; and Garcia, J. N., Aguiar, J. A., Gill, M., Alvarez, A., Morales, J., Ferrero, J., Gonzalez, B., Padron, G., Menendez, A., (1995) Biotecnologia Aplicada 12, 152-155). All proteins were epitope-tagged and His₆-tagged for further detection and purification. The proteins were expressed at high levels and recovered at high purity (see Experimental Procedures).

Functionality of Parts within Chimeric Activators:

The biological activity of the targeting element, EGF, was verified in the chimeric activators by testing its ability to stimulate phosphorylation of tyrosine-1068 in EGFR. Activation of EGFR was evaluated in HeLa cells by treating them with the four chimeric proteins, a commercial recombinant EGF as a positive control, and IFNα2a tagged with c-myc and His₆as a negative control. FIG. 11 illustrates the induction of phosphorylation of the EGFR by the different chimeric proteins as well for the rEGF control (lanes 2 to 7). HeLa cells were stimulated for 5 minutes with vehicle (PBS; lane 1) EGF (lane 2), chimeric activators containing wild-type EGF linked to wild-type or mutant IFNα2a (lanes 3-7), or wild-type IFNα2a protein expressed from Pichia pastoris in the same manner as the chimeric activators (lane 8). EGF receptor immunoprecipitated from stimulated HeLa cell lysates were separated by SDS-PAGE, then immunoblotted for Tyr1068-phosphorylated EGF receptor (top) or total EGF receptor (bottom). Cells treated only with PBS (vehicle) or with tagged IFNα do not show detectable activity (lanes 1 and 8). To test the activity of the IFNα portion of the chimeric activators, the phosphorylation of STAT1 tyrosine 701 (a consequence of IFN-α receptor activation; FIG. 12) was examined by Western blot. These experiments demonstrated that the EGF and IFNα2a components of the chimeric proteins were both active and that the mutations K133A, R144A, and R149A reduced the activity of the tagged IFNα2a to a degree similar to the reductions previously reported (Piehler, J., Roisman, L. C., Schreiber, G., (2000) J Biol Chem 275(51), 40425-40433).

Activity of IFNα2a-EGF Chimeric Activators Depends on EGFR:

It was tested whether the IFNα2a-EGF chimeric proteins could signal through IFNAR in an EGFR-dependent manner by comparing their activity with the activity of the corresponding IFNα2a (mutant) protein in cells expressing both EGFR and IFNAR. Two different epithelial cell lines were used with varying levels of EGFR expression: A431 cells, which show high expression of EGFR (˜2×10⁶EGFR/cell), and HeLa cells, which show moderate expression of EGFR (2×10⁴EGFR/cell) (Masui, H., Kawamoto, T., Sato, J. D., Wolf, B., Sato, G., Mendelsohn, J., (1984) Cancer Res 44(3), 1002-1007). In FIG. 12, starved HeLa (A), A431 (B), Daudi (C), or Daudi-EGFR (D) cells were incubated for 30 minutes with PBS (vehicle), commercial IFNα A, EGF, IFNα/EGF chimeric activator proteins containing wild-type or mutant IFNα-2a (CAwt CAK133A, CAR144A, or CAR149A), or the corresponding wild-type or mutant IFNα2a proteins produced from Pichia. Lysates were prepared and immunoblots performed probing with an anti-STAT1(pTyr701) antibody, and with an anti-actin antibody as a loading control (in some examples, similar immunoblots were prepared in which lanes were scanned with a densitometer and the phospho-STAT1 signal normalized to the actin signal). HeLa, A431, and Daudi-EGFR cells express both EGFR and IFNAR, while Daudi cells express only IFNAR. Quantification by FACs analysis confirmed the expression levels of EGFR and IFNAR. The results indicated that an IFNα2a-EGF chimeric activator (without a mutation) and IFNα2a alone induced interferon signaling with about equal efficiency (FIGS. 12A and B, lanes 4-9), and that the IFNα2a mutant proteins K133A, R144A, and R149A, which respectively are reduced by 10×, 40×, and 200× for IFNAR binding (Table 1), show correspondingly low levels of IFNα signaling (FIGS. 12A and B, lanes 13-15, 19-22 and 26-29).

The chimeric activators with EGF fused to the mutant IFNα2a showed higher levels of IFNα signaling than the corresponding IFNα2a mutants alone, however. For example, in HeLa and A431 cells pSTAT1 was activated when cells were treated with CAR44A and CAR9A (FIGS. 12A and B, lanes 16-18 and 23-25) but not when the cells are treated with the corresponding IFNα2a mutants, even at higher concentrations (FIGS. 12A and B, lanes 22 and 29). No synergistic effect was seen when cells were treated with a combination EGF and any of the various IFNα2a mutants□ (data not shown).

As a second way to test whether the enhancement of IFNα signaling depends on binding to EGFR, EGFR was introduced into the Daudi cell line, which does not normally express this receptor and compared IFNα signaling in this engineered line to that seen in the parent cell line. The Daudi cell line is derived from a human Burkitt's lymphoma cell, and its proliferation and survival are inhibited by IFNα (Evinger, M., Pestka, S., (1981) Methods in Enzymology 79(Pt B), 362-368). The function of the chimeric activators on Daudi and Daudi-EGFR cells clearly depended on the presence of the receptor for the targeting element (FIGS. 12C and D). The CAR149A protein stimulated STAT1 phosphorylation only in Daudi-EGFR cells (FIG. 12D, lanes 23-25) and not in the Daudi parental cell line (FIG. 12C, lanes 26-29). The CAwt and IFNα2a proteins were active in both cell lines, as expected, whereas the IFNα2aR149A mutant showed only slight activity at high concentrations. Chimeric activators containing the intermediate-strength mutations CAK133A and CAR144A gave intermediate levels of signaling in Daudi cells, consistent with their predicted properties, and showed quantitative enhancements in signaling relative to IFNα2aK133A and IFNα2aR144A in Daudi-EGFR cells (FIG. 12D, lanes 10-22).

The activities of the chimeric activators differed on the various cell lines (FIG. 12). Without wishing to be bound by theory, these cell-type differences may be due to differences at the level of receptor expression, although the HeLa, Daudi, and A431 cell lines have different tissue origins and oncogenic mutations, so that any comparison of results between these lines can only be suggestive. Daudi cells have 10-20 times more IFNAR molecules at the cell surface than do HeLa and A431 cells, which may explain the greater level of IFNAR activation in Daudi cells, for example in response to CAR144A and IFNα2a(R144A).

As an additional control, it was tested whether signaling by IFNα2a(mutant)-EGF chimeric activators could be inhibited by an antibody against the receptor for the targeting element (FIG. 13). In FIG. 13, HeLa cells were pre-treated for 2 hours with 1 μg/mL of mAb 528, a mouse monoclonal antibody which prevents EGF from binding to EGFR (even-numbered lanes), followed by treatment for 30 minutes with vehicle (lanes 1-2), or 1.5 nM of commercial IFNα A (lanes 3-4), IFNα/EGF chimeric activator proteins containing wild-type or mutant IFNα-2a (CAwt, lanes 5-6; CAK133A, lanes 9-10; CAAR144A, lanes 13-14; or CAR149A, lanes 17-18), or the corresponding wild-type or mutant IFNα2a proteins (lanes 7-8, 11-12, 15-16, and 19-20). Pre-treatment of HeLa cells for 2 h. with the mouse monoclonal anti-EGFR antibody 528 inhibits the activation of the STAT1 signaling pathway by the K144A and R149A mutant chimeric activators (FIG. 13, lanes 13-14 and 17-18), but not the activation caused by the non-chimeric IFNα2a and mutants. Neither the wild-type IFNα2a nor the CAwt showed inhibition (FIG. 13, lanes 5-6, 9-10), as expected. The 528 antibody does not itself activate the EGF or the IFNα signal cascades. Treatment with mAb 528 appeared to have no effect on signaling induced by the CA-K133A protein. Since the IFNα element retains significant binding to the IFNAR, it is possible that this chimera was able to displace the antibody from the EGFR during the 30-minute course of the experiment.

EGFR-Dependent Inhibition of Cell Proliferation by Chimeric Activators:

The ability of the chimeric proteins to suppress the proliferation of Daudi and Daudi-EGFR cells is shown in FIG. 14. In FIG. 14, Daudi and Daudi-EGFR cells were grown for 60 hours in the presence of various concentrations of IFNα2a-EGF chimeric proteins or the corresponding IFNα2a proteins purified from Pichia. The relative number of viable cells was determined by the production of formazan, which absorbs at A460, from tetrazolium. Curves were fit to the data using a 4-parameter fit (Microcal Origin 5.0). In both cell lines, a dose-dependent growth inhibition was observed. When Daudi cells were treated with the chimeric activators and their IFNα2a counterparts, essentially no difference in their IC₅₀s was found (FIGS. 14A-C). Furthermore, the ability to inhibit proliferation diminished according to the ability to bind to IFNAR and activate STAT1.

The chimeric activators, relative to their IFNα counterparts, showed enhanced inhibition of cell proliferation and survival of Daudi-EGFR cells (FIGS. 14E and F). The chimeric activators containing the mutations K133A and R144A were about 10-fold and 100-fold more potent, respectively, than the corresponding IFNα2a mutants alone. CAR149A weakly inhibited proliferation in a pattern that could not be fit to a sigmoid curve (data not shown) and its activity relative to the corresponding IFNα2a mutant therefore could not be quantified.

The behavior of the Daudi-EGFR cells was somewhat affected by the presence of EGFR, which may contribute pro-survival signals. The IC₅₀s of wild-type and mutant IFNαs were about 5- to 6-fold higher in Daudi-EGFR (FIG. 14). The maximal extent of proliferation inhibition was also less than for cells treated with IFNα mutants alone. These results are consistent with previous observations that EGF can antagonize the antiproliferative and pro-death effects of IFNα (Caraglia, M., Abbruzzese, A., Leardi, A., Pepe, S., Budillon, A., Baldassare, G., Selleri, C., Lorenzo, S. D., Fabbrocini, A., Giuberti, G., Vitale, G., Lupoli, G., Bianco, A. R., Tagliaferri, P., (1999) Cell Death Differ 6(8), 773-780).

Accordingly, in the experiments described herein, it was evaluated whether the cell-type specificity of an extracellular signaling protein could be altered by a combination of genetic fusion followed by quantitative modulation. The results have implications for understanding the natural design of multisubunit proteins and ligand-receptor interactions, as well as for the design of artificial proteins targeted to cancer cells and other types of disease-causing cells.

In some embodiments, the goal of a particular design was to alter the cell-type specificity of IFNα so that it would only activate its receptor on cells bearing EGFR. EGF was attached to IFNα2a with a flexible linker, so that both modules could simultaneously bind to their receptors. IFNα2a also was mutated so that its ability to bind to its receptor would be significantly reduced, using a set of previously defined mutations that reduce the equilibrium binding of IFNα2a for its receptor by 10-, 40- and 200-fold (Piehler, J., Roisman, L. C., Schreiber, G., (2000) J Biol Chem 275(51), 40425-40433). The purpose was to generate a chimeric protein that would be essentially unable to bind directly to IFNARs, but would bind to EGFR with high affinity. By virtue of the high local concentration of the chimera on the cell surface, the IFNα2a module would then be able to bind to its receptor.

Several lines of evidence indicated that the resulting chimerized, mutated proteins induced IFNα signaling in an EGFR-dependent manner. First, a comparison of IFNα2a(mutant)-EGF chimeras with their unchimerized IFNα2a(mutant) counterparts in HeLa and A431 cells, which express both EGFR and IFNAR, showed that the chimeric proteins were more potent in inducing STAT1 phosphorylation, which results specifically from the activation of IFNAR (FIG. 12). As expected, the differential effect was particularly pronounced for chimeric activators carrying mutations that significantly reduce IFNα binding to its receptor. In contrast, IFNα2a-EGF (CA-wt) was essentially indistinguishable from wild-type IFNα2a; this result is expected because the binding of IFNα to its receptor is quantitatively similar to that for EGF. Second, the activities of the chimerized and unchimerized proteins were compared on Daudi cells and Daudi cells engineered to express EGFR. These results indicated that the enhanced stimulation of STAT1 phosphorylation by the EGF chimeras depended on the presence of EGFR on the cell surface. The improved selectivity of the mutant chimeric activators seen with HeLa and A431 cells was reproduced in Daudi-EGFR cells, but not in parental Daudi cells. Third, the stimulation of STAT1 phosphorylation could be inhibited by an anti-EGFR antibody.

The chimeric activator proteins described here induced a biological response in an EGFR-dependent manner. The proliferation and survival of Daudi cells is inhibited by IFNα2a. Daudi cells expressing EGFR were found to be more sensitive than parental Daudi cells to IFNα2a(mutant)-EGF chimeric activators by up to more than order of magnitude (FIG. 14). In a therapeutic context, the Daudi-EGFR cells may be considered to represent target cells, the parental Daudi cells may represent non-target cells where receptor activation results in side effects, and the differential effect corresponds to the therapeutic index of a protein drug. Thus, by reducing the binding of a given activator and attaching it to a targeting element, the therapeutic index can be improved by more than an order of magnitude.

According to aspects of the invention, the artificial localization/activation system described herein is reminiscent of interactions seen in a number of biological systems. For example, during signal transduction, kinases such as Raf and PDK1 are recruited to the inner face of the cytoplasmic membrane (McKay, M. M., Morrison, D. K., (2007) Oncogene 26(22), 3113-3121), which may enhance the rate of signal transduction as predicted by Adam and Delbruck (Adam, G., Delbruck, M., (1968) Reduction of dimensionality in biological diffusion processes—in: Rich A, Davidson N, editors, Structural chemistry and molecular biology, San Francisco: W. H. Freeman and Co. p. 198-215), by reducing the dimensionality in which substrates can diffuse. In the case of PDK1, a distinct targeting element, the PH domain, interacts with PIP₃in the membrane so that an activity element, the kinase domain itself, can act on its substrates. The binding of HIV gp120 to its target cells also occurs by a two-step process, in which cell-specific targeting occurs through CD4, followed by an activation step mediated by a chemokine receptor (Chan, D. C., Kim, P. S., (1998) Cell 93(5), 681-684; and Blair W S, Lin P-F, Meanwell N A, Wallace O B., (2000) Drug Discovery Today 5(5), 183-194). The interaction between IL-2 and its receptor can occur through an initial contact with a non-signaling receptor subunit, which is followed by a lower-affinity interaction with signaling receptors (Stauber, D. J., Debler, E. W., Horton, P. A., Smith, K. A., Wilson, I. A., (2003) Proc Natl Acad Sci USA 103(8), 2788-2793); IL-2 is somewhat analogous to CA-K133A, which has a reduced binding to IFNAR that can be augmented by an additional receptor subunit, with EGFR playing a similar role to the IL-2Rα subunit. These results suggest that such natural interactions can evolve from rather arbitrary associations of transmembrane proteins—for example, there does not need to be any pre-existing interaction between CD4 and chemokine receptors or between IL-2Rα and the other IL-2 receptors for HIV or IL-2 respectively to bind to these combinations of proteins.

Aspects of the invention take advantage, at least in part, of intellectual developments in quantitative systems biology and differ from other targeting approaches in two key respects. First, anticipating that the improvement in cell-type specificity of a chimeric activator might be modest in an initial design, an activator with well-characterized side effects was chosen: IFNα2a by itself is already an approved drug for certain diseases. Second, the chimeric molecule was designed to bind simultaneously to two receptors so that the effect of a reduction-of-function mutation in the activity element is reduced or eliminated by the high local concentration of this element in the neighborhood of its receptor after binding to the targeting receptor.

In some embodiments, aspects of the invention can use a tumor-specific antibody as a targeting element. The molecular designs reported here depended in part on structural models of both the IFNα/IFNAR2 and EGF/EGFR complexes. Use of antibody V regions in chimeric activators will become more feasible as more structures of antibody-receptor complexes are solved (Franklin, M. C., Carey, K. D., Vajdos, F. F., Leahy, D. J., de Vos, A. M., Sliwkowski, M. X., (1994) Cancer Cell 5(4), 317-328; and Cho, H-S., Mason, K., Ramyar, K. X., Stanley, A. M., Gabelli, S. B., Denney Jr, D. W., Leahy, D. J., (2003) Nature 421(6924), 756-760).

In summary, artificial signaling molecules were constructed based on quantitative principles. According to aspects of the invention, these principles may be used to design and produce chimeric molecules that are useful for therapeutic applications. In addition, further analysis of these principles may allow the further improvement of protein therapeutics and a deeper understanding of the forces that shape natural biological system design.

The abbreviations used in the description of these examples are as follows: CA, chimeric activator; EGF, epidermal growth factor; EGFR, epidermal growth factor receptor; IFNα2a, interferon-alpha2a; IFNAR, IFNα receptor; IL-2, interleukine-2; Mut⁺, methanol utilization wild-type; Mut^S, methanol utilization slow; TGFα, tumor growth factor α; STAT-1, signal transducer and activator 1.

Example 8: Antibody-TRAIL Chimeric Activators for Treatment of Cancer

TRAIL, also known as Apo2L, is a member of the TNF family of proteins, and binds to ‘death receptors’ such as DR5. TRAIL acts similarly to TNF, but it is thought that TRAIL causes only cell death without accompanying inflammation. The following sequences were designed in which TRAIL is fused to the V regions of the antibody MR1-1, which is described above.

PROTEIN SEQUENCE: ATR14: SEQ ID NO: 18: QVKLQQSGGGLVKPGASLKLSCVTSGFTFRKFGMSWVRQTSDKRLEWVAS ISTGGYNTYYSDNVKGRFTISRENAKNTLYLQMSSLKSEDTALYYCTRGY SPYSYAMDYWGQGTTVTVS (HEAVY) SEQ ID NO: 19: SSGGGSGGGGSGGGGS SEQ ID NO: 20: DIELTQSPASLSVATGEKVTIRCMTSTDIDDDMNWYQQKPGEPPKFLISE GNTLRPGVPSRFSSSGTGTDFVFTIENTLSEDVGDYYCLQSWNVPLTFGd GTKLEIK (Light) LINKER: SEQ ID NO: 21: GGGGSGGGSSGGGSSSGGGGSGGGGSSGGGSGGGS TRAIL: SEQ ID NO: 22: RERGPQRVAAHITGTRGRSNTLSSPNSKNEKALGRKINSWESSRSGHSFL SNIHLRNGELVIHEKGFYYIYSQTYFRFQEEIKENTKNDKQMVQYIYKYT SYPAPILLMKSARNSCWSKDAEYGLYSIYQGGIFELKENDRIFVSVTNEH LIDMDREASFFGAFLVG MR1-1: SEQ ID NO: 23: QVKLQQSGGGLVKPGASLKLSCVTSGFTFRKFGMSWVRQTSDKRLEWVAS ISTGGYNTYYSDNVKGRFTISRENAKNTLYLQMSSLKSEDTALYYCTRGY SPYSYAMDYWGQGTTVTVSSSGGGSGGGGSGGGGSDIELTQSPASLSVAT GEKVTIRCMTSTDIDDDMNWYQQKPGEPPKFLISEGNTLRPGVPSRFSSS GTGTDFVFTIENTLSEDVGDYYCLQSWNVPLTFGdGTKLEIKGGGGSGGG SSGGGSSSGGGGSGGGGSSGGGSGGGSRERGPQRVAAHITGTRGRSNTLS SPNSKNEKALGRKINSWESSRSGHSFLSNIHLRNGELVIEEKGFYYIYSQ TYFRFQEEIKENTKNDKQMVQYIYKYTSYPAPILLMKSARNSCWSKDAEY GLYSIYQGGIFELKENDRIFVSVTNEHLIDMDEEASFFGAFLVG DNA SEQUENCE: SEQ ID NO: 24: CAAGTTAAGTTGCAACAATCCGGTGGTGGTTTGGTTAAGCCAGGTGCTTC TTTGAAGTTGTCTTGTGTTACTTCTGGTTTTACTTTTAGAAAGTTTGGTA TGTCTTGGGTTAGACAAACTTCTGATAAGAGATTGGAATGGGTTGCTTCT ATTTCTACTGGTGGTTACAACACTTACTACTCTGATAACGTTAAGGGTAG ATTTACTATTTCCAGAGAGAACGCTAAGAACACTTTGTACTTGCAAATGT CTTCTTTGAAGTCTGAAGATACTGCTTTGTACTACTGTACTAGAGGTTAC TCTCCATACTCTTACGCTATGGATTACTGGGGTCAAGGTACTACTGTTAC TGTTTCTTCCTCCGGTGGAGGTTCCGGTGGTGGAGGATCTGGTGGTGGTG GTTCTGATATTGAGTTGACTCAATCTCCAGCTTCTTTGTCTGTTGCTACT GGTGAGAAGGTTACTATTAGATGTATGACTTCTACTGATATTGATGATGA TATGAACTGGTACCAACAAAAGCCAGGTGAACCACCAAAGTITTTGATTT CTGAAGGTAACACTTTGAGACCAGGTGTTCCATCCAGATTTTCTTCTTCT GGTACTGGTACTGATTTTGTTTTTACTATTGAGAACACTTTGTCTGAAGA TGTTGGTGATTACTACTGTTTGCAATCTTGGAACGTTCCATTGACTTTTG GTGATGGTACTAAGTTGGAGATTAAGGGAGGAGGTGGTTCCGGTGGTGGT TCTTCCGGAGGTGGTTCTTCCTCTGGAGGTGGTGGTTCAGGTGGAGGTGG TTCCTCTGGAGGTGGTTCTGGTGGAGGTTCCAGAGAAAGAGGTCCACAAA GAGTTGCTGCTCACATTACTGGTACTAGAGGTAGATCTAACACTTTGTCT TCTCCAAACTCTAAGAACGAAAAGGCTTTGGGTAGAAAGATTAACTCTTG GGAGTCTTCCAGATCTGGTCATTCTTTCTTGTCTAACTTGCATTTGAGAA ACGGTGAATTGGTTATTCATGAGAAGGGTTTCTACTACATTTACTCTCAA ACTTACTTTAGATTTCAAGAAGAAATTAAGGAGAACACTAAGAACGATAA GCAAATGGTTCAATACATTTACAAGTACACTTCTTACCCAGCTCCAATTT TGTTGATGAAGTCTGCTAGAAACTCTTGTTGGTCTAAGGATGCTGAATAC GGTTTGTACTCTATTTACCAAGGTGGTATTTTCGAATTGAAGGAGAACGA TAGAATTTTCGTTTCTGTTACTAACGAACATTTGATTGATATGGATCACG AAGCTTCTTTCTTTGGTGCTTTTTTGGTTGGT

The sequences are highlighted so that the first and third segments (regular text) are the heavy chain V region and the light chain V region respectively. The second (bolded text) is a linker, the fourth (underlined text) is a longer linker, and the fifth segment (italicized text) is TRAIL or an active fragment of TRAIL. In the case of the sequence shown, the active fragment corresponds to amino acids 115-281 and is 1.5 times more bioactive than the full-length TRAIL (Hymowitz et al. Biochemistry, Vol. 39, No. 4, p. 633 (2000)).

Three different mutant forms of TRAIL can be used, containing the mutations:

Q205A Y216A Y237A

The chimeric proteins containing normal TRAIL and the mutations X, Y, and Z were tested for their ability to induce apoptosis in the glioblastoma cells U87MG and their engineered derivative U87MG-EGFRvIII. EGFRvIII is a deleted derivative of EGFR that is found in some cancers and contains a novel peptide junction that is recognized by the antibody MR1-1.

The following results will be obtained. Plus signs indicate levels of apoptosis by viability and apoptosis signaling assays. Apoptosis assessed by viability assay will be measure by using the cell proliferation reagent WST-1. Apoptosis signaling will be measure by caspase activation using antibodies directed against caspase-8 and active caspase-3.

U87MG U87MG-EGFRvIII TRAIL (+) ++++ ++++ TRAIL (Q205A) ++ ++ TRAIL (Y216A) + + TRAIL (Y237A) − − MR1-1 - TRAIL (+) ++++ ++++ MR1-1 - TRAIL (Q205A) ++ ++++ MR1-1 - TRAIL (Y216A) + +++ MR1-1 - TRAIL (Y237A) − ++

Example 9: Use of an Anti-CEA Antibody Instead of MR1-1

Sequences of chimeric activators also were designed using the antibody V regions from a humanized version of the antibody T84.66, which is directed against carcinoembryonic antigen (CEA). Carcinoembryonic antigen is a protein that is highly expressed on colon cancers, lung cancers, breast cancers, and other types of cancer. It is expressed in only small amounts on normal tissues in the gastrointestinal tract. CEA is also highly expressed in the tumor cell lines GW39, LS147T and SW1417.

The CEA protein has seven extra cellular immunoglobulin-family domains and is attached to the cell surface by means of a lipid anchor at its C-terminus; this protein contains no intracellular amino acids. A large number of antibodies against CEA have been identified, of which T84.66 and MFE-23 are particularly well characterized. The antibody T84.66 was chosen because it binds somewhere within the two most membrane-proximal domains (Hass et al. Cancer Research [1991] 51:1876), while MFE-23 binds to a much more membrane-distal domain that might lie more than 200 angstroms from the cell surface (Boehm and Perkins, FEBS Letters [2000] 475:11). The T84.66 binding site therefore appears to be about the same height from the cell membrane as the TRAIL N- and C-termini, and also the IFNα N- and C-termini, when these ligands are bound to their receptors.

Based on these considerations, a chimeric activator was designed containing humanized T84.66 V regions and TRAIL.

PROTEIN SEQUENCE: T84.66: SEQ ID NO: 25: EVQLVESGGGLVQPGGSLRLSCAASGFNIKDTYMHWVRQAPGKGLEWVAR IDPANGNSKYVPKFQGRATISADTSKNTAYLQMNSLRAEDTAVYYCAPFG YYVSDYAMAYWGQGTLVTVSS (HEAVY) SEQ ID NO: 26: SSSGGGSGGGGSGGGGS SEQ ID NO: 27: DIQLTQSPSSLSASVGDRVTITCRAGESVDIFGVGFLHWYQQKPGKAPKL LIYRASNLESGVPSRFSGSGSRTDFTLTISSLQPEDFATYYCQQTNEDPY TF GQGTKVEIK (light) LINKER: SEQ ID NO: 28: GGGGSGGGSSGGGSSSGGGGSGGGGSSGGGSGGGS TRAIL: SEQ ID NO: 29: RERGPQRVAAHITGTRGRSNTLSSPNSKNEKALGRKINSWESSRSGHSFL SNLHLRNGELVIHEKGFYYIYSQTYFRFQEEIKENTKNDKQMVQYIYKYT SYPAPILLMKSARNSCWSKDAEYGLYSIYQGGIFELKENDRIFVSVTNEH LIDMDHEASFFGAFLVG T84.66: SEQ ID NO: 30: EVQLVESGGGLVQPGGSLRLSCAASGFNIKDTYMHWVRQAPGKGLEWVAR IDPANGNSKYVPKFQGRATISADTSKNTAYLQMNSLRAEDTAVYYCAPFG YYVSDYAMAYWGQGTLVTVSSSSSGGGSGGGGSGGGGSDIQLTQSPSSLS ASVGDRVTITCRAGESVDIFGVGFLHWYQQKPGKAPKLLIYRASNLESGV PSRFSGSGSRTDFTLTISSLQPEDFATYYCQQTNEDPYTFGQGTKVEIKG GGGSGGGSSGGGSSSGGGGSGGGGSSGGGSGGGSRERGPQRVAAHITGTR GRSNTLSSPNSKNEKALGRKINSWESSRSGHSFLSNLHLRNGELVIHEKG FYYIYSQTYFRFQEEIKENTKNDKQMVQYIYKYTSYPAPILLMKSARNSC WSKDAEYGLYSIYQGGIFELKENDRIFVSVTNEHLIDMDHEASFFGAFLV G DNA SEQUENCE: SEQ ID NO: 31: GAAGTTCAATTGGTTGAATCTGGAGGTGGTTTGGTTCAACCAGGTGGTTC TTTGAGATTGTCTTGTGCTGCTTCTGGTTTTAACATTAAGGATACTTACA TGCATTGGGTTAGACAAGCTCCAGGTAAGGGTTTGGAATGGGTTGCTAGA ATTGATCCAGCTAACGGTAACTCTAAGTACGTTCCAAAGTTTCAAGGTAG AGCTACTATTTCTGCTGATACTTCTAAGAACACTGCTTACTTGCAAATGA ACTCTTTGAGAGCTGAAGATACTGCTGTTTACTACTGTGCTCCATTTGGT TACTACGTTTCTGATTACGCTATGGCTTACTGGGGTCAAGGTACTTTGGT TACTGTTTCTTCCTCCTCTTCTGGTGGAGGTTCTGGAGGTGGTGGATCTG GTGGAGGTGGTTCTGATATTCAATTGACTCAATCTCCATCTTCTTTGTCT GCTTCTGTTGGTGATAGAGTTACTATTACTTGTAGAGCTGGTGAATCTGT TGATATTTTTGGTGTTGGTTTTTTGCATTGGTACCAACAAAAGCCAGGTA AGGCTCCAAAGTTGTTGATTTACAGAGCTTCTAACTTGGAATCTGGTGTT CCATCCAGATTTTCTGGTTCTGGTTCCAGAACTGATTTTACTTTGACTAT TTCTTCTTTGCAACCAGAAGATTTTGCTACTTACTACTGTCAACAAACTA ACGAAGATCCATACACTTTTGGTCAAGGTACTAAGGTTGAAATTAAGGGT GGAGGAGGTTCTGGTGGTGGATCTTCCGGAGGTGGTTCTTCCTCTGGAGG TGGTGGTTCAGGTGGAGGTGGTTCCTCTGGAGGTGGTTCTGGTGGAGGTT CCAGAGAAAGAGGTCCACAAAGAGTTGCTGCTCACATTACTGGTACTAGA GGTAGATCTAACACTTTGTCTTCTCCAAACTCTAAGAACGAAAAGGCTTT GGGTAGAAAGATTAACTCTTGGGAGTCTTCCAGATCTGGTCATTCTTTCT TGTCTAACTTGCATTTGAGAAACGGTGAATTGGTTATTCATGAGAAGGGT TTCTACTACATTTACTCTCAAACTTACTTTAGATTTCAAGAAGAAATTAA GGAGAACACTAAGAACGATAAGCAAATGGTTCAATACATTTACAAGTACA CTTCTTACCCAGCTCCAATTTTGTTGATGAAGTCTGCTAGAAACTCTTGT TGGTCTAAGGATGCTGAATACGGTTTGTACTCTATTTACCAAGGTGGTAT TTTCGAATTGAAGGAGAACGATAGAATTTTCGTTTCTGTTACTAACGAAC ATTTGATTGATATGGATCACGAAGCTTCTTTCTTTGGTGCTTTTTTGGTT GGT

Protein activity is measured as in the previous example but using LS147T and SW1417 cell lines.

Example 10: Antibody-Erythropoietin Chimeric Activators for Treatment of Anemia

Erythropoietin (Epo) is a hormone that stimulates production of red blood cells. Epo can be used to treat anemia that may be part of many disease conditions, but is used primarily in two settings. First, kidney failure patients usually do not produce adequate levels of Epo, which is expressed mainly in the kidneys, and are therefore anemic. Second, cancer patients often become anemic as a result of chemotherapy treatment, which kills dividing cells including red blood cell precursors.

Use of erythropoietin can also affect platelet production, possibly because receptors for Epo are also found on hematopoietic precursor cells that give rise to platelets. In addition, Epo receptors are sometimes found on cancer cells, and Epo may enhance tumor cell growth and angiogenesis. It would be useful to have a form of Epo that only stimulated red blood cell production and did not bind to Epo receptors on other cells, such as cancer cells or early hematopoietic stem cells that can give rise to other cell types.

By way of background, a person is considered to be anemic if their hemoglobin levels are less than 12 grams/deciliter for women or <14 g/dl for men. These values correspond to a hematocrit of 37% for women and 40% for men, and a red blood cell count of 4×10¹²/l for women and 4.5×10¹²for men. Usually when people are treated with Epo, the levels of red blood cells are not fully restored, since this is associated with an increased rate of heart attack and stroke.

Recent studies suggest that Epo may in fact accelerate tumor growth in human patients (reviewed by Khuri, F R [2007] New England Journal of Medicine 356:24:2445-2448; and Crawford, [2007] Journal of Clinical Oncology 25:9:1021-1023). This is disappointing, because it had been thought that increasing red blood cell counts in cancer patients would increase their quality of life, and also increase the oxygenation of tumors, making them more sensitive to radiation and other types of treatments.

In one study, patients with non-small cell lung cancer were given erythropoietin or a placebo, and the treated group was found to have decreased overall survival (Wright et al. 25:9:1027-1032). In another study, breast cancer patients received Epo or a placebo, and again the treated group had decreased survival (Leyland-Jones et al. [2005] Journal of Clinical Oncology 23:25:5960-5972). In this study, the patients in each group with higher hemoglobin levels survived longer, so it does not appear that the increase in red blood cells caused by Epo was the cause of the decreased survival. In an important pair of studies, Henke et al. studied the effect of Epo treatment on patients with head and neck cancer, and found that the treated group survived less well than the placebo group (Henke et al. [2003] Lancet 362:9392:1255-60). They then tested the tumors from these patients for expression of Epo receptors, and found that, in the Epo-treated group, patients with tumors expressing Epo receptors did not survive as long as patients whose tumors did not express Epo receptors. In the placebo group, patients did about equally well regardless of whether their tumors expressed Epo receptors (Henke et al. [2006] Journal of Clinical Oncology 24:29:4708-4713). These results strongly indicate that Epo can shorten the survival of cancer patients by bind to Epo receptors on tumor cells and enhancing the growth or survival of the tumor cells.

Glycophorin is a highly expressed protein on the surface of red blood cells. Glycophorin is also expressed on the precursors of red blood cells (Southcott et al. Blood 12:4425). During production of red blood cells, precursor hematopoietic stem cells (HSCs) undergo a series of differentiation steps as follows:

- HSCs→BFU-E→CFU-E→terminal red blood cells
  where BFU-E and CFU-E are ‘blast-forming unit’ and ‘colony-forming unit’. BFU-E cells produce about 50,000 red blood cells, while CFU-E cells produce about 1,000 red blood cells. CFU-E cells are particularly dependent on erythropoietin for survival and cell division (Adamson et al. Blood Cells [1978] 4:89). By constructing a molecule that is targeted to glycophorin-expressing cells, red blood cell production may be stimulated without affecting other cell types.

Glycophorin A exists in two allelic forms, M and N, which define the M and N blood groups. These forms differ at the N-terminus as follows (Czerwinski et al [1998] The Journal of Immunology 160: 4406-4417)

1 2 3 4 5 M: NH2 Ser Ser Thr Thr Gly . . . . (SEQ ID NO: 32) N: NH2 Leu Ser Thr Thr Glu . . . . (SEQ ID NO: 33)

Catimel B. et al. Journal of Immunological Methods [1993] 165:183 described a monoclonal antibody, 10F7MN that recognizes the N and M-type of glycophorin A. It should be noted that certain serine and threonine residues in glycophorin are 0-glycosylated, and the 10F7MN antibody actually recognized a combination of the amino acid and sugar structures. Based on the sequence of the 10F7MN V regions and human erythropoietin, a series of chimeric activators were designed with the following general structure: 10F7MN (heavy chain V region)-short linker-10F7MN (light chain V region)-long linker-erythropoietin. The specific sequence design shown below uses the original mouse-derived V regions of 10F7MN, but it is also possible to use a humanized pair of V regions. (Use of other monoclonal antibody directed against glycophorin is also possible, such as GPA105, [Wasniowska et al., Mol. Immunol. {1992} 29:6:783-91] or 5F4).

PROTEIN SEQUENCE: 10F7MN: SEQ ID NO: 34: MAQVKLQQSGAELVKPGASVKLSCKASGYTFNSYFMHWMKQRPVQGLEW IGMIRPNGGTTDYNEKFKNKATLTVDKSSNTAYMQLNSLTSGDSAVYYC ARWEGSYYALDYWGQGTTVTVSS (HEAVY) SEQ ID NO: 35: GGGGSGGGGSSGGGGSS SEQ ID NO: 36: DIELTQSPAIMSATLGEKVTMTCRASSNVKYMYWYQQKSGASPKLWIYY TSNLASGVPGRFSGSGSGTSYSLTISSVEAEDAATYYCQQFTSSPYTFG GGTKLEIKRAAA (light) Linker: SEQ ID NO: 37: GGGGSGGGSSGGGSSSGGGGSGGGGSSGGGSGGGS EPO: SEQ ID NO: 38: APPRLICDSRVLQRYLLEAKEAENITTGCAEHCSLNENITVPDTKVNF YAWKRMEVGQQAVEVWQGLALLSEAVLRGQALLVNSSQPWEPLQLHVD KAVSGLRSLTTLLRALGAQKEAISPPDAASAAPLRTITADTFRKLFRV YSNFLRGKLKLYTGEACRTGDR 10F7MN: SEQ ID NO: 39: MAQVKLQQSGAELVKPGASVKLSCKASGYTFNSYFMHWMKQRPVQGLE WIGMIRPNGGTTDYNEKFKNKATLTVDKSSNTAYMQLNSLTSGDSAVY YCARWEGSYYALDYWGQGTTVTVSSGGGGSGGGGSSGGGGSSDIELTQ SPAIMSATLGEKVTMTCRASSNVKYMYWYQQKSGASPKLWIYYTSNLA SGVPGRFSGSGSGTSYSLTISSVEAEDAATYYCQQFTSSPYTFGGGTK LEIKRAAAGGGGSGGGSSGGGSSSGGGGSGGGGSSGGGSGGGSAPPRL ICDSRVLQRYLLEAKEAENITTGCAEHCSLNENITVPDTKVNFYAWKR MEVGQQAVEVWQGLALLSEAVLRGQALLVMSSQPWEPLQLHVDKAVSG LRSLTTLLRALGAQKEAISPPDAASAAPLRTITADTFRKLFRVYSNFL RGKLKLYTGEACRTGDR DNA SEQUENCE: SEQ ID ND: 40: ATGGCTCAAGTTAAGTTGCAACAATCTGGTGCTGAATTGGTTAAGCCA GGTGCTTCTGTTAAGTTGTCTTGTAAGGCTTCTGGTTACACCTTCAAC TCTTACTTTATGCATTGGATGAAGCAAAGACCAGTTCAAGGTTTGGAA TGGATTGGTATGATTAGACCAAACGGTGGTACTACCGATTACAACGAG AAGTTTAAGAACAAGGCTACTTTGACTGTTGATAAGTCCTCTAACACT GCTTACATGCAATTGAACTCTTTGACTTCTGGTGATTCTGCTGTTTAC TACTGTGCTAGATGGGAAGGTTCTTACTACGCTTTGGATTACTGGGGT CAAGGTACCACTGTTACTGTTTCTTCCGGTGGAGGTGGATCTGGTGGT GGAGGATCTTGAGGAGGTGGTGGATCTTCCGATATTGAGTTGACTCAA TCTCCAGCTATTATGTCTGCTACCTTGGGTGAGAAGGTTACTATGACT TGTAGAGCTTCATCTAACGTTAAGTACATGTACTGGTACCAACAGAAG TCTGGTGCTTCTCCAAAGTTGTGGATTTACTACACTTCTAACTTGGCT TCTGGTGTTCCAGGTAGATTTTCTGGTTCAGGTTCTGGTACTTCCTAC TCTTTGACTATTTCCTCTGTTGAAGCTGAAGATGCTGCTACTTACTAC TGTCAACAATTCACTTCTTCCCCATACACTTTTGGAGGAGGTACTAAG TTGGAAATCAAGAGAGCTGCCGCAGGTGGAGGTGGTTCCGGAGGAGGA TCTTCCGGTGGTGGATCTTCTTCTGGAGGTGGAGGATCCGGTGGTGGA GGATCATCTGGTGGAGGATCTGGTGGTGGTTCCGCTCCACCTAGATTG ATTTGTGATTCCAGAGTTTTGGAAAGATACTTGTTGGAAGCTAAGGAG GCTGAAAAGATTACTACTGGTTGTGCTGAACATTGTTCTTTGAACGAG AAGATTACTGTTCCAGATACTAAGGTTAACTTTTACGCTTGGAAGAGA ATGGAAGTTGGTCAGCAAGCTGTTGAAGTTTGGCAAGGTTTGGCTTTG TTGTCTGAAGCTGTTTTGAGAGGTCAAGCTTTGTTGGTTAAGTCTTCT CAACCATGGGAACCATTGCAATTGCATGTTGATAAGGCTGTTTCTGGT TTGAGATCTTTGACTACCTTGTTGAGAGCTTTGGGTGCTCAAAAGGAA GCTATTTCTCCTCCAGATGCTGCTTCTGCCGCTCCATTGAGAACTATT ACTGCTGATACTTTTAGAAAGTTGTTTAGAGTTTACTCTAACTTCTTG AGAGGTAAGTTGAAGTTGTACACTGGTGAAGCTTGTAGAACTGGTGAT AGA

(The length of the long linker may need to be varied depending on which anti-glycophorin antibody is used and where the epitope is.)

This molecule will be expressed in Pichia pastoris. Because Epo is glycosylated at a number of sites and it will ultimately be useful to have a molecule with mammalian-type glycosylation, a 10F7MN-Epo chimeric activator also will be expressed in a mammalian cell line such as CHO cells.

To reduce the activity of the Epo portion, a mutation that reduces the affinity of Epo for its receptor will be introduced. Elliott et al. (Blood [1997] 89:2:493-502) described a series of mutations in erythropoietin that reduce its activity. In some embodiments, at least one or more of the following mutations may be used:

N147A N147K R150A R150E

To test the chimeric activators, a test system that uses one of the following cell lines can be constructed and used: TF-1, UT-7 or ERY-1. These are cells that respond to Epo. The cell line can be transfected with an expression construct that expresses human glycophorin, and the chimeric activators can be tested in this pair of cell lines.

EPO activity will be measured by proliferation and signaling assays. Proliferation will be assessed by using WST-1 reagent while pSTAT5 will be measured for EPO receptor activation.

The following results will be obtained:

TF-1 TF-1_Glycophorin A EPO ++++ ++++ EPO (N147A) ++ ++ EPO (R150A) − + + EPO (R150E) − + + EPO (N147K) − − 10F7MN - EPO ++++ ++++ 10F7MN - EPO (N147A) ++ ++++ 10F7MN - EPO (R150A) + +++ 10F7MN - EPO (R150E) − ++ 10F7MN - EPO (N147K) − +

For a test in an animal system, the following strategy can be used. Glycophorin is a protein that has changed rapidly in evolution, so that the epitopes recognized by existing anti-human glycophorin are not found in most other animals. Lethally irradiated mice that have been reconstituted with human hematopoietic stem cells can be used.

Example 11 1. General Model for Chimera Design

Aspects of theoretical chimera design appear to be a difficult task, and no theoretical approaches have been focused on the field. Many variables are involved, both physical and kinetic, as well as concentrations, and dynamics. In addition, the size of the receptors need to be taken into account for an optimal chimera design and maximum selectivity. Ligands may be linked by a long amino acid chain, wherein the length is a determinant of the chimera performance, and it needs to be carefully designed according to the physical and kinetic characteristics of the system.

Over the past years, theoretical efforts have been mainly focused on understanding and modeling single receptor-ligand interaction and internalization. Here a successful theoretical approach for single receptor signaling has been extended to chimeras interacting with an arbitrary number of different receptors. To test the results, the case of a simple homodimer and a heterodimer were explored, and the theoretical predictions were compared with experimental data. In addition, the theoretical prediction of the optimal length of the linker in the case of a heterodimer was compared with experimental results.

Herein a general theory for chimera design is presented, for testing mutant ligands with known affinity and for designing optimal linker length for increased selectivity. The theory is presented for chimeras designed by binding of an arbitrary number n linked by amino acid chains of different lengths.

The process of binding is assumed to occur in the following steps: the chimera binds initially to one of the receptors (receptor i) with a rate of binding k_on;iand dissociation k_off;i, internalization by endocytosis of the free receptor k_t;iand active receptor k_e;iand receptor recycling Q_r;irates equivalent to the non chimeric ligand. This first reaction of ligand-receptor i recruits chimeric proteins to the cell membrane, increasing the local concentration of ligand j in the surface of the cell, enhancing interaction of ligand j and its receptor.

The effect of the two dimensional diffusion of the receptors is neglected (if compared with other dynamical processes in the system, it can be considered instantaneous).

2. Equations for the General System

Certain equations described herein are useful to model generalized chimeric binding systems, with an additional term that accounts for the coupling between ligand concentration due to the chimera. The general equations for a set of n ligands and n receptors are as follows.

$\begin{matrix} \frac{{dR}_{i}}{dt} = - k_{i, on} R_{i} L + k_{i, off} C_{i} - k_{i, t} R_{i} + Q_{i, R} - R_{i} \sum_{j = 1, j \neq i}^{n} (k_{i, j, on}^{'} L_{i, j}) & (13) \\ \frac{{dC}_{i}}{dt} = k_{i, on} R_{i} L + k_{i, off} C_{i} - k_{i, e} C_{i} + R_{i} \sum_{j = 1, j \neq i}^{n} (k_{i, j, on}^{'} L_{i, j}) & (14) \\ \frac{d L}{dt} = \frac{1}{N_{Aυ} V} \sum_{i = 1}^{n} (k_{i, off} C_{i} - k_{i, on} R_{i} L) & (15) \end{matrix}$

where R_iand C_iare the total number of empty and bound receptor i. L is the concentration of chimera in solution. The last term of equations 13 and 14 reflects the increase in local concentration of ligand i due to the binding of the ligand j to its receptor.

Once the ligand j is bound to the receptor j, an increase in the local concentration of ligand i close to the cell membrane is created, and the ligand i can be assumed to be distributed in a volume gasket which depends on the distance between ligand i and j. This local concentration of i due to the binding of the j ligand-receptor complex can be calculated as follows.

$\begin{matrix} L_{i, j} = \frac{C_{j}^{'}}{N_{Aυ} V_{0, i, j}} = \frac{3 C_{j}^{'}}{4 π} \frac{1}{{(r + a_{i, j})}^{3} - r^{3}} & (16) \end{matrix}$

where N_Avis the Avogadro's number, r is the average cell radius and C_0jis the concentration of the C_jresult of the regular binding mechanism, i.e., the number of complexes C_jbounded to a chimera that it is not bound to another receptor, responsive of the local concentration increase.

$\begin{matrix} \frac{{dC}_{j}^{'}}{dt} = k_{j, on} R_{j} L - k_{j, off} C_{j} - k_{j, e} C_{j} & (18) \end{matrix}$

Regarding the binding mechanism between a receptor and a free ligand or a chimeric ligand, it is reasonable to assume certain scaling in the reaction rate, due to the geometrical characteristics of the problem. So, in the last term of equations 13 and 14 the reaction rate needs to be rescaled having in mind that reaction ligand-receptor-i only occurs when the ligand is in the close vicinity of the receptor. The mechanism is illustrated in FIG. 16, and the reaction only occurs in the dark volume of the semi-sphere of radius a_i;j

This way, the rescaled reaction rate is in the form:

$\begin{matrix} k_{i, j, on}^{'} = k_{j, on} \frac{V_{i, j}^{'}}{V_{i, j}} = \frac{3 h_{i}}{4} \frac{(a_{i, j}^{2} - a_{0, i, j}^{2})}{a_{i, j}^{3}} & (19) \end{matrix}$

here, h_iis the height of the gasket, which corresponds to the location where the ligand can bind to the receptor. a_0;jis the radius of the receptor j.

It is assumed that the free end of the chimera is distributed over time in the two regions V_{0 i;j}and V_i;jproportionally to their size, so the reaction rate needs to be scaled according to this.

The quantity a_i;jis the distance between ligand i and j. a_0;i;jis the minimum linker distance, and depends on geometrical characteristics of the receptors involved.

α_0,i,j=√{square root over ((α_j,0+α_i,0)²+|l_i−l_j|²)} (21)

For a given ligand concentration L, the previous equations will give the number of free molecules of the receptor i in the cell surface (R_i), and the number of complex ligand-receptor molecules in the surface prior to internalization (C_i).

3. Chimera Dimer

The theory is now restricted to a case of a hetero-dimer, e.g., two different ligands linked to a receptor. This particular situation is the common scenario for chimera design. As a numerical approach, values are used for the case of EGF linked to different mutants of the IF molecule. The result will be compared with experimental values that predict greater selectivity for various mutants compared with the wild type case.

The model consists of 7 variables, one for each configuration of each of the two receptors and one for the ligand concentration. The interacting components with their corresponding relevant chemical parameters are illustrated in FIG. 15. The components of the model are subjected to 4 reversible and 3 irreversible reactions:

R₁+LC′₁k_1,on,k_1,off (1)

R₂+LC′₂k_2,on,k_2,off (2)

L₂+R₂C₂k′_2,on,k_2,off (3)

L₁+R₁C₁k′_1,on,k_1,off (4)

C₁,C₂,C′₁,C′₂→ k_1,3,k_2,e (5)

R₁,R₂→ k_1,t,k_2,t (6)

→R₁,R₂Q₁,Q₂ (7)

Where R1 and R2 are the amount of the two cell surface receptors that the chimera ligand L is targeting. The variables C₁, C₂, C₁′ and C₂′ correspond to different configurations of the active ligand-receptor complexes.

Reactions 1 and 2 account for the primary reaction of complex formation of the two species, with their respective affinity (k_1,on; k_2,on) and dissociation rates (k_1,off; k_2,off). Since every chimera ligand molecule L has two distinct active sites, it can interact with each of the receptors to form two types of complexes C₁′ and C₂′. The quantities C₁′ and C₂′ represent the total amount of complexes where one of the two active sites of the chimera is free and able to interact with its complementary receptor. This way, when the primary complexes C′1 and C′2 are formed through reaction 1 or 2, a local concentration of the remaining active site is created on the cell surface, which favors the formation of the complementary complex.

In other words, when a C₁′ complex is formed through reaction 1, a local concentration of ligand with only the second binding site available is created on the cell surface. This local concentration, referred to as L₂, is able to interact with R₂through reaction 3 to form a C₂complex. In the same way, the C₂′ complexes formed through reaction 2 give rise to L1, favoring the formation of the complex C₁through reaction 4. These local concentrations L₁and L₂are distributed in a spherical gasket of inner diameter equal to the cell diameter r and height equal to the size of the linker a between the two ligands of the chimera.

Expressions for the calculation of the L1 and L2 local concentrations are:

$\begin{matrix} L_{1} = \frac{C_{2}^{'}}{N_{A υ} V_{0}} = \frac{3 C_{2}^{'}}{4 π} \frac{1}{{(r + a)}^{3} - r^{3}} & (8) \\ L_{2} = \frac{C_{1}^{'}}{N_{A υ} V_{0}} = \frac{3 C_{1}^{'}}{4 π} \frac{1}{{(r + a)}^{3} - r^{3}} & (9) \end{matrix}$

where N_Avis the Avogadro's number and V₀is the gasket volume. The only contribution to the local concentration comes from the complexes C₀₁and C₀₂, since the complexes C₁and C₂formed through reactions 3 and 4 don't have any free binding sites.

The equations for the first ligand-receptor system are as follows:

$\begin{matrix} \frac{{dR}_{1}}{dt} = - k_{1, on} R_{1} L + k_{1, on}^{'} R_{1} L_{1} + k_{1, off} C_{1} - k_{1, t} R_{1} + Q_{r} & (22) \\ \frac{{dC}_{1}}{dt} = k_{1, on} R_{1} L + k_{1, on}^{'} R_{1} L_{1} - k_{1, off} C_{1} - k_{1, e} C_{1} & (23) \\ \frac{{dR}_{2}}{dt} = - k_{2, on} R_{2} L - k_{2, on}^{'} R_{2} L_{2} + k_{2, off} C_{2} - k_{2, t} R_{2} + Q_{r} & (24) \\ \frac{{dC}_{2}}{dt} = k_{2, on} R_{2} L + k_{2, on}^{'} R_{2} L_{2} - k_{2, off} C_{2} - k_{2, e} C_{2} & (25) \\ \frac{d L}{dt} = \frac{1}{N_{A υ} V} (k_{1, off} C_{1} - k_{1, on} R_{1} L + k_{2, off} C_{2} - k_{2, on} R_{2} L) & (26) \\ L_{1} = \frac{C_{2}^{'}}{N_{A υ} V_{0}} = \frac{3 C_{2}^{'}}{4 π} \frac{1}{{(r + a)}^{3} - r^{3}} & (27) \\ L_{2} = \frac{C_{1}^{'}}{N_{A υ} V_{0}} = \frac{3 C_{1}^{'}}{4 π} \frac{1}{{(r + a)}^{3} - r^{3}} & (28) \end{matrix}$

with L being the total concentration of ligand. C₀₁and C₀₂are the number of receptors that are linked only to one of the ligands i.e., the ones that contribute to increase the local concentration of the other receptor. These values can be calculated as follows. In this case

$\begin{matrix} a_{1; 2} = a_{2; 1} = a & (29) \\ \frac{{dC}_{1}^{'}}{dt} = k_{1, on} R_{1} L - k_{1, off} C_{1}^{'} - k_{2, e} C_{1}^{'} & (30) \\ \frac{{dC}_{2}^{'}}{dt} = k_{2, on} R_{2} L - k_{2, off} C_{1}^{'} - k_{2, e} C_{1}^{'} & (31) \end{matrix}$

FIG. 17 represents the concentration of complex ligand-receptor 1 in the surface of the cell, for different values of total number of receptors R₁.

The equations for the second receptor are equivalent to the first one, but with an additional term which accounts for the ligand concentration that the receptor sees from the first ligand-receptor complex.

The effective ligand concentration that the second receptor sees depends on the amount of complex ligand-receptor 1 C₁in the surface of the cell at any time. An additional term is added in the second set of equations, which account for the local concentration of ligand close to the cell surface. This concentration is calculated in Equation 27 assuming that the molecules are distributed in a volume gasket V₀on the cell surface of height the length of the linker. This assumption is justified by the fact that diffusion of the receptors is very fast compared with the internalization times of the receptors.

The value of k_0on;2needs to be scaled taking into account the fact that the reaction with the ligand linked to a surface is constrained by structural and geometric aspects of the systems. The fact that receptor diameter is comparable with linker size and that different heights of receptors in the outer part of the cell membrane has to be introduced into the problem.

While the dissociation rates for each binding reaction k_1;off, k_2;offare equivalent in reaction 1 and 3, and in reaction 2 and 4, the same is not true for the affinity rates. Reactions 3 and 4 occur now between molecules diffusing in a two-dimensional space, with one of them freely moving in three dimensions while attached to the cell surface receptor through one binding site.

This special configuration induces as set constrains that reduce and modulate the affinity rates k_1;onand k_2;on. First of all, reaction between two molecules in a two dimensional surface is modulated by diffusion rate.

$\begin{matrix} k_{1, on}^{'} = {(\frac{1}{k_{1, on}} + \frac{1}{k_{1, diff}})}^{- 1} & (10) \end{matrix}$

where the diffusion rate k_diff(expressed in the appropriate units of M_{−1 min-1}) for two-dimensional collision is calculated based on physical considerations as follows:

$\begin{matrix} k_{1, diff} = \frac{2 π D_{1}}{\ln (b_{1} / a)} N_{A υ} l_{1} & (11) \end{matrix}$

D₁and l₁are the diffusion coefficient and the height of the receptor R₁, correspondingly.

Parameter b₁is the average distance between free receptors in the cell, calculated considering homogeneous distribution of receptors on the cell, and calculated as follows:

$\begin{matrix} b = \sqrt{\frac{4 r^{2}}{R}} & (12) \end{matrix}$

The rest of the reactions account for the trafficking of the receptor-ligand complexes inside the cell. Reaction 5 and Reaction 6 account for the internalization of the signaling complexes and receptors, respectively, while reaction 7 accounts for the constant production of fresh receptors.

Chimeras are fusions of usually two or more ligands that target different extracellular receptors. Chimeras have been successfully tested experimentally for targeting selectively cells with different receptor concentration in their surface. Experimental results described herein demonstrate that the combination of chimera design with ligand mutation successfully increases selectivity in interferon targeting in cells overexpressing EGFR.

The fact that the ligand spends time in the regions where it can not react with its receptors will clearly reduce the reaction rate. These aspects were introduced by defining a new reaction rate in the following way.

$\begin{matrix} k_{on, 1, 2}^{'} = k_{on, 1} \frac{V^{'}}{V} \approx k_{on, 1} \frac{3 h_{1}}{4} \frac{(a^{2} - a_{0, 1, 2}^{2})}{a^{3}} & (32) \\ k_{on, 2, 1}^{'} = k_{on, 2} \frac{V^{'}}{V} \approx k_{on, 2} \frac{3 h_{2}}{4} \frac{(a^{2} - a_{0, 2, 1}^{2})}{a^{3}} & (33) \end{matrix}$

For the numerical analysis, the parameter values listed in Table 3 were used, unless specified. The parameters correspond to measured values of the wild type EGFR and wild type IFN-R in Hela cells. The advantage is that experimental data is already available to validate the model predictions.

To test the model predictions, reproduction was attempted of experimental observations, where different chimeras where designed with various mutants of a IF1 ligand. The different mutant designs were shown to have increased selectivity. The dependence on the total amount of C₂for various interferon mutants, which exhibit different affinities with the IR, was analyzed. The goal was to test the selectivity of the chimeric protein among cells with higher EGFR expression levels. Results are shown in FIG. 18.

TABLE 3 numerical kinetic and physical parameters Parameter Value R_{1, T} 2 × 10⁴ k_{1, off} 0.24 min⁻¹ k_{1, e} 0.15 nM⁻¹ k_{1, D} 2.47 nM h₁ 0.005 μm a_{0, 1} 0.01 μm l₁ lhjfldf R_{2, T} 2 × 10² k_{2, off}WT 0.011 min⁻¹ k_{2, D}WT 3.7 nM k_{2, off}K133A 0.018 min⁻¹ k_{2, D}K133A 26 nM k_{2, off}K144A 0.073 min⁻¹ k_{2, D}K144A 120 nM k_{2, off}K149A 0.043 min⁻¹ k_{2, D}K149A 538 nM k_{2, e} 0 ???? nM⁻¹ h₂ 0.005 μm a_{0, 2} 0.01 μm l₂ lhjfldf L₀ 0.5 nM a 125 × 10⁻⁴ μm D 5.1 μm s⁻¹ r 8.5 μm

In all cases, the number of IF receptors is higher in the case of a chimeric protein, due to the concentration of chimera localized in the surface of the cell. These results are in good qualitative agreement with the experimental results. Selectivity of the mutants depends, among other parameters, on the number of IF receptors necessary to induce apoptotic signaling in the cell. Signaling from the IF pathway can be measured to scale the numerical values obtained from the simulations.

It is reasonable to assume that for a relatively small number of active IF receptors in the cell, the pathway is saturated. Based on an analysis of the experimental data of the wild type IF without linker at a concentration of 0.5 nM, the pathway is saturated already or close to saturation. If this information is compared with the model results presented herein, it turns out that the pathway is close to saturation when the number of total active IF receptors at t=30 min is around 7. From here, selectivity occurs for active IF receptors below this value. On the other hand, experimentally measured signal is negligible in the case of mutant R144A at concentration 0.5 nM. In this case the model predicts a number of IFN receptors at time t=30 min of C₂=0.69.

These values can be used to scale the model from number of active IF receptors with actual signal measured in the cell.

4. Third Case Scenario: Optimal Linker Size

The model can be used to calculate the optimal linker size depending on the properties of the system (e.g., the number of receptors, ligand receptor affinity, structure of the membrane receptors, etc.). As a numerical example, the number of IFN receptors active for different linker sizes was calculated for the different mutants. The linker length dependence at high linker sizes reduces because the local concentration of chimera reduces with the length of the linker. At low values, the dependence is governed by the physical characteristics of the receptors, (a₀,h).

5. Appendix A: Diffusion Time Versus Internalization Time

One of the additional issues in the linker length design concerns the time spent by receptor 1 to find the complex C₁in the cell membrane. This time is dependent on the diffusion coefficient of the membrane receptors, as well as the linker length and the average distance between the two receptors. To estimate this time, the equation for two dimensional diffusion was used. The average distance between two receptors, b_i;j, depends on the concentration and distribution of receptors i and j on the cell surface. To calculate this distance, it is assumed that the cell has a spherical shape, and that receptors are evenly distributed through the whole cell surface.

$\begin{matrix} τ = \frac{b^{2}}{2 D} \log (\frac{b}{2 a}) & (34) \end{matrix}$

In this equation, 2a is the effective target size and D is the diffusion coefficient (assuming both receptor has the same diffusion rate). The distance between the target and the empty receptor depends on the concentration of the complex C₁, which is time dependent. The collision rate is given by

$\begin{matrix} b = \frac{C_{1}}{2} \frac{1}{4 π R_{cell}^{2}} & (35) \end{matrix}$

where r is the average cell radius. The collision rate was computed (inverse of the collision time) for this case study (with Hela cells, EGFR and IF). FIG. 20 is a time plot of the rate of collision.

It should be appreciated that the analysis described herein may be used to design optimal linker lengths for chimeric activators described herein (where the chimeric activators are designed to bind to cell surface receptors, and wherein one of the binding elements may be mutated to have a lower binding affinity for its receptor). However, aspects of the invention also may be used to optimize linker lengths for other chimeric molecules where two components that bind to different binding sites are connected via a linker.

Example 12: Chimeric Activators for Treating Asthma

In some embodiments, chimeric activators can be designed to target cells associated with diseases such as asthma. In one example a chimeric activator can be designed to kill or inactivate B cells that produce IgE. In some embodiments, an IgE receptor may be used as a targeting element and FasL may be used as an activity element.

OTHER EMBODIMENTS

It will be clear that the invention may be practiced other than as particularly described in the foregoing description and examples. In some embodiments, methods of the invention include modifying, assaying, and/or optimizing one or more of the targeting or activity elements and/or the linker. Numerous modifications and variations of the present invention are possible in light of the above teachings and, therefore, are within the scope of the claims. Preferred features of each aspect of the invention are as for each of the other aspects mutatis mutandis. The documents including patents, patent applications, journal articles, abstracts, laboratory manuals, books, or other disclosures mentioned herein are hereby incorporated by reference in their entirety. In the event of conflict, the disclosure of present application controls, other than in the event of clear error. Further, the hard copy of the sequence listing submitted herewith and the corresponding computer readable form are both incorporated herein by reference in their entireties.

Claims

1. An isolated nucleic acid encoding a chimeric activator, the nucleic acid comprising in frame a first sequence, a second sequence, and optionally a third sequence, wherein the first sequence encodes an activity element, the second sequence encodes a targeting element, and the third sequence encodes a linker, and wherein the first sequence includes a mutation that reduces the binding affinity of the activity element for a natural cell surface receptor.

2. An isolated chimeric activator protein encoded by claim 1.

3. An isolated nucleic acid of claim 1, wherein the first, second, and third sequences are arranged to encode a chimeric activator protein that comprises the targeting element at its N-terminal end, the activity element at its C-terminal end, and the linker connecting the C-terminal end of the targeting element to the N-terminal end of the activity element.

4. An isolated nucleic acid of claim 1, wherein the first, second, and third sequences are arranged to encode a chimeric activator protein that comprises the activity element at its N-terminal end, the targeting element at its C-terminal end, and the linker connecting the C-terminal end of the activity element to the N-terminal end of the targeting element.

5. A chimeric activator protein of claim 2, wherein said chimeric activator protein selectively binds to cancer cells relative to normal cells.

6. A nucleic acid of claim 1, wherein the activity element is a cytokine.

7. A nucleic acid of claim 1, wherein the targeting element is an antibody.

8. A nucleic acid of claim 1, wherein the targeting element is an antibody fragment.

9. A nucleic acid of claim 1, wherein the targeting element is an Fc region.

10. A nucleic acid of claim 1, wherein the activity element activates apoptosis.

11. A nucleic acid of claim 1, wherein the activity element is an interferon.

12. A nucleic acid of claim 11, wherein the activity element is a mutant interferon 2 alpha.

13. A nucleic acid of claim 12, wherein the activity element is interferon 2 alpha (K133A).

14. A nucleic acid of claim 12, wherein the activity element is interferon 2 alpha (R144A).

15. A nucleic acid of claim 12, wherein the activity element is interferon 2 alpha (R149A).

16. A nucleic acid of claim 1, wherein the targeting element is a ligand.

17. A nucleic acid of claim 16, wherein the targeting element is epidermal growth factor.

18. An isolated nucleic acid comprising one or more nucleic acid sequences selected from the group consisting of SEQ ID NO. 1, SEQ ID NO. 3, SEQ ID NO. 5, SEQ ID NO. 7, SEQ ID NO. 9, SEQ ID NO. 11, SEQ ID NO. 13, and SEQ ID NO. 15.

19. An isolated protein comprising an amino acid sequence selected from the group consisting of SEQ ID NO. 2, SEQ ID NO. 4, SEQ ID NO. 6, SEQ ID NO. 8, SEQ ID NO. 10, SEQ ID NO. 12, SEQ ID NO. 14, and SEQ ID NO. 16.

20. A nucleic acid of claim 1, wherein the targeting element is MR1-1, a CEA-binding antibody, or a glycophorin-binding antibody.

21. A nucleic acid of claim 1 or 19, wherein the activity element is a TRAIL or EPO activity element.

22. An isolated chimeric activator protein encoded by the nucleic acid of claim 19.

23. An isolated chimeric activator protein encoded by the nucleic acid of claim 20.

24. A recombinant protein comprising

a first element that binds to a first receptor on a target cell;

a second element that binds to a second receptor on the target cell; and

optionally a linker that connects the first and second elements,

wherein the linker allows the first and second elements to bind simultaneously to the first and second receptors on the target cell, wherein the first element comprises a mutation that reduces its binding affinity for its receptors, and wherein the first element transmits a signal to the host cell when it is bound to the first receptor.

25. The recombinant protein of claim 24, wherein the first element binds to its receptor as a monomer.

26. The recombinant protein of claim 24, wherein the second element binds to its receptor as a monomer.

27. The recombinant protein of claim 24, wherein the linker is between about 25 and about 70 amino acids long.

28. The recombinant protein of claim 24, wherein the linker is flexible.

29. A chimeric activator comprising an activity element and a targeting element optionally joined by a linker, wherein the targeting element binds to a first binding site on a target cell, and wherein the activity element binds to a second binding site on a target cell, and wherein the linker length has been optimized for maximizing binding efficiency of the activity element to the second binding site when the targeting element is bound to the first binding site.

30. The chimeric activator of claim 29 wherein the first binding site is a ligand binding site, a receptor, or an epitope on a cell surface.

31. The chimeric activator of claim 29 wherein the second binding site is a signal-transduction receptor on a cell surface.

32. The chimeric activator of claim 29 wherein the targeting element is an antibody, an antibody fragment, an Fc region, a natural or synthetic ligand, or a protein interaction motif.

33. The chimeric activator of claim 29 wherein the activity element is a cytokine, a cytotoxic protein, a regulatory protein, or an active fragment of any one thereof.

34. The chimeric activator of claim 29 wherein the linker length is at least equal to the minimum distance between the first and second binding sites on the cell surface.

35. The chimeric activator of claim 29 wherein the linker length is at least twice the minimum distance between the first and second binding sites on the cell surface.

36. The chimeric activator of claim 29 wherein the linker length is at most five-six times the minimum distance between the first and second binding sites on the cell surface.

37. The chimeric activator of claim 29 wherein the activity element is mutated such that the binding affinity of the activity element for the second binding site is lower than the binding affinity of the targeting element for the first binding site.

38. The chimeric activator of claim 29, wherein the activity element is an enzyme.

39. A method for manufacturing a chimeric activator comprising an activity element and a targeting element joined by a linker, wherein the targeting element binds to a first binding site on a target cell, and wherein the activity element binds to a second binding site on a target cell, and wherein the linker length has been optimized for maximizing binding efficiency of the activity element to the second binding site when the targeting element is bound to the first binding site, the method comprising:

i) optimizing the linker length as a function of the concentration of the first and second binding sites, the size of the activity element and targeting element, the minimum distance between the binding sites of the targeting element and the activity element, and the affinities of the activity element and the targeting element for the first and second binding sites; and

ii) preparing a chimeric activator having an optimal linker length.

40. A method for manufacturing a chimeric activator comprising an activity element and a targeting element joined by a linker, wherein the targeting element binds to a first binding site on a target cell, and wherein the activity element binds to a second binding site on a target cell, and wherein the linker length has been optimized for maximizing binding efficiency of the activity element to the second binding site when the targeting element is bound to the first binding site, the method comprising:

i) mutating the activity element such that the binding affinity of the activity element for the second binding site is lower than the binding affinity of the targeting element for the first binding site;

i) optimizing the linker length as a function of the concentration of the first and second binding sites, the size of the activity element and targeting element, the minimum distance between the binding sites of the targeting element and the activity element, and the affinities of the activity element and the targeting element for the first and second binding sites; and

iii) preparing a chimeric activator.

41. A method for targeted cellular regulation, the method comprising:

administering to a subject a biologically effective amount of a chimeric activator comprising an activity element and a targeting element joined by a linker, wherein the targeting element binds to a first binding site on a target cell, and wherein the activity element binds to a second binding site on a target cell, and wherein the linker length has been optimized for maximizing binding efficiency of the activity element to the second binding site when the targeting element is bound to the first binding site.

42. A method for treating cancer, the method comprising:

administering to a subject having a cancer a therapeutically effective amount of a composition comprising a chimeric activator comprising an activity element and a targeting element joined by a linker, wherein the targeting element binds to a first binding site on a target cell, and wherein the activity element binds to a second binding site on a target cell, and wherein the linker length has been optimized for maximizing binding efficiency of the activity element to the second binding site when the targeting element is bound to the first binding site.